Proteopedia - User contributions [en]

Proteopedia:Development

2026-09-08T07:46:32Z

Angel Herraez: /* pending issues for Alcalá, November 2026 */

See also:
* [[Proteopedia:Wishlist]]
* [[Proteopedia:Problems]]

==pending issues for Alcalá, November 2026==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''

(In the new server installation)

* SAT:
** color palette: restyling, colors ordered by HSL
** manage several isosurfaces in one model: a selector, color them individually, hide/display toggle
** add a choice of standard color palettes for surfaces (mostly gradients)
** add tooltips to describe surface coloring and possibility to have it added to the caption, as it was done for structure palettes

* New method for smooth transitions between scenes: fade-out, fade-in

* StructureSection:
** Links to Proteopedia pages may render wrong when some are inside StructureSection and some are outside
** Pages with more than one StructureSection have content misplaced

* Use PNGJ rather than state for saving the scenes

* Improve model pop-up window (JSmolPopup.htm and js)
** fix behaviour of resize buttons (in parent or popup)
** better refresh (avoid errors)
** descriptive window title, copying original caption
** adapt to parent page with more that one JSmol panels - make utility buttons specific for each applet

* Tutorial pages:
** fix Ramachandran_principle_and_phi_psi_angles
** fix Ramachandran_Plot_Inspection

* Print3D
** check validity of output when 'scene' is selected as rendering style - dimensions, thicknesses
*** available print styles are restricted for large structures; when 'scene' is chosen, apparently restriction is not applied

* Adapt to handle new 12-character PDB_xxxxxxxx codes.

==Online & at home, August-September 2024==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''
* An update of initialview script for seeded pages: combination into a single file, modularisation, fix for rendering of multimodel files.
* Introduced conditionalLoad function for deciding to skip simplified view, based on molecular weight of the biological unit with all models.
* New functions.spt combines many utility functions (including conditionalLoad)

* New look for toggle buttons (spin, quality, labels), popup button, load full button, resize buttons.
* Multimodel files: new toggle buttons: first/all models, animation on/off.

See [[Development/2024-09|details]].

==Rehovot, March 2023==
(12-20 March) ''[[User:Angel_Herraez|AH]], [[User:Jaime_Prilusky|JP]]'' and [[User:Joel_L._Sussman|JS]]:

=== Sequence Tool ===
This widget reads the information in any pdb- or mmcif-formatted file included in a Proteopedia page and parses its content to display the protein sequence (for all chains) alongside the JSmol 3D-view panel.
The sequence includes information combined from both the COORD and SEQRES records in the PDB file, hence including physical gaps, numbering gaps, sequence microheterogeneity and inserted residues.

The visitor of the page may interactively explore the structure and the sequence:
* A click on a letter in the sequence listing will display the full information of that residue and will highlight it in the 3D structure view.
* A click on any atom in the 3D view will highlight the matching residue in the sequence listing.
* A search box accepts a residue number, or a residue letter, or a partial sequence; matches will be displayed on both the sequence and the structure.

This tool is included in all pages automatically generated in Proteopedia for any new structure
deposited in the Protein Data Bank (seeded pages) and may be included at will in user-generated
pages. Documentation is at [[Seqtool]]

=== Colouring schemes for AI-predicted structures ===
Procedures were developed to apply several colouring schemes in the 3D structure view that reflect the reliability or uncertainty in the coordinates of each residue in predicted 3D protein structures coming form several platforms and databases, namely:
* [https://robetta.bakerlab.org RoseTTAFold], with RMSD data for each atom or residue.
* [https://alphafold.ebi.ac.uk AlphaFold], with pLDDT score for each atom or residue.
* [https://esmatlas.com/about#fold ESMFold], with pLDDT score for each atom or residue.
The functionality for applying these colour schemes was added through buttons in the SAT, and it is offered automatically depending on which data source provides the uploaded structure files.

The colour reference (legend) is automatically included below the caption area under the 3D view, for any new scene that was created using the colouring option.
[[Image:AI-predicted coloring schemes.png]]

===Prediction of structure===
A new area inside 'load molecule' section of SAT allows to enter a raw or Fasta-formatted protein
sequence, sends it to the ESMfold server and retrieves the resulting predicted structure into
Proteopedia. The structure is also loaded on SAT, ready for preparing a scene.

==Alcalá, Spain, March 2021==
[[User:Angel_Herraez|AH]] modified Html5mediator.php to allow embedding videos from [https://vimeo.com Vimeo]

==Rehovot December 2020==
[[User:Jaime_Prilusky|JP]]:
* Enabled Proteopedia to manage scenes with multiple isosurfaces.
* Modified SAT to allow adding multiple isosurfaces to a scene and to edit scenes with multiple isosurfaces.
* Incorporated CSS class bg- and text- to allow coloring of captions and text.

==Rehovot October 2020==
[[User:Jaime_Prilusky|JP]]: Modified SAT's scene searching approach to ease reuse scenes from other pages. SAT now scan the page being edited for ''name='##/wgArticleId/'' and build the scenes dropdown on [load scene] tab with all the scenes from all the wgArticleIds found.

==Rehovot, January 2019==
[[User:Jaime_Prilusky|JP]] and [[User:Joel_L._Sussman|JS]]: Morphing on Proteopedia at [[Special:Morph]]. Provide two structures (either PDB ids, upload files or a combination or both) and optional chain selection and click Morph. Morphing takes place between a few minutes, thanks to PyMOL and SCHRODINGER, and you’ll be able to directly upload the resulting morph to Proteopedia for SAT scene development, or download a PDB or .pse file.

==Rehovot, October 2018==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working together during AH's visit to Weizmann Institute, 12 to 19 October 2018.''
* JSmol was upgraded to version 14.29.16
* A conflict was solved between display of PDB file information (e.g. resolution, nr.of NMR models) and display of caption.
* SAT: the chosen options for a scene (description, caption, spin status, scene transitions...) are now stored together with the scene and hence they are reused as defaults when the scene is edited.
* More work on connecting the Sequence display with the Structure.
* Use WebGL for rendering, enabled per user (new toggle in the Preferences page). Note that not all features in JSmol are implemented in WebGL, so customised scenes may lack features; you can check a list of supported and unsupported features [http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/WebGL#Support_for_JmolScript_features here]. This is experimental and still needs some work (e.g. Simplified and Full model do not make sense in WebGL; also we need to verify proper display of ligands)
* Work on a new design for the home page.

== Rehovot, August 2018 ==
[[User:Jaime_Prilusky|JP]] JSmol applet displays "I'm ready. Click on a green link" when there's no defined structure or scene to render. Before, it remained with the "Loading, please wait ..." statement forever, since there was nothing to load.

== Alcalá, Spain, March 2018 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 19 to 22 March 2018.''

* Files can now be dragged from local disk and dropped onto the SAT. A copy of the file will be automatically uploaded and stored in Proteopedia and will be subsequently used by the scenes that are created from that SAT.
* The SAT, under ''Load molecule'', now has an option to load the ''Biological Assembly'' rather than the ''Asymmetric Unit'' (which was previously the only choice and will still be the default).
* Additional work on the special interface for display of knowledge about mutations of some deeply studied proteins. Different renderings, added onto the protein's 3D structure, were implemented for each kind of feature that results from the mutation.

== Amherst, MA, USA, January 2018 ==
Proteopedia 10th Anniversary Conference
* An option to use the latest version of JSmol while viewing any Proteopedia page has been added to the user's [[Special:Preferences|personal preferences]] section: click on the ‘Misc’ tab and check the option to ‘use the latest JSmol version’; then, save your preferences.
** JSmol files will be retrieved from <nowiki>https://chemapps.stolaf.edu/jmol/jsmol</nowiki>
* Advanced users will found now in Proteopedia’s Scene Authoring Tool (SAT), under the JSmol panel, a button to quickly open JSmol Script Console and a text input field to enter scripting commands and Execute them. This allows to easily execute additional scripting JSmol commands besides those currently implemented as buttons and pulldowns.

== Essen, Germany, June 2017 ==
[[User:Jaime_Prilusky|JP]] Added option to load= attribute to indicate if to load Asymmetric Unit or Biological Assembly for a PDB structure, by adding _au or _ba to the PDB id ( i.e load=2ace_au load=2ace_ba ). Default behaviour, when only the PDB id is provided, remains the same: loads Biological Assembly if available, otherwise the Asymmetric Unit.

== Rehovot, Israel, June 2017 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during AH's visit to Weizmann, 30 May to 13 June 2017, with constant feedback from [[User:Joel_L._Sussman|JS]]''

During this period we addressed an update in the back-end features of the Proteopedia platform. The major aim was to improve the user experience in the platform, as well as adding some new features.

Several features were implemented in Proteopedia and were immediately made available online for the users. Changes were applied to the design of Proteopedia pages, particularly aiming to speed up the loading and increase responsiveness of pages for the user. The drop of web browser support for Java applets along the previous years led us (2014) to implement the use of the JSmol viewer for structures, in place of the former Jmol viewer. However, that brought the inconvenience of a slower response. In these new developments (2017), we made some changes that reduce the delay associated to including JSmol in the pages.

* The JSmol object is now written to the page not during, but after page loading has completed.
** Even though page loading speed is not perceivable enhanced, such delayed insertion has allowed to implement several other functionalities added to Proteopedia pages.
* A rotating image (animated gif) for the model or scene is displayed initially in place of the JSmol object (when such gif file is already available). Therefore, the initial delay on page loading is now suppressed and it will take place only when the user requests JSmol to load. This allows much quicker loading of the page.
** Proteopedia Main Page is now using those animated images with its front models (selected randomly out of a short list). This results in a much more quickly responding page.
** A new button [''Display Interactive Model''] is shown below the image, for the user to decide showing the JSmol model instead of the initial replacement image.
** The image is replaced with the JSmol model also whenever the user clicks on a green link.
** An automated procedure allows to generate and save the animated GIFs for Proteopedia seeded pages, as well as for user-authored pages. This procedure is to be used programmatically for the full collection, or manually just by privileged users.
* The JSmol panel in all pages is now resizable. This will allow adjustment by the users, according to their device screen size, the diverse needs and the intended use, e.g. projection in the classroom.
** Two new buttons were added in the tool area below the JSmol panel, to increase and decrease the size in discrete steps (20%, within a range from 200 to 800 px).
** The [''popup''] button is still available as an independent option.
* The popup window now has a new extra button, [''update''], that allows to refresh the state of model, retrieving it again from the calling page. This avoids the need to call again the popup window and load again the JSmol object (so it yields a quicker experience). It also allows, for example, to work in the page on the main monitor while displaying the enlarged model (popup) in a second monitor or projector.
* All the above-mentioned new options have also been added as part of the [[http://proteopedia.org/w/User:Jaime_Prilusky/JSmolExtension|JSmol Extension for MediaWiki]], for use in other websites.
* When entering page ''Edit mode'', JSmol for the ''Scene Authoring Tool'' (SAT) is not inserted until the user opens the SAT by clicking on the [show] button. This results in a much more quickly responding page, allowing for quick editing of the page text if changing scenes was not intended. The delay that used to be on loading the page has now been shifted to when the user decides to open the SAT (and only the first time).
* Whenever a model is loaded (seeded pages at least), information is filled into the page content, under the JSmol page:
** The PDB id (read from the server).
** Number of models if NMR. This is read from the server or from within JSmol.
** Resolution if applicable. (Implementation is pending)
** Type of model: ''biological assembly'' or ''asymmetric unit''. This is read from the Proteopedia server.
* When creating a scene, the user may specify a caption; this will be saved together with the scene and will be displayed in the page when any user clicks on the green link to loads that scene into the JSmol panel. This caption is inserted in the area below the model.
** The caption will be updated whenever a new scene is loaded (as long as the scene was prepared and saved including a caption).
* For seeded pages, any user has now a choice to display the model of either ''biological assembly'' or ''asymmetric unit'', as long as the files are available in the server for that particular protein. If only one is available, only the relevant option is presented in the interface.
* When a page is written in a language other than English and its title has been set as recommended (that is, ''Title of page (language)''), the JSmol interface (context menu) is now displayed in the language matching the page. This possibility is limited to those languages for which there is a Jmol localisation; otherwise, the default for JSmol is the system language, otherwise US English. Examples: [[1eve_%28Spanish%29|Spanish]], [[1eve_%28French%29|French]], [[1eve_%28German%29|German]], [[1eve_%28Italian%29|Italian]], [[1eve_%28Czech%29|Czech]], [[1eve_%28Russian%29|Russian]], [[1eve_%28Turkish%29|Turkish]], [[1eve_%28Chinese%29|Chinese]].

Additionally, we started development of a wholly new approach: to develop a visual interface that incorporates knowledge about mutations of some deeply studied proteins, their effect on structure and stability of the molecule, so as to gain insights into what structural alterations are relevant to pathogenicity.

* A special page will hold the sequence and mutation data. This page may be edited as usual, by authorised users.
* The display page, also editable,
** Has a regular content area, editable by users.
** Reads the data from the matching data page (access limited).
** Includes a scrollable panel showing the sequence of the protein, with all mutations listed.
** Includes the JSmol model.
** Clicking on the mutations displays them in the 3D model, focusing on the affected residue, with highlights on the neighbouring residues and display of clashes.
** The display in JSmol may be animated between wild type and mutated residue.

== Alcalá, Spain, October 2016 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 10 to 13 October 2016.''

=== Template for ConSurf ===
A mediawiki template, [[Template:ConSurf|{ {ConSurf} }]], was written that inserts the standard ConSurf subsection, including description, links and the checkbox to apply the evolutionary conservation colouring, applied to the protein specified by the user editing any page.

Pending:
* Write documentation or help, possibly combining it with [[Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link|existing help]]

=== Update of style applied by the "high quality" button ===

This button is located under every model (JSmol panel).

It formerly toggled the <code>antialiasDisplay</code> state.

It is now changed to also toggle the use of <code>cartoonFancy</code>.

Note: the high quality mode is abandoned during rotation, but gives a nicer look when stopped, e.g. for copying an image. It may be retained during rotation if the default in Proteopedia, <code>platformSpeed 5</code>, is changed to at least 6 e.g. using the <code>pspeed</code> option in the applet tag (not advisable in general for responsiveness in mobile platforms).

=== Direct insertion of the scene link from SAT into the body text ===

When a scene is saved within the SAT, the former method required the author to copy some resulting code with the scene green link from a textbox in the SAT to the editable section (wikitext) of the page content.

The improvement implemented adds the scene code automatically at the current cursor position within the editable content.

Pending:
* Adequate help needs to be written and inserted, particularly to instruct the user to have the cursor in the right place before saving the scene.
* Maybe remove or hide the textbox in the SAT, to avoid duplicity or confusion.

=== Generation of animated image with rotating model ===

A link, “Export Animated Image” has been added in the area below the JSmol panel. This allows to obtain an animated GIF of the current scene, useful for display in presentations or web pages independent from Proteopedia.

The animation is produced server-side (using Jmol.jar and ImageMagick).

Technical: the use of the capture command in Jmol proved to be impossible without a graphic display; therefore, we had to resort to using a loop with incremental rotation and single image export at each step, then combine them all into a single animated gif.
A full 360° spin is implemented, with some user choices like axis of rotation, overall duration of one full turn in the animation, dimensions and smoothness of the animation.

Pending:
* Add better help / explanation of the process, and how to download the resulting image. #DONE
* Implement also the “rocking” motion as an alternative animated display. #DONE

=== Compaction of JSmol pop-up menu ===

The menu has been increasing in length and complexity along Jmol versions. Some actions were taken so that if fits better in available window space. Only css was used, which overrides the default css rules included in the JSmol library.
* Reduced line height for each submenu entry (not only first level entries but also all submenus)
* The languages submenu is now scrollable within a limited height.
Pending:
* Investigate: the popup menu in the SAT seems to be able to open upwards when there is no space at the bottom of window. Achieving this would be desirable for JSmol in general. It may be caused by action of some other jQuery UI code, in effect only in the SAT but absent in JSmol’s copy of UI.

=== Rendering of nucleotide ligands ===

In the default initial rendering, ligands are displayed as spacefill cpk. However, JSmol fails to identify single nucleotides as ligands (they are evaluated as single-residue nucleic acids and so rendered as cartoon, i.e. invisible).

Code was added to <code>initialview02v3.spt</code> so that single nucleotides are rendered like ligands (e.g. GDP, GTP often bound to G-proteins, or ATP in kinases)

=== Access to SAT not available ===

The banner and link to open the SAT is not displayed while the page is being edited and the Preview has been requested. As a consequence, if the user under<code> My preferences > Editing </code>checks the<code> Show preview on first edit </code>option, he will never see the SAT.

A hint for this was added to [[Help:Contents#Creating_Molecular_Scenes]]

=== Issues detected that need further work or investigation ===

==== Using assembly CIF ====
Limitations associated to using mmCIF assemblies as the source of models.
* <code>biopolymers</code> are not detected by Jmol (as chosen from the pop-up menu), or not available due to asemblies?
* Need to check the status of retrieval of biological unit vs. asymmetric unit. #DONE
* Ned to check different behaviour in applet tag than in SAT, e.g. the display of tetramer vs. dimer – likely related to the use of <code>getlateststructure</code> or <code>getfrozenstructure</code> and the recent switch to using assemblies
* Some ligands are not listed under Hetero in the popup menu. Example: [UIR] in [[Trypsin]] or [[1y3v]]

==== Transitions between scenes ====
SAT offers some options for transitions (skip zoom-out, skip transition), the behaviour of which needs to be re-checked. They might be not working, or rather be incompatible with the option of reloading the model for each new scene.

==== Update caption below structure for each scene ====
Below the JSmol model a caption is displayed, with text specified in the applet tag. When a different scene is loaded, this caption should get updated.

(Remains to be implemented) #DONE

==== Choice of templates for a new page ====
When a new page is started, it is created with a template. The possibility of offering a gallery of templates or layouts was suggested.

This was not addressed for lack of specific ideas. Not clear if it would be useful. #DISREGARDED

==== Category:Pyrho ====
[[:Category:Pyrho]] which is very frequent, inserts a bad link to Wikipedia (non existing page).

==== Localisation ====
* When a page is written in a non-English language, the language of the JSmol interface could be changed to match. [[Aricept_Complexed_with_Acetylcholinesterase_%28French%29|Example in French]] #DONE

Proteopedia:Development

2026-08-30T08:34:37Z

Angel Herraez: /* pending issues for Alcalá, November 2026 */

See also:
* [[Proteopedia:Wishlist]]
* [[Proteopedia:Problems]]

==pending issues for Alcalá, November 2026==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''

(In the new server installation)

* SAT:
** color palette: restyling, colors ordered by HSL
** manage several isosurfaces in one model: a selector, color them individually, hide/display toggle
** add a choice of standard color palettes for surfaces (mostly gradients)
** add tooltips to describe surface coloring and possibility to have it added to the caption, as it was done for structure palettes

* New method for smooth transitions between scenes: fade-out, fade-in

* StructureSection:
** Links to Proteopedia pages may render wrong when some are inside StructureSection and some are outside
** Pages with more than one StructureSection have content misplaced

* Use PNGJ rather than state for saving the scenes

* Improve model pop-up window (JSmolPopup.htm and js)
** fix behaviour of resize buttons (in parent or popup)
** better refresh (avoid errors)
** descriptive window title, copying original caption
** adapt to parent page with more that one JSmol panels - make utility buttons specific for each applet

* Tutorial pages:
** fix Ramachandran_principle_and_phi_psi_angles
** fix Ramachandran_Plot_Inspection

* Print3D
** check validity of output when 'scene' is selected as rendering style - dimensions, thicknesses
*** available print styles are restricted for large structures; when 'scene' is chosen, apparently restriction is not applied

==Online & at home, August-September 2024==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''
* An update of initialview script for seeded pages: combination into a single file, modularisation, fix for rendering of multimodel files.
* Introduced conditionalLoad function for deciding to skip simplified view, based on molecular weight of the biological unit with all models.
* New functions.spt combines many utility functions (including conditionalLoad)

* New look for toggle buttons (spin, quality, labels), popup button, load full button, resize buttons.
* Multimodel files: new toggle buttons: first/all models, animation on/off.

See [[Development/2024-09|details]].

==Rehovot, March 2023==
(12-20 March) ''[[User:Angel_Herraez|AH]], [[User:Jaime_Prilusky|JP]]'' and [[User:Joel_L._Sussman|JS]]:

=== Sequence Tool ===
This widget reads the information in any pdb- or mmcif-formatted file included in a Proteopedia page and parses its content to display the protein sequence (for all chains) alongside the JSmol 3D-view panel.
The sequence includes information combined from both the COORD and SEQRES records in the PDB file, hence including physical gaps, numbering gaps, sequence microheterogeneity and inserted residues.

The visitor of the page may interactively explore the structure and the sequence:
* A click on a letter in the sequence listing will display the full information of that residue and will highlight it in the 3D structure view.
* A click on any atom in the 3D view will highlight the matching residue in the sequence listing.
* A search box accepts a residue number, or a residue letter, or a partial sequence; matches will be displayed on both the sequence and the structure.

This tool is included in all pages automatically generated in Proteopedia for any new structure
deposited in the Protein Data Bank (seeded pages) and may be included at will in user-generated
pages. Documentation is at [[Seqtool]]

=== Colouring schemes for AI-predicted structures ===
Procedures were developed to apply several colouring schemes in the 3D structure view that reflect the reliability or uncertainty in the coordinates of each residue in predicted 3D protein structures coming form several platforms and databases, namely:
* [https://robetta.bakerlab.org RoseTTAFold], with RMSD data for each atom or residue.
* [https://alphafold.ebi.ac.uk AlphaFold], with pLDDT score for each atom or residue.
* [https://esmatlas.com/about#fold ESMFold], with pLDDT score for each atom or residue.
The functionality for applying these colour schemes was added through buttons in the SAT, and it is offered automatically depending on which data source provides the uploaded structure files.

The colour reference (legend) is automatically included below the caption area under the 3D view, for any new scene that was created using the colouring option.
[[Image:AI-predicted coloring schemes.png]]

===Prediction of structure===
A new area inside 'load molecule' section of SAT allows to enter a raw or Fasta-formatted protein
sequence, sends it to the ESMfold server and retrieves the resulting predicted structure into
Proteopedia. The structure is also loaded on SAT, ready for preparing a scene.

==Alcalá, Spain, March 2021==
[[User:Angel_Herraez|AH]] modified Html5mediator.php to allow embedding videos from [https://vimeo.com Vimeo]

==Rehovot December 2020==
[[User:Jaime_Prilusky|JP]]:
* Enabled Proteopedia to manage scenes with multiple isosurfaces.
* Modified SAT to allow adding multiple isosurfaces to a scene and to edit scenes with multiple isosurfaces.
* Incorporated CSS class bg- and text- to allow coloring of captions and text.

==Rehovot October 2020==
[[User:Jaime_Prilusky|JP]]: Modified SAT's scene searching approach to ease reuse scenes from other pages. SAT now scan the page being edited for ''name='##/wgArticleId/'' and build the scenes dropdown on [load scene] tab with all the scenes from all the wgArticleIds found.

==Rehovot, January 2019==
[[User:Jaime_Prilusky|JP]] and [[User:Joel_L._Sussman|JS]]: Morphing on Proteopedia at [[Special:Morph]]. Provide two structures (either PDB ids, upload files or a combination or both) and optional chain selection and click Morph. Morphing takes place between a few minutes, thanks to PyMOL and SCHRODINGER, and you’ll be able to directly upload the resulting morph to Proteopedia for SAT scene development, or download a PDB or .pse file.

==Rehovot, October 2018==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working together during AH's visit to Weizmann Institute, 12 to 19 October 2018.''
* JSmol was upgraded to version 14.29.16
* A conflict was solved between display of PDB file information (e.g. resolution, nr.of NMR models) and display of caption.
* SAT: the chosen options for a scene (description, caption, spin status, scene transitions...) are now stored together with the scene and hence they are reused as defaults when the scene is edited.
* More work on connecting the Sequence display with the Structure.
* Use WebGL for rendering, enabled per user (new toggle in the Preferences page). Note that not all features in JSmol are implemented in WebGL, so customised scenes may lack features; you can check a list of supported and unsupported features [http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/WebGL#Support_for_JmolScript_features here]. This is experimental and still needs some work (e.g. Simplified and Full model do not make sense in WebGL; also we need to verify proper display of ligands)
* Work on a new design for the home page.

== Rehovot, August 2018 ==
[[User:Jaime_Prilusky|JP]] JSmol applet displays "I'm ready. Click on a green link" when there's no defined structure or scene to render. Before, it remained with the "Loading, please wait ..." statement forever, since there was nothing to load.

== Alcalá, Spain, March 2018 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 19 to 22 March 2018.''

* Files can now be dragged from local disk and dropped onto the SAT. A copy of the file will be automatically uploaded and stored in Proteopedia and will be subsequently used by the scenes that are created from that SAT.
* The SAT, under ''Load molecule'', now has an option to load the ''Biological Assembly'' rather than the ''Asymmetric Unit'' (which was previously the only choice and will still be the default).
* Additional work on the special interface for display of knowledge about mutations of some deeply studied proteins. Different renderings, added onto the protein's 3D structure, were implemented for each kind of feature that results from the mutation.

== Amherst, MA, USA, January 2018 ==
Proteopedia 10th Anniversary Conference
* An option to use the latest version of JSmol while viewing any Proteopedia page has been added to the user's [[Special:Preferences|personal preferences]] section: click on the ‘Misc’ tab and check the option to ‘use the latest JSmol version’; then, save your preferences.
** JSmol files will be retrieved from <nowiki>https://chemapps.stolaf.edu/jmol/jsmol</nowiki>
* Advanced users will found now in Proteopedia’s Scene Authoring Tool (SAT), under the JSmol panel, a button to quickly open JSmol Script Console and a text input field to enter scripting commands and Execute them. This allows to easily execute additional scripting JSmol commands besides those currently implemented as buttons and pulldowns.

== Essen, Germany, June 2017 ==
[[User:Jaime_Prilusky|JP]] Added option to load= attribute to indicate if to load Asymmetric Unit or Biological Assembly for a PDB structure, by adding _au or _ba to the PDB id ( i.e load=2ace_au load=2ace_ba ). Default behaviour, when only the PDB id is provided, remains the same: loads Biological Assembly if available, otherwise the Asymmetric Unit.

== Rehovot, Israel, June 2017 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during AH's visit to Weizmann, 30 May to 13 June 2017, with constant feedback from [[User:Joel_L._Sussman|JS]]''

During this period we addressed an update in the back-end features of the Proteopedia platform. The major aim was to improve the user experience in the platform, as well as adding some new features.

Several features were implemented in Proteopedia and were immediately made available online for the users. Changes were applied to the design of Proteopedia pages, particularly aiming to speed up the loading and increase responsiveness of pages for the user. The drop of web browser support for Java applets along the previous years led us (2014) to implement the use of the JSmol viewer for structures, in place of the former Jmol viewer. However, that brought the inconvenience of a slower response. In these new developments (2017), we made some changes that reduce the delay associated to including JSmol in the pages.

* The JSmol object is now written to the page not during, but after page loading has completed.
** Even though page loading speed is not perceivable enhanced, such delayed insertion has allowed to implement several other functionalities added to Proteopedia pages.
* A rotating image (animated gif) for the model or scene is displayed initially in place of the JSmol object (when such gif file is already available). Therefore, the initial delay on page loading is now suppressed and it will take place only when the user requests JSmol to load. This allows much quicker loading of the page.
** Proteopedia Main Page is now using those animated images with its front models (selected randomly out of a short list). This results in a much more quickly responding page.
** A new button [''Display Interactive Model''] is shown below the image, for the user to decide showing the JSmol model instead of the initial replacement image.
** The image is replaced with the JSmol model also whenever the user clicks on a green link.
** An automated procedure allows to generate and save the animated GIFs for Proteopedia seeded pages, as well as for user-authored pages. This procedure is to be used programmatically for the full collection, or manually just by privileged users.
* The JSmol panel in all pages is now resizable. This will allow adjustment by the users, according to their device screen size, the diverse needs and the intended use, e.g. projection in the classroom.
** Two new buttons were added in the tool area below the JSmol panel, to increase and decrease the size in discrete steps (20%, within a range from 200 to 800 px).
** The [''popup''] button is still available as an independent option.
* The popup window now has a new extra button, [''update''], that allows to refresh the state of model, retrieving it again from the calling page. This avoids the need to call again the popup window and load again the JSmol object (so it yields a quicker experience). It also allows, for example, to work in the page on the main monitor while displaying the enlarged model (popup) in a second monitor or projector.
* All the above-mentioned new options have also been added as part of the [[http://proteopedia.org/w/User:Jaime_Prilusky/JSmolExtension|JSmol Extension for MediaWiki]], for use in other websites.
* When entering page ''Edit mode'', JSmol for the ''Scene Authoring Tool'' (SAT) is not inserted until the user opens the SAT by clicking on the [show] button. This results in a much more quickly responding page, allowing for quick editing of the page text if changing scenes was not intended. The delay that used to be on loading the page has now been shifted to when the user decides to open the SAT (and only the first time).
* Whenever a model is loaded (seeded pages at least), information is filled into the page content, under the JSmol page:
** The PDB id (read from the server).
** Number of models if NMR. This is read from the server or from within JSmol.
** Resolution if applicable. (Implementation is pending)
** Type of model: ''biological assembly'' or ''asymmetric unit''. This is read from the Proteopedia server.
* When creating a scene, the user may specify a caption; this will be saved together with the scene and will be displayed in the page when any user clicks on the green link to loads that scene into the JSmol panel. This caption is inserted in the area below the model.
** The caption will be updated whenever a new scene is loaded (as long as the scene was prepared and saved including a caption).
* For seeded pages, any user has now a choice to display the model of either ''biological assembly'' or ''asymmetric unit'', as long as the files are available in the server for that particular protein. If only one is available, only the relevant option is presented in the interface.
* When a page is written in a language other than English and its title has been set as recommended (that is, ''Title of page (language)''), the JSmol interface (context menu) is now displayed in the language matching the page. This possibility is limited to those languages for which there is a Jmol localisation; otherwise, the default for JSmol is the system language, otherwise US English. Examples: [[1eve_%28Spanish%29|Spanish]], [[1eve_%28French%29|French]], [[1eve_%28German%29|German]], [[1eve_%28Italian%29|Italian]], [[1eve_%28Czech%29|Czech]], [[1eve_%28Russian%29|Russian]], [[1eve_%28Turkish%29|Turkish]], [[1eve_%28Chinese%29|Chinese]].

Additionally, we started development of a wholly new approach: to develop a visual interface that incorporates knowledge about mutations of some deeply studied proteins, their effect on structure and stability of the molecule, so as to gain insights into what structural alterations are relevant to pathogenicity.

* A special page will hold the sequence and mutation data. This page may be edited as usual, by authorised users.
* The display page, also editable,
** Has a regular content area, editable by users.
** Reads the data from the matching data page (access limited).
** Includes a scrollable panel showing the sequence of the protein, with all mutations listed.
** Includes the JSmol model.
** Clicking on the mutations displays them in the 3D model, focusing on the affected residue, with highlights on the neighbouring residues and display of clashes.
** The display in JSmol may be animated between wild type and mutated residue.

== Alcalá, Spain, October 2016 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 10 to 13 October 2016.''

=== Template for ConSurf ===
A mediawiki template, [[Template:ConSurf|{ {ConSurf} }]], was written that inserts the standard ConSurf subsection, including description, links and the checkbox to apply the evolutionary conservation colouring, applied to the protein specified by the user editing any page.

Pending:
* Write documentation or help, possibly combining it with [[Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link|existing help]]

=== Update of style applied by the "high quality" button ===

This button is located under every model (JSmol panel).

It formerly toggled the <code>antialiasDisplay</code> state.

It is now changed to also toggle the use of <code>cartoonFancy</code>.

Note: the high quality mode is abandoned during rotation, but gives a nicer look when stopped, e.g. for copying an image. It may be retained during rotation if the default in Proteopedia, <code>platformSpeed 5</code>, is changed to at least 6 e.g. using the <code>pspeed</code> option in the applet tag (not advisable in general for responsiveness in mobile platforms).

=== Direct insertion of the scene link from SAT into the body text ===

When a scene is saved within the SAT, the former method required the author to copy some resulting code with the scene green link from a textbox in the SAT to the editable section (wikitext) of the page content.

The improvement implemented adds the scene code automatically at the current cursor position within the editable content.

Pending:
* Adequate help needs to be written and inserted, particularly to instruct the user to have the cursor in the right place before saving the scene.
* Maybe remove or hide the textbox in the SAT, to avoid duplicity or confusion.

=== Generation of animated image with rotating model ===

A link, “Export Animated Image” has been added in the area below the JSmol panel. This allows to obtain an animated GIF of the current scene, useful for display in presentations or web pages independent from Proteopedia.

The animation is produced server-side (using Jmol.jar and ImageMagick).

Technical: the use of the capture command in Jmol proved to be impossible without a graphic display; therefore, we had to resort to using a loop with incremental rotation and single image export at each step, then combine them all into a single animated gif.
A full 360° spin is implemented, with some user choices like axis of rotation, overall duration of one full turn in the animation, dimensions and smoothness of the animation.

Pending:
* Add better help / explanation of the process, and how to download the resulting image. #DONE
* Implement also the “rocking” motion as an alternative animated display. #DONE

=== Compaction of JSmol pop-up menu ===

The menu has been increasing in length and complexity along Jmol versions. Some actions were taken so that if fits better in available window space. Only css was used, which overrides the default css rules included in the JSmol library.
* Reduced line height for each submenu entry (not only first level entries but also all submenus)
* The languages submenu is now scrollable within a limited height.
Pending:
* Investigate: the popup menu in the SAT seems to be able to open upwards when there is no space at the bottom of window. Achieving this would be desirable for JSmol in general. It may be caused by action of some other jQuery UI code, in effect only in the SAT but absent in JSmol’s copy of UI.

=== Rendering of nucleotide ligands ===

In the default initial rendering, ligands are displayed as spacefill cpk. However, JSmol fails to identify single nucleotides as ligands (they are evaluated as single-residue nucleic acids and so rendered as cartoon, i.e. invisible).

Code was added to <code>initialview02v3.spt</code> so that single nucleotides are rendered like ligands (e.g. GDP, GTP often bound to G-proteins, or ATP in kinases)

=== Access to SAT not available ===

The banner and link to open the SAT is not displayed while the page is being edited and the Preview has been requested. As a consequence, if the user under<code> My preferences > Editing </code>checks the<code> Show preview on first edit </code>option, he will never see the SAT.

A hint for this was added to [[Help:Contents#Creating_Molecular_Scenes]]

=== Issues detected that need further work or investigation ===

==== Using assembly CIF ====
Limitations associated to using mmCIF assemblies as the source of models.
* <code>biopolymers</code> are not detected by Jmol (as chosen from the pop-up menu), or not available due to asemblies?
* Need to check the status of retrieval of biological unit vs. asymmetric unit. #DONE
* Ned to check different behaviour in applet tag than in SAT, e.g. the display of tetramer vs. dimer – likely related to the use of <code>getlateststructure</code> or <code>getfrozenstructure</code> and the recent switch to using assemblies
* Some ligands are not listed under Hetero in the popup menu. Example: [UIR] in [[Trypsin]] or [[1y3v]]

==== Transitions between scenes ====
SAT offers some options for transitions (skip zoom-out, skip transition), the behaviour of which needs to be re-checked. They might be not working, or rather be incompatible with the option of reloading the model for each new scene.

==== Update caption below structure for each scene ====
Below the JSmol model a caption is displayed, with text specified in the applet tag. When a different scene is loaded, this caption should get updated.

(Remains to be implemented) #DONE

==== Choice of templates for a new page ====
When a new page is started, it is created with a template. The possibility of offering a gallery of templates or layouts was suggested.

This was not addressed for lack of specific ideas. Not clear if it would be useful. #DISREGARDED

==== Category:Pyrho ====
[[:Category:Pyrho]] which is very frequent, inserts a bad link to Wikipedia (non existing page).

==== Localisation ====
* When a page is written in a non-English language, the language of the JSmol interface could be changed to match. [[Aricept_Complexed_with_Acetylcholinesterase_%28French%29|Example in French]] #DONE

Proteopedia:Development

2026-08-29T10:31:07Z

Angel Herraez: plans for November visit to Alcalá

See also:
* [[Proteopedia:Wishlist]]
* [[Proteopedia:Problems]]

==pending issues for Alcalá, November 2026==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''

(In the new server installation)

* SAT:
** polish color palette
** manage several isosurfaces in one model: color them, including a selector
** add a choice of standard color palettes for surfaces (mostly gradients)
** add tooltips to describe surface coloring and possibility to have it added to the caption, as for structure palettes

* New method for smooth transitions between scenes: fade-out, fade-in

* Links to Proteopedia pages may end wrong when some are inside StructureSection and some are outside

* Pages with more than one StructureSection have content misplaced

* Use PNGJ rather than state for saving the scenes

* Improve model pop-up window (JSmolPopup.htm and js)
** fix behaviour of resize buttons (in parent or popup)
** better refresh (avoid errors)
** better window title, copy of original caption
** adapt to parent page with more that one JSmol panels - make utility buttons specific for each applet

* Tutorials
** fix Ramachandran_principle_and_phi_psi_angles
** fix Ramachandran_Plot_Inspection

* Print3D
** check validity of output when 'scene' is selected as rendering style - dimensions, thichknesses

==Online & at home, August-September 2024==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''
* An update of initialview script for seeded pages: combination into a single file, modularisation, fix for rendering of multimodel files.
* Introduced conditionalLoad function for deciding to skip simplified view, based on molecular weight of the biological unit with all models.
* New functions.spt combines many utility functions (including conditionalLoad)

* New look for toggle buttons (spin, quality, labels), popup button, load full button, resize buttons.
* Multimodel files: new toggle buttons: first/all models, animation on/off.

See [[Development/2024-09|details]].

==Rehovot, March 2023==
(12-20 March) ''[[User:Angel_Herraez|AH]], [[User:Jaime_Prilusky|JP]]'' and [[User:Joel_L._Sussman|JS]]:

=== Sequence Tool ===
This widget reads the information in any pdb- or mmcif-formatted file included in a Proteopedia page and parses its content to display the protein sequence (for all chains) alongside the JSmol 3D-view panel.
The sequence includes information combined from both the COORD and SEQRES records in the PDB file, hence including physical gaps, numbering gaps, sequence microheterogeneity and inserted residues.

The visitor of the page may interactively explore the structure and the sequence:
* A click on a letter in the sequence listing will display the full information of that residue and will highlight it in the 3D structure view.
* A click on any atom in the 3D view will highlight the matching residue in the sequence listing.
* A search box accepts a residue number, or a residue letter, or a partial sequence; matches will be displayed on both the sequence and the structure.

This tool is included in all pages automatically generated in Proteopedia for any new structure
deposited in the Protein Data Bank (seeded pages) and may be included at will in user-generated
pages. Documentation is at [[Seqtool]]

=== Colouring schemes for AI-predicted structures ===
Procedures were developed to apply several colouring schemes in the 3D structure view that reflect the reliability or uncertainty in the coordinates of each residue in predicted 3D protein structures coming form several platforms and databases, namely:
* [https://robetta.bakerlab.org RoseTTAFold], with RMSD data for each atom or residue.
* [https://alphafold.ebi.ac.uk AlphaFold], with pLDDT score for each atom or residue.
* [https://esmatlas.com/about#fold ESMFold], with pLDDT score for each atom or residue.
The functionality for applying these colour schemes was added through buttons in the SAT, and it is offered automatically depending on which data source provides the uploaded structure files.

The colour reference (legend) is automatically included below the caption area under the 3D view, for any new scene that was created using the colouring option.
[[Image:AI-predicted coloring schemes.png]]

===Prediction of structure===
A new area inside 'load molecule' section of SAT allows to enter a raw or Fasta-formatted protein
sequence, sends it to the ESMfold server and retrieves the resulting predicted structure into
Proteopedia. The structure is also loaded on SAT, ready for preparing a scene.

==Alcalá, Spain, March 2021==
[[User:Angel_Herraez|AH]] modified Html5mediator.php to allow embedding videos from [https://vimeo.com Vimeo]

==Rehovot December 2020==
[[User:Jaime_Prilusky|JP]]:
* Enabled Proteopedia to manage scenes with multiple isosurfaces.
* Modified SAT to allow adding multiple isosurfaces to a scene and to edit scenes with multiple isosurfaces.
* Incorporated CSS class bg- and text- to allow coloring of captions and text.

==Rehovot October 2020==
[[User:Jaime_Prilusky|JP]]: Modified SAT's scene searching approach to ease reuse scenes from other pages. SAT now scan the page being edited for ''name='##/wgArticleId/'' and build the scenes dropdown on [load scene] tab with all the scenes from all the wgArticleIds found.

==Rehovot, January 2019==
[[User:Jaime_Prilusky|JP]] and [[User:Joel_L._Sussman|JS]]: Morphing on Proteopedia at [[Special:Morph]]. Provide two structures (either PDB ids, upload files or a combination or both) and optional chain selection and click Morph. Morphing takes place between a few minutes, thanks to PyMOL and SCHRODINGER, and you’ll be able to directly upload the resulting morph to Proteopedia for SAT scene development, or download a PDB or .pse file.

==Rehovot, October 2018==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working together during AH's visit to Weizmann Institute, 12 to 19 October 2018.''
* JSmol was upgraded to version 14.29.16
* A conflict was solved between display of PDB file information (e.g. resolution, nr.of NMR models) and display of caption.
* SAT: the chosen options for a scene (description, caption, spin status, scene transitions...) are now stored together with the scene and hence they are reused as defaults when the scene is edited.
* More work on connecting the Sequence display with the Structure.
* Use WebGL for rendering, enabled per user (new toggle in the Preferences page). Note that not all features in JSmol are implemented in WebGL, so customised scenes may lack features; you can check a list of supported and unsupported features [http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/WebGL#Support_for_JmolScript_features here]. This is experimental and still needs some work (e.g. Simplified and Full model do not make sense in WebGL; also we need to verify proper display of ligands)
* Work on a new design for the home page.

== Rehovot, August 2018 ==
[[User:Jaime_Prilusky|JP]] JSmol applet displays "I'm ready. Click on a green link" when there's no defined structure or scene to render. Before, it remained with the "Loading, please wait ..." statement forever, since there was nothing to load.

== Alcalá, Spain, March 2018 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 19 to 22 March 2018.''

* Files can now be dragged from local disk and dropped onto the SAT. A copy of the file will be automatically uploaded and stored in Proteopedia and will be subsequently used by the scenes that are created from that SAT.
* The SAT, under ''Load molecule'', now has an option to load the ''Biological Assembly'' rather than the ''Asymmetric Unit'' (which was previously the only choice and will still be the default).
* Additional work on the special interface for display of knowledge about mutations of some deeply studied proteins. Different renderings, added onto the protein's 3D structure, were implemented for each kind of feature that results from the mutation.

== Amherst, MA, USA, January 2018 ==
Proteopedia 10th Anniversary Conference
* An option to use the latest version of JSmol while viewing any Proteopedia page has been added to the user's [[Special:Preferences|personal preferences]] section: click on the ‘Misc’ tab and check the option to ‘use the latest JSmol version’; then, save your preferences.
** JSmol files will be retrieved from <nowiki>https://chemapps.stolaf.edu/jmol/jsmol</nowiki>
* Advanced users will found now in Proteopedia’s Scene Authoring Tool (SAT), under the JSmol panel, a button to quickly open JSmol Script Console and a text input field to enter scripting commands and Execute them. This allows to easily execute additional scripting JSmol commands besides those currently implemented as buttons and pulldowns.

== Essen, Germany, June 2017 ==
[[User:Jaime_Prilusky|JP]] Added option to load= attribute to indicate if to load Asymmetric Unit or Biological Assembly for a PDB structure, by adding _au or _ba to the PDB id ( i.e load=2ace_au load=2ace_ba ). Default behaviour, when only the PDB id is provided, remains the same: loads Biological Assembly if available, otherwise the Asymmetric Unit.

== Rehovot, Israel, June 2017 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during AH's visit to Weizmann, 30 May to 13 June 2017, with constant feedback from [[User:Joel_L._Sussman|JS]]''

During this period we addressed an update in the back-end features of the Proteopedia platform. The major aim was to improve the user experience in the platform, as well as adding some new features.

Several features were implemented in Proteopedia and were immediately made available online for the users. Changes were applied to the design of Proteopedia pages, particularly aiming to speed up the loading and increase responsiveness of pages for the user. The drop of web browser support for Java applets along the previous years led us (2014) to implement the use of the JSmol viewer for structures, in place of the former Jmol viewer. However, that brought the inconvenience of a slower response. In these new developments (2017), we made some changes that reduce the delay associated to including JSmol in the pages.

* The JSmol object is now written to the page not during, but after page loading has completed.
** Even though page loading speed is not perceivable enhanced, such delayed insertion has allowed to implement several other functionalities added to Proteopedia pages.
* A rotating image (animated gif) for the model or scene is displayed initially in place of the JSmol object (when such gif file is already available). Therefore, the initial delay on page loading is now suppressed and it will take place only when the user requests JSmol to load. This allows much quicker loading of the page.
** Proteopedia Main Page is now using those animated images with its front models (selected randomly out of a short list). This results in a much more quickly responding page.
** A new button [''Display Interactive Model''] is shown below the image, for the user to decide showing the JSmol model instead of the initial replacement image.
** The image is replaced with the JSmol model also whenever the user clicks on a green link.
** An automated procedure allows to generate and save the animated GIFs for Proteopedia seeded pages, as well as for user-authored pages. This procedure is to be used programmatically for the full collection, or manually just by privileged users.
* The JSmol panel in all pages is now resizable. This will allow adjustment by the users, according to their device screen size, the diverse needs and the intended use, e.g. projection in the classroom.
** Two new buttons were added in the tool area below the JSmol panel, to increase and decrease the size in discrete steps (20%, within a range from 200 to 800 px).
** The [''popup''] button is still available as an independent option.
* The popup window now has a new extra button, [''update''], that allows to refresh the state of model, retrieving it again from the calling page. This avoids the need to call again the popup window and load again the JSmol object (so it yields a quicker experience). It also allows, for example, to work in the page on the main monitor while displaying the enlarged model (popup) in a second monitor or projector.
* All the above-mentioned new options have also been added as part of the [[http://proteopedia.org/w/User:Jaime_Prilusky/JSmolExtension|JSmol Extension for MediaWiki]], for use in other websites.
* When entering page ''Edit mode'', JSmol for the ''Scene Authoring Tool'' (SAT) is not inserted until the user opens the SAT by clicking on the [show] button. This results in a much more quickly responding page, allowing for quick editing of the page text if changing scenes was not intended. The delay that used to be on loading the page has now been shifted to when the user decides to open the SAT (and only the first time).
* Whenever a model is loaded (seeded pages at least), information is filled into the page content, under the JSmol page:
** The PDB id (read from the server).
** Number of models if NMR. This is read from the server or from within JSmol.
** Resolution if applicable. (Implementation is pending)
** Type of model: ''biological assembly'' or ''asymmetric unit''. This is read from the Proteopedia server.
* When creating a scene, the user may specify a caption; this will be saved together with the scene and will be displayed in the page when any user clicks on the green link to loads that scene into the JSmol panel. This caption is inserted in the area below the model.
** The caption will be updated whenever a new scene is loaded (as long as the scene was prepared and saved including a caption).
* For seeded pages, any user has now a choice to display the model of either ''biological assembly'' or ''asymmetric unit'', as long as the files are available in the server for that particular protein. If only one is available, only the relevant option is presented in the interface.
* When a page is written in a language other than English and its title has been set as recommended (that is, ''Title of page (language)''), the JSmol interface (context menu) is now displayed in the language matching the page. This possibility is limited to those languages for which there is a Jmol localisation; otherwise, the default for JSmol is the system language, otherwise US English. Examples: [[1eve_%28Spanish%29|Spanish]], [[1eve_%28French%29|French]], [[1eve_%28German%29|German]], [[1eve_%28Italian%29|Italian]], [[1eve_%28Czech%29|Czech]], [[1eve_%28Russian%29|Russian]], [[1eve_%28Turkish%29|Turkish]], [[1eve_%28Chinese%29|Chinese]].

Additionally, we started development of a wholly new approach: to develop a visual interface that incorporates knowledge about mutations of some deeply studied proteins, their effect on structure and stability of the molecule, so as to gain insights into what structural alterations are relevant to pathogenicity.

* A special page will hold the sequence and mutation data. This page may be edited as usual, by authorised users.
* The display page, also editable,
** Has a regular content area, editable by users.
** Reads the data from the matching data page (access limited).
** Includes a scrollable panel showing the sequence of the protein, with all mutations listed.
** Includes the JSmol model.
** Clicking on the mutations displays them in the 3D model, focusing on the affected residue, with highlights on the neighbouring residues and display of clashes.
** The display in JSmol may be animated between wild type and mutated residue.

== Alcalá, Spain, October 2016 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 10 to 13 October 2016.''

=== Template for ConSurf ===
A mediawiki template, [[Template:ConSurf|{ {ConSurf} }]], was written that inserts the standard ConSurf subsection, including description, links and the checkbox to apply the evolutionary conservation colouring, applied to the protein specified by the user editing any page.

Pending:
* Write documentation or help, possibly combining it with [[Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link|existing help]]

=== Update of style applied by the "high quality" button ===

This button is located under every model (JSmol panel).

It formerly toggled the <code>antialiasDisplay</code> state.

It is now changed to also toggle the use of <code>cartoonFancy</code>.

Note: the high quality mode is abandoned during rotation, but gives a nicer look when stopped, e.g. for copying an image. It may be retained during rotation if the default in Proteopedia, <code>platformSpeed 5</code>, is changed to at least 6 e.g. using the <code>pspeed</code> option in the applet tag (not advisable in general for responsiveness in mobile platforms).

=== Direct insertion of the scene link from SAT into the body text ===

When a scene is saved within the SAT, the former method required the author to copy some resulting code with the scene green link from a textbox in the SAT to the editable section (wikitext) of the page content.

The improvement implemented adds the scene code automatically at the current cursor position within the editable content.

Pending:
* Adequate help needs to be written and inserted, particularly to instruct the user to have the cursor in the right place before saving the scene.
* Maybe remove or hide the textbox in the SAT, to avoid duplicity or confusion.

=== Generation of animated image with rotating model ===

A link, “Export Animated Image” has been added in the area below the JSmol panel. This allows to obtain an animated GIF of the current scene, useful for display in presentations or web pages independent from Proteopedia.

The animation is produced server-side (using Jmol.jar and ImageMagick).

Technical: the use of the capture command in Jmol proved to be impossible without a graphic display; therefore, we had to resort to using a loop with incremental rotation and single image export at each step, then combine them all into a single animated gif.
A full 360° spin is implemented, with some user choices like axis of rotation, overall duration of one full turn in the animation, dimensions and smoothness of the animation.

Pending:
* Add better help / explanation of the process, and how to download the resulting image. #DONE
* Implement also the “rocking” motion as an alternative animated display. #DONE

=== Compaction of JSmol pop-up menu ===

The menu has been increasing in length and complexity along Jmol versions. Some actions were taken so that if fits better in available window space. Only css was used, which overrides the default css rules included in the JSmol library.
* Reduced line height for each submenu entry (not only first level entries but also all submenus)
* The languages submenu is now scrollable within a limited height.
Pending:
* Investigate: the popup menu in the SAT seems to be able to open upwards when there is no space at the bottom of window. Achieving this would be desirable for JSmol in general. It may be caused by action of some other jQuery UI code, in effect only in the SAT but absent in JSmol’s copy of UI.

=== Rendering of nucleotide ligands ===

In the default initial rendering, ligands are displayed as spacefill cpk. However, JSmol fails to identify single nucleotides as ligands (they are evaluated as single-residue nucleic acids and so rendered as cartoon, i.e. invisible).

Code was added to <code>initialview02v3.spt</code> so that single nucleotides are rendered like ligands (e.g. GDP, GTP often bound to G-proteins, or ATP in kinases)

=== Access to SAT not available ===

The banner and link to open the SAT is not displayed while the page is being edited and the Preview has been requested. As a consequence, if the user under<code> My preferences > Editing </code>checks the<code> Show preview on first edit </code>option, he will never see the SAT.

A hint for this was added to [[Help:Contents#Creating_Molecular_Scenes]]

=== Issues detected that need further work or investigation ===

==== Using assembly CIF ====
Limitations associated to using mmCIF assemblies as the source of models.
* <code>biopolymers</code> are not detected by Jmol (as chosen from the pop-up menu), or not available due to asemblies?
* Need to check the status of retrieval of biological unit vs. asymmetric unit. #DONE
* Ned to check different behaviour in applet tag than in SAT, e.g. the display of tetramer vs. dimer – likely related to the use of <code>getlateststructure</code> or <code>getfrozenstructure</code> and the recent switch to using assemblies
* Some ligands are not listed under Hetero in the popup menu. Example: [UIR] in [[Trypsin]] or [[1y3v]]

==== Transitions between scenes ====
SAT offers some options for transitions (skip zoom-out, skip transition), the behaviour of which needs to be re-checked. They might be not working, or rather be incompatible with the option of reloading the model for each new scene.

==== Update caption below structure for each scene ====
Below the JSmol model a caption is displayed, with text specified in the applet tag. When a different scene is loaded, this caption should get updated.

(Remains to be implemented) #DONE

==== Choice of templates for a new page ====
When a new page is started, it is created with a template. The possibility of offering a gallery of templates or layouts was suggested.

This was not addressed for lack of specific ideas. Not clear if it would be useful. #DISREGARDED

==== Category:Pyrho ====
[[:Category:Pyrho]] which is very frequent, inserts a bad link to Wikipedia (non existing page).

==== Localisation ====
* When a page is written in a non-English language, the language of the JSmol interface could be changed to match. [[Aricept_Complexed_with_Acetylcholinesterase_%28French%29|Example in French]] #DONE

Print3D help/Error messages

2026-08-27T17:24:45Z

Angel Herraez: warnings issued by Jmol when trying to produce the Print3D output

These are warnings issued by Jmol when trying to produce the Print3D output.

They must be ignored (provided they are harmless) in order for the process to complete in the server and the output page be displayed.

Please add any you find:

* BioModelset need to delete the DataList map
* no isosurface points were found!

User:Angel Herraez/Sandbox 11

2026-08-24T16:47:21Z

Angel Herraez:

<div style="display:none;">[https://proteopedia.org test]</div>
<StructureSection load='' size='350' side='right' caption='' scene=''>

Covalent Lysine-Cysteine protein crosslinks were first reported in 2016, interpreted at the time as Lys-CH<sub>2</sub>-Cys<ref name="methylene">PMID: 27261771</ref><ref name="matthews">PMID: 34180568</ref>. In 2019, Jimin Wang provided evidence for oxygen rather than methylene as the linker<ref name="jimin">PMID: 30592103</ref><ref name="dauterletter">PMID: 30666728</ref>. In 2021, Wensien ''et al.'' with the Tittmann group (Goettingen), studying [[Transaldolase]], put the Lysine-cysteine "Nitrogen-Oxygen-Sulfur" (NOS) protein crosslink on firm ground

=== First link to PDB (inside structureSection): correct ===
A survey of the data in the [[Protein Data Bank]] revealed that the NOS bond likely exists "in diverse protein families across all domains of life (including ''Homo sapiens'')

== Smooth transitions ==

<scene name='/scripts/11/1109340/1crn/1'>smoothed scene</scene> BAD

<jmol>
<jmolLink>
<target>jmolApplet1</target>
<text>smoothed scene link</text>
<script>script /wiki/extensions/Proteopedia/spt/functions.spt; script /scripts/11/1109340/1crn/1.spt;</script>
</jmolLink>
</jmol> GOOD

</StructureSection>

=== Second link to PDB (outside structureSection): incorrect ===

A survey of the data in the [[Protein Data Bank]] revealed that the NOS bond likely exists "in diverse protein families across all domains of life (including ''Homo sapiens'')

__NOTOC__
==2026==

==={{Font color|#ff8000|Education & Communication}}===

<div style="display:none"><ref group="edu2026">PMID: 41854287</ref></div>
<references group="edu2026" />

==={{Font color|#00b000|BioMedical Research}}===

<div style="display:none">
<ref group="res2026">PMID: 42527684</ref>
<ref group="res2026">PMID: 42375539</ref>
<ref group="res2026">PMID: 42395897</ref>
<ref group="res2026">PMID: 42344113</ref>
<ref group="res2026">PMID: 41504448</ref>
</div>
<references group="res2026" />

==2021-2025==

==={{Font color|#ff8000|Education & Communication}}===

:* [https://www.google.com/books/edition/Food_Chemistry_in_Small_Bites/QLk_EQAAQBAJ O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.]

<div style="display:none">
<ref group="edu2021">PMID: 39976303</ref>
<ref group="edu2021">PMID: 39291955</ref>
<ref group="edu2021">PMID: 35001912</ref>
</div>
<references group="edu2021" />

==={{Font color|#00b000|BioMedical Research}}===
====2025====

:* [https://www.biorxiv.org/content/10.1101/2025.04.11.648320v1.full Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.]

<div style="display:none">
<ref group="res2025">PMID: 41390121</ref>
<ref group="res2025">PMID: 41331102</ref>
<ref group="res2025">PMID: 41047069</ref>
<ref group="res2025">PMID: 41072766</ref>
<ref group="res2025">PMID: 40284663</ref>
<ref group="res2025">PMID: 39299531</ref>
<ref group="res2025">PMID: 39758030</ref>
</div>
<references group="res2025" />

<div style="display:none">
<ref group="res2025">PMID: 41060696</ref>
</div>
<references group="res2025" />
<blockquote><span style="background-color:#fffce0;">
For AlphaFold3-predicted structures, "Average '''pLDDT''' scores were calculated using FirstGlance in Jmol."
</span>
</blockquote>

Template:Banner BAMBED

2026-08-24T16:05:03Z

Angel Herraez: tring to fix the problem with existing template not producing the name of the journal

<div style="border:1px solid #E1A524; margin:0 auto; display:table;">
<div style="background-color:#FDE2C4; border:1px solid white; padding:2px; text-align:center;">
''This page, as it appeared on [{{fullurl:{{PAGENAME}}|oldid={{{OLDID}}}}} {{{DATE}}}], was featured in [https://doi.org/{{{BAMBEDDOI}}} this article] in the journal [[BAMBED|Biochemistry and Molecular Biology]].''
</div>
</div>

Template:Banner BAMBED

2026-08-24T16:02:30Z

Angel Herraez: tring to fix the problem with existing template not producing the name of the journal

<div style="border:1px solid #E1A524; margin:0 auto; display:table;">
<div style="display:none;">[[BAMBED]]</div>
<div style="background-color:#FDE2C4; border:1px solid white; padding:2px; text-align:center;">
''This page, as it appeared on [{{fullurl:{{PAGENAME}}|oldid={{{OLDID}}}}} {{{DATE}}}], was featured in [https://doi.org/{{{BAMBEDDOI}}} this article] in the journal [[BAMBED|Biochemistry and Molecular Biology]].''
</div>
</div>

Template:Banner BAMBED

2026-08-24T16:00:36Z

Angel Herraez: tring to fix the problem with existing template not producing the name of the journal

<div style="border:1px solid #E1A524; margin:0 auto; display:table;">
<div style="display:none;">[[Protein_Data_Bank]]</div>
<div style="background-color:#FDE2C4; border:1px solid white; padding:2px; text-align:center;">
''This page, as it appeared on [{{fullurl:{{PAGENAME}}|oldid={{{OLDID}}}}} {{{DATE}}}], was featured in [https://doi.org/{{{BAMBEDDOI}}} this article] in the journal [[BAMBED|Biochemistry and Molecular Biology]].''
</div>
</div>

User:Angel Herraez/Sandbox 11

2026-08-24T10:21:34Z

Angel Herraez:

<div style="display:none;">[https://proteopedia.org test]</div>
<StructureSection load='' size='350' side='right' caption='' scene=''>

Covalent Lysine-Cysteine protein crosslinks were first reported in 2016, interpreted at the time as Lys-CH<sub>2</sub>-Cys<ref name="methylene">PMID: 27261771</ref><ref name="matthews">PMID: 34180568</ref>. In 2019, Jimin Wang provided evidence for oxygen rather than methylene as the linker<ref name="jimin">PMID: 30592103</ref><ref name="dauterletter">PMID: 30666728</ref>. In 2021, Wensien ''et al.'' with the Tittmann group (Goettingen), studying [[Transaldolase]], put the Lysine-cysteine "Nitrogen-Oxygen-Sulfur" (NOS) protein crosslink on firm ground

=== First link to PDB (inside structureSection): correct ===
A survey of the data in the [[Protein Data Bank]] revealed that the NOS bond likely exists "in diverse protein families across all domains of life (including ''Homo sapiens'')

== Smooth transitions ==

<scene name='/scripts/11/1109340/1crn/1'>smoothed scene</scene> BAD

<jmol>
<jmolLink>
<target>jmolApplet1</target>
<text>smoothed scene link</text>
<script>script /wiki/extensions/Proteopedia/spt/functions.spt; script /scripts/11/1109340/1crn/1.spt;</script>
</jmolLink>
</jmol> GOOD

</StructureSection>

=== Second link to PDB (outside structureSection): incorrect ===

A survey of the data in the [[Protein Data Bank]] revealed that the NOS bond likely exists "in diverse protein families across all domains of life (including ''Homo sapiens'')

__NOTOC__
==2026==

==={{Font color|#ff8000|Education & Communication}}===

<ref>PMID: 41854287</ref><references />

==={{Font color|#00b000|BioMedical Research}}===

<ref group="xtra">PMID: 42527684</ref><ref group="xtra">PMID: 42375539</ref><ref group="xtra">PMID: 42395897</ref><ref group="xtra">PMID: 42344113</ref><ref group="xtra">PMID: 41504448</ref><references group="xtra" />

==2021-2025==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 39976303</ref><references group="xtra" />

* [https://www.google.com/books/edition/Food_Chemistry_in_Small_Bites/QLk_EQAAQBAJ O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.]

<ref group="xtra">PMID: 39291955</ref><references group="xtra" />

<ref group="xtra">PMID: 35001912</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2025====
<ref group="xtra">PMID: 41390121</ref><references group="xtra" />

<ref group="xtra">PMID: 41060696</ref><references group="xtra" />
<blockquote><span style="background-color:#fffce0;">
For AlphaFold3-predicted structures, "Average '''pLDDT''' scores were calculated using FirstGlance in Jmol."
</span>
</blockquote>

<ref group="xtra">PMID: 41331102</ref><references group="xtra" />

<ref group="xtra">PMID: 41047069</ref><references group="xtra" />

<ref group="xtra">PMID: 41072766</ref><references group="xtra" />

<ref group="xtra">PMID: 40284663</ref><references group="xtra" />

<ref group="xtra">PMID: 39299531</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2025.04.11.648320v1.full Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.]

<ref group="xtra">PMID: 39758030</ref><references group="xtra" />

User:Angel Herraez/Sandbox 11

2026-08-24T10:13:54Z

Angel Herraez:

<div style="display:none;">[https://proteopedia.org test]</div>
<StructureSection load='' size='350' side='right' caption='' scene=''>

Covalent Lysine-Cysteine protein crosslinks were first reported in 2016, interpreted at the time as Lys-CH<sub>2</sub>-Cys<ref name="methylene">PMID: 27261771</ref><ref name="matthews">PMID: 34180568</ref>. In 2019, Jimin Wang provided evidence for oxygen rather than methylene as the linker<ref name="jimin">PMID: 30592103</ref><ref name="dauterletter">PMID: 30666728</ref>. In 2021, Wensien ''et al.'' with the Tittmann group (Goettingen), studying [[Transaldolase]], put the Lysine-cysteine "Nitrogen-Oxygen-Sulfur" (NOS) protein crosslink on firm ground

=== First link to PDB (inside structureSection): correct ===
A survey of the data in the [[Protein Data Bank]] revealed that the NOS bond likely exists "in diverse protein families across all domains of life (including ''Homo sapiens'')

== Smooth transitions ==

<scene name='/scripts/11/1109340/1crn/1'>smoothed scene</scene> BAD

<jmol>
<jmolLink>
<target>jmolApplet1</target>
<text>smoothed scene link</text>
<script>script /wiki/extensions/Proteopedia/spt/functions.spt; script /scripts/11/1109340/1crn/1.spt;</script>
</jmolLink>
</jmol> GOOD

</StructureSection>

=== Second link to PDB (outside structureSection): incorrect ===

A survey of the data in the [[Protein Data Bank]] revealed that the NOS bond likely exists "in diverse protein families across all domains of life (including ''Homo sapiens'')

__NOTOC__
==2026==

==={{Font color|#ff8000|Education & Communication}}===

<ref>PMID: 41854287</ref><references />

==={{Font color|#00b000|BioMedical Research}}===

<ref group="xtra">PMID: 42527684</ref><references group="xtra" />

<ref group="xtra">PMID: 42375539</ref><references group="xtra" />

<ref group="xtra">PMID: 42395897</ref><references group="xtra" />

<ref group="xtra">PMID: 42344113</ref><references group="xtra" />

<ref group="xtra">PMID: 41504448</ref><references group="xtra" />

==2021-2025==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 39976303</ref><references group="xtra" />

* [https://www.google.com/books/edition/Food_Chemistry_in_Small_Bites/QLk_EQAAQBAJ O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.]

<ref group="xtra">PMID: 39291955</ref><references group="xtra" />

<ref group="xtra">PMID: 35001912</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2025====
<ref group="xtra">PMID: 41390121</ref><references group="xtra" />

<ref group="xtra">PMID: 41060696</ref><references group="xtra" />
<blockquote><span style="background-color:#fffce0;">
For AlphaFold3-predicted structures, "Average '''pLDDT''' scores were calculated using FirstGlance in Jmol."
</span>
</blockquote>

<ref group="xtra">PMID: 41331102</ref><references group="xtra" />

<ref group="xtra">PMID: 41047069</ref><references group="xtra" />

<ref group="xtra">PMID: 41072766</ref><references group="xtra" />

<ref group="xtra">PMID: 40284663</ref><references group="xtra" />

<ref group="xtra">PMID: 39299531</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2025.04.11.648320v1.full Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.]

<ref group="xtra">PMID: 39758030</ref><references group="xtra" />

Template:BAMBED

2026-08-24T09:53:54Z

Angel Herraez: Undo revision 4482891 by Angel Herraez (talk)

<div style="border:1px solid #E1A524; margin:0 auto; display:table;">
<div style="background-color:#FDE2C4; border:1px solid white; padding:2px; text-align:center;">
''This page, as it appeared on [{{fullurl:{{PAGENAME}}|oldid={{{OLDID}}}}} {{{DATE}}}], was featured in [http://doi.org/{{{BAMBEDDOI}}} this article]
in the journal Biochemistry and Molecular Biology Education.''
</div>
</div>

Template:BAMBED

2026-08-24T09:52:28Z

Angel Herraez: tring to fix the problem with existing template not producing the name of the journal - temporary fix

<div style="border:1px solid #E1A524; margin:0 auto; display:table;">
<div style="display:none;">[[BAMBED]] (temporary fix)</div>
<div style="background-color:#FDE2C4; border:1px solid white; padding:2px; text-align:center;">
''This page, as it appeared on [{{fullurl:{{PAGENAME}}|oldid={{{OLDID}}}}} {{{DATE}}}], was featured in [http://doi.org/{{{BAMBEDDOI}}} this article]
in the journal [[BAMBED|Biochemistry and Molecular Biology Education]].''
</div>
</div>

User:Angel Herraez/Sandbox Rama

2026-08-23T17:54:47Z

Angel Herraez: Blanked the page

User:Angel Herraez/Sandbox Rama

2026-08-23T17:52:51Z

Angel Herraez:

<title>Ramachandran Animation</title>

<script type="text/javascript" src="/wiki/extensions/Jmol/JSmol/JSmol.min.js"></script>
<script type="text/javascript" src="/wiki/extensions/Jmol/JSmol/js/Jmol2.js"></script>
<script type="text/javascript" src="/wiki/Tutorial/Ramachandran_principle_and_phi_psi_angles/pp.js"></script>
<script language="javascript">

// QUERY PARAMETERS
var offerTrail = false;
var clashesOrange = false;

var qparam = document.location.search;
if (match(qparam, "trail"))
offerTrail = true;
if (match(qparam, "orange"))
clashesOrange = true;

Jmol.Info =
{
use: "HTML5",
j2sPath: "/wiki/extensions/Jmol/JSmol/j2s",
}
delete Jmol._tracker; // avoid error messages on AWS

</script>

<link rel="stylesheet" type="text/css" href="/wiki/Tutorial/Ramachandran_principle_and_phi_psi_angles/pp.css">
<link rel="stylesheet" type="text/css" href="/wiki/Tutorial/Ramachandran_principle_and_phi_psi_angles/input.css">

<div style="display:none;background-color:#fe8;padding:60px;font-size:140%;border:5px solid red;" id="divmsie">
</div>

<div style="display:none;background-color:#ffa;padding:10px;font-size:110%;border:1px solid red;" id="divedge">
<center>

</div>

<div style="font-size:150%;text-align:center;font-weight:bold;">
<br>
The Ramachandran Principle
</div>
<div style="font-size:130%;text-align:center;font-weight:bold;">
Phi (φ) and Psi (ψ) Angles in Proteins
</div>

<br>
<div style="width:80%;text-align:center;margin-left:10%;font-size:120%;">
The Ramachandran Principle says that
<a href="http://proteopedia.org/w/Protein_primary%2C_secondary%2C_tertiary_and_quaternary_structure" target="_blank">alpha helices, beta strands, and turns</a>
are the most likely conformations for a
<a href="http://proteopedia.org/w/Chain" target="_blank">polypeptide chain</a>
to adopt, because most other conformations are impossible
due to steric collisions between atoms.
</div>
<br>
<div style="width:90%;text-align:center;margin-left:5%;font-size:100%;">
This interactive tutorial is also available as an
<a href="http://tinyurl.com/RamachandranPrinciple" target="_blank">Animated Slideshow</a>
or
<a href="https://tinyurl.com/RamachandranPrincipleYoutube" "="" target="_blank">YouTube Video</a>,
and there is a
<a href="http://proteopedia.org/w/User:Eric_Martz/Ramachandran_Principle_Quiz" target="_blank">Quiz</a>.
</div>

<br>

<div style="font-size:110%;">

<center>
<table border="1" style="border-collapse:collapse;">
<tbody><tr>
<td style="padding:10px;">
<div id="scrollingdiv" style="height:490px;overflow:auto;">

<p>
At right is a fragment of a

<a href="http://proteopedia.org/wiki/index.php/Chain" target="_blank">polypeptide chain</a>.

In the center is a single complete alanine residue.
Check <b>Alanine</b> to identify its atoms<sup>1</sup>. The other atoms are fragments of adjacent
<a href="http://proteopedia.org/wiki/index.php/Amino_Acids" target="_blank">amino acids</a><sup>2</sup>.

<span style="background-color:#ffff80;padding:3px;">
<i>Drag with your mouse to rotate the model.</i>
</span>

</p><p>

The Alanine is covalently bonded to other amino acids through
<font color="#ff40ff"><b>peptide bonds</b></font>.
Check
<font color="#ff40ff"><b>Peptide Bonds</b></font> to locate them.

</p><p>

The double bonds between

<a href="http://proteopedia.org/wiki/index.php/Backbone_representations" target="_blank">main chain (backbone)</a>

<font color="#808080"><b><big>C</big></b></font>
and
<font color="#ff2020"><b><big>O</big></b></font>
delocalize, making the peptide bonds also have partial double bonds
(<i>half-dotted bonds</i>).
This prevents the peptide bond from rotating.

</p><p>

Each peptide bond holds six atoms
in a plane. Check <b>Planes</b> to see them.

</p><p>

The
<font color="#505050"><b>alpha carbon
(C<span style="font-family:"Times New Roman", Times, serif;">α</span>)</b></font>
in the center of each amino acid
is held in the main chain by two rotatable bonds. The

<a href="#dihedral">dihedral (torsion) angles</a>
of these bonds are called<sup>3</sup>
<font color="#00b000"><b>Phi</b></font>
and
<font color="#00b000"><b>Psi</b></font>
(in Greek letters,
<font color="#00b800"><b>φ</b></font>
and
<font color="#00b800"><b>ψ</b></font>).

<span style="background-color:#ffff80;padding:3px;">
<i>Use the radio buttons (top of right panel) to identify the rotatable main-chain bonds,
and click the -20° and +20° buttons to see them rotate.</i>
</span>

</p><p></p><center>
<hr width="50%">
Click the <b>Reset</b> button.
</center>

<p></p><p>
The balls shown are much smaller than the atoms they represent.
Check <b>van der Waals</b> to see the real sizes of the atoms<sup>4</sup>.
In fact, most
<font color="#00b800"><b>Phi</b></font>
and
<font color="#00b800"><b>Psi</b></font>
angle combinations are impossible because two atoms cannot occupy the same space.

</p><p>

Check <b>Show Clashes</b> to see where non-bonded atoms are overlapping, and thus
in physically impossible positions.
(This model simulation allows two atoms to overlap, unlike real atoms.)

</p><p>
Check <b>White</b> to make clashes easier to see.
Rotate
<font color="#00b800"><b>Phi</b></font>
and
<font color="#00b800"><b>Psi</b></font>
to find angle combinations where there are no clashes.

</p><p>
In the early 1960’s,
<a href="https://en.wikipedia.org/wiki/G._N._Ramachandran" target="_blank">G. N. Ramachandran</a>
(University of Madras, India) and coworkers
computationally determined the phi and psi angles that avoid steric collisions,
initially treating the atoms simply as rigid spheres<sup>5, 6</sup>.
They showed that the physically allowed angle combinations (that avoid clashes) correspond largely
to the secondary structures observed in proteins:
<a href="http://proteopedia.org/wiki/index.php/Secondary_structure" target="_blank">
alpha helices, beta sheets, and turns</a>.

</p><p>
Ramachandran and team also showed that the major effect of sidechains on the allowed phi and psi
angles is due to C<sub>β</sub> <sup>2</sup>.
Sidechains larger than that of alanine affect the allowed
angles by only a few percent <sup>7, 8</sup>.

</p><p>

The <i>Ramachandran Plot</i> below shows the phi and psi angles actually observed in
proteins.

</p></div></td>
<td>


<script language="javascript">
jmolApplet("500",
"script /wiki/Tutorial/Ramachandran_principle_and_phi_psi_angles/pp1.spt;javascript jmolIsReady();");
</script>
</td>


<td style="padding:10px;width:190px;">



<table border="0">
<tbody><tr><td colspan="2">



<span style="font-size:150%;font-weight:bold;background-color:#d0d0d0;padding-left:6px;padding-right:6px;padding-top:6px;" title="Chemical element color key">

<font color="#383838">C<span style="font-family:"Times New Roman", Times, serif;">α</span>
</font>

<font color="#808080">C</font>
<font color="#ffffff">H</font>
<font color="#3050ff">N</font>
<font color="#ff2020">O</font>

</span>

<br><br><br>




</td></tr><tr><td>

<label class="rcontainer" id="idrcont0">
<input type="radio" name="ppradioid" id="ppradioid_0" onclick="doRadio()" checked="">Phi φ
<span class="rcheckmark"></span>
</label>

 </td><td>

<label class="rcontainer" id="idrcont1" style="color:#a0a0a0;font-weight:normal;">
<input type="radio" name="ppradioid" id="ppradioid_1" onclick="doRadio()">Psi ψ
<span class="rcheckmark"></span>
</label>


</td></tr><tr><td id="phiangle" style="font-size:130%;font-weight:bold;color:#00c800;">
165°
</td><td id="psiangle" style="font-size:130%;text-align:right;font-weight:normal;color:#a0a0a0;">
165°

</td></tr><tr><td colspan="2" style="text-align:center;">


<span title="Rotate 10 degrees counter-clockwise">
<input type="button" class="rotationbutton" name="rminus" id="rminus" value="-20°" onclick="jmolScript(rotateminus)">
</span>

<span title="Rotate 10 degrees clockwise">
<input type="button" class="rotationbutton" name="rplus" id="rplus" value="+20°" onclick="jmolScript(rotateplus)">
</span>

</td></tr></tbody></table>




<br>


<span title="A single complete amino acid.">
<label class="container">
<input type="checkbox" name="idalanine" id="idalanine">Alanine
<span class="checkmark"></span>
</label>
</span>


<label class="container">
<input type="checkbox" name="idpeptidebonds" id="idpeptidebonds"><font color="#ff40ff">Peptide Bonds</font>
<span class="checkmark"></span>
</label>


<span title="Six atoms are held in a plane by each peptide bond.">
<label class="container">
<input type="checkbox" name="idplanes" id="idplanes">Planes
<span class="checkmark"></span>
</label>
</span>

<br>


<span title="Atoms shown actual sizes.">
<label class="container">
<input type="checkbox" name="idvdw" id="idvdw">van der Waals<sup>4</sup>
<span class="checkmark"></span>
</label>
</span>


<div name="divwhite" id="divwhite" style="display:none;">
<label class="container">
<input type="checkbox" name="idwhite" id="idwhite">    White
<span class="checkmark" style="margin-left:20px;"></span>
</label>
</div>


<label class="container">
<input type="checkbox" name="idclashes" id="idclashes">Show Clashes
<span class="checkmark"></span>
</label>

<div name="divtrailclashes" id="divtrailclashes" style="display:none;" title="Previous clashes remain during rotation.">
<label class="container">
<input type="checkbox" name="idtrailclashes" id="idtrailclashes" onclick="doTrailClashes()">    Trail Clashes
<span class="checkmark" style="margin-left:20px;"></span>
</label>
</div>

<script>
// ALTERNATE ONCLICK EVENTS FOR PROTEOPEDIA
// NOTE THAT THE FUNCTION NAME MUST BE GIVEN WITHOUT "()"

document.getElementById("idalanine").addEventListener("click", doAlanine);
document.getElementById("idpeptidebonds").addEventListener("click", doPeptideBonds);
document.getElementById("idplanes").addEventListener("click", doPlanes);
document.getElementById("idvdw").addEventListener("click", doVDW);
document.getElementById("idwhite").addEventListener("click", doWhite);
document.getElementById("idclashes").addEventListener("click", doClashes);
document.getElementById("idtrailclashes").addEventListener("click", doTrailClashes);

</script>

<br>

<center>

<input type="button" class="resetbutton" onclick="location.reload()" value="Reset">
</center>

</td></tr>
</tbody></table>
</center>


<div style="margin-left:20px;">
<img src="/wiki/Tutorial/Ramachandran_principle_and_phi_psi_angles/Ramachandran_plot_general_100K.jpg" align="right" border="0" width="600">
<a name="plot"></a><p><a name="plot"><br></a>
At right is a <i>Ramachandran Plot</i> <sup>9, 10</sup> with 100,000 data points taken from
high-resolution
crystal structures<sup>11</sup>. Each data point represents the
<a href="http://biomodel.uah.es/model5/prot/diedros_en.htm" target="_blank">combination of phi and psi angles</a>
occurring in a single
amino acid. Residues in an
<a href="http://proteopedia.org/wiki/index.php/Alpha_helix" target="_blank">alpha-helical</a>
conformation are marked
<b><span style="font-size:150%;font-family:"Times New Roman", Times, serif;">α</span></b>,
and those in a
<a href="http://proteopedia.org/wiki/index.php/Sheets_in_Proteins" target="_blank">beta strand</a>
conformation, <big><b>β</b></big>.

The cluster of data in the upper right quadrant represents mostly
<a href="http://proteopedia.org/wiki/index.php/Turns_in_Proteins" target="_blank">turns</a>.

</p><p>

This plot excludes glycine (whose sidechain is a single hydrogen), proline
(whose sidechain is covalently linked back to the main chain), and amino acids that precede
proline. These special cases have
<a href="https://en.wikipedia.org/wiki/Ramachandran_plot#Gallery" target="_blank">different distributions</a> on Ramachandran plots.

</p>

<p><span style="background:#ffd0d0;padding:10px;line-height:2;">
Challenge your understanding with the
<a href="http://proteopedia.org/w/User:Eric_Martz/Ramachandran_Principle_Quiz" target="_blank"><b>PRACTICE QUIZ</b></a>.
</span></p>

</div>

<b>Related Resources</b><br>
<ul><li>

<a name="dihedral">Dihedral (torsion) angles</a>
are explained with animated models rotating clockwise and counter-clockwise in the
<a href="https://tinyurl.com/RamachandranPrinciple" target="_blank">Slideshow</a> and the
<a href="https://tinyurl.com/RamachandranPrincipleYoutube" target="_blank">YouTube Video</a>.

</li><li>

There is also a
simple visualization of phi and psi angles at
<a href="http://biomodel.uah.es/model5/prot/diedros_en.htm" target="_blank">Dihedral angles in proteins</a>
by Angel Herráez.

</li><li>

<a href="http://proteopedia.org/w/Tutorial:Ramachandran_Plot_Inspection" target="_blank">Tutorial: Ramachandran Plot Inspection</a>: an interactive Ramachandran plot with
many controls and details, by Angel Herráez. Also
<a href="http://biomodel.uah.es/model1j/prot/Ramachandran.htm" target="_blank">in Spanish</a>.

</li><li>

<a href="http://proteopedia.org/w/Ramachandran_Plot" target="_blank">Ramachandran Plot</a>: detailed explanation with example proteins and their
plots displayed in JSmol. Here you can show the Ramachandran plot for any protein structure.

</li><li>

A list of all related resources in English and Spanish:
<a href="http://proteopedia.org/w/Dihedral/Index" target="_blank">Dihedral/Index</a>.

</li><li>

<a href="http://proteopedia.org/wiki/index.php/Backbone_representations" target="_blank">Backbone representations</a> explains the relations between backbone traces
and main chain polypeptide bonds, as well as smoothed traces and ribbons.

</li></ul>

<br clear="right"><center>
<table style="background-color:#f0ffe0;border-collapse:collapse;border:1px solid green;" cellpadding="10">
<tbody><tr><td style="text-align:center;">
This tutorial is available in two locations:
<a href="http://proteopedia.org/w/Tutorial:Ramachandran_principle_and_phi_psi_angles" target="_blank">Proteopedia.Org</a>
and
<a href="http://bioinformatics.org/molvis/phipsi" target="_blank">Bioinformatics.Org</a>.

<br>
There is also a
<a href="https://tinyurl.com/RamachandranPrinciple" target="_blank"><b>Slideshow</b></a>, a
<a href="https://tinyurl.com/RamachandranPrincipleYoutube" target="_blank"><b>YouTube Video</b></a>, and a
<a href="http://proteopedia.org/w/User:Eric_Martz/Ramachandran_Principle_Quiz" target="_blank"><b>Practice Quiz</b></a>.

<div style="font-size:80%;text-align:right;">
<a href="/wiki/Tutorial/Ramachandran_principle_and_phi_psi_angles/options.htm" target="_blank">Advanced Options</a>
</div>

</td></tr></tbody></table></center><br>

<br>
<b>Notes & References</b><br>
<ol>

<li>The outlines of the black dots that identify the atoms in Alanine are smaller than
the actual (van der Waals) sizes of those atoms. Check <b>van der Waals</b> to see the actual
sizes.

</li><br><li>
Each amino acid contributes 3 atoms directly to the
<a href="http://proteopedia.org/wiki/index.php/Backbone_representations" target="_blank">main chain (backbone)</a>
of covalent bonds:

<b>-<font color="#3050ff">N</font>-<font color="#383838">C<span style="font-family:"Times New Roman", Times, serif;">α</span></font>-<font color="#808080">C</font></b>

The model here includes -C-C-<b>N-C-C</b>-N-C-.
The central
<font color="#383838">C<span style="font-family:"Times New Roman", Times, serif;">α</span></font> has alanine's sidechain, -CH<sub>3</sub>.
Alanine's sidechain carbon is termed C<sub>β</sub>.

</li><br><li>
Edsall JT, Flory PJ, Kendrew JC, Liquori AM, Nemethy G, Ramachandran GN, Scheraga HA.
A proposal of standard conventions and nomenclature for the description of
polypeptide conformation. J Biol Chem. 1966 Feb 25;241(4):1004-8.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=5905118" target="_blank">PMID:5905118</a>

</li><br><li>
Actually, the <i>van der Waals</i> checkbox shows the atoms at 88% of their true
<a href="https://en.wikipedia.org/wiki/Van_der_Waals_radius" target="_blank">van der Waals radii</a>.
In the above simulation, clashes are reported when 88% of the true radii overlap.
This is in accord with the observations of
Ramachandran and Sasisekharan<sup>6</sup>, who found that allowed interatomic distances
for non-bonded atoms are ~0.4 Å less than their van der Waals radii<sup>10</sup>.
The van der Waals radius of carbon is 1.7 Å. Thus, the van der Waals distance between
the centers of two non-bonded carbon atoms is 3.4 Å. However the minimum allowed distance
is about 0.4 Å less, which is 12% less. Thus 88% of the true van der Waals radii was
used in the above simulation for detection of "clashes".

</li><br><li>
Ramachandran, G. N., Ramakrishnan, C., Sasisekharan, V.
Stereochemistry of polypeptide chain configurations.
J Mol Biol. 1963 Jul;7:95-9.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=13990617" target="_blank">PMID:13990617</a>

</li><br><li>
Ramachandran, G. N., Sasisekharan V. Conformation of polypeptides and proteins.
Adv Protein Chem. 1968;23:283-438.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=4882249" target="_blank">PMID:4882249</a>

</li><br><li>
Ramakrishnan, C., Ramachandran, G. N.
Stereochemical criteria for polypeptide and protein chain conformations. II.
Allowed conformations for a pair of peptide units. Biophys J. 1965 Nov;5(6):909-33.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=5884016" target="_blank">PMID:5884016</a>

</li><br><li>
Chakrabarti P, Pal D. The interrelationships of side-chain and main-chain conformations in
proteins. Prog Biophys Mol Biol. 2001;76(1-2):1-102.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=11389934" target="_blank">PMID:11389934</a>

</li><br><li>
The plot shown<sup>11</sup> is
<a href="https://en.wikipedia.org/wiki/Ramachandran_plot#/media/File:Ramachandran_plot_general_100K.jpg" target="_blank">
available in the Wikimedia Commons</a>
courtesy of Jane and David Richardson.

</li><br><li>
Ramachandran and Sasisekharan<sup>6</sup> determined inter-atomic distances of
closest approach of non-bonded atoms from crystal structures. For each pair of elements
(their Table VI), they determined an allowed distance, and a partially allowed distance.
Distances less than the partially allowed values are “very unlikely” to occur due to
steric repulsion. The allowed distances are 0.3 to 0.5 Å less than the
<a href="https://en.wikipedia.org/wiki/Van_der_Waals_radius" target="_blank">van der Waals radii</a>.
(their page 327).
The partially allowed distances are usually 0.1 Å, sometimes 0.2 Å,
less than the allowed distances.

</li><br><li>
Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG,
Richardson JS, Richardson DC.
Structure validation by C-alpha geometry: phi, psi and C-beta deviation.
Proteins. 2003 Feb 15;50(3):437-50.
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=12557186" target="_blank">PMID:12557186</a>

</li></ol>

<br>
<center>
<hr width="60%">

This page is by
<a href="http://martz.molviz.org" target="_blank">Eric Martz</a>.

<br>
License:
<a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" target="_blank">
Attribution-NonCommercial-ShareAlike 4.0 International</a>.

<br>
Released May 27, 2018. Enhanced June 24 and July 16, 2018.

<br>
Many thanks to
<a href="https://www.stolaf.edu/people/hansonr/" target="_blank">Bob Hanson</a>
and the
<a href="http://jmol.sourceforge.net/history/" target="_blank">JSmol Team</a>,
and to
<a href="http://proteopedia.org/w/User:Jaime_Prilusky" target="_blank">Jaime Prilusky</a>
for adaptation to Proteopedia.Org.

<hr width="60%">
</center>

<br><br><br><br>
</div>

User:Angel Herraez/Sandbox Rama

2026-08-23T17:49:34Z

Angel Herraez: Angel Herraez changed the content model of the page User:Angel Herraez/Sandbox Rama from "wikitext" to "plain text": test content model

test
<script> a = 3; b = a+10; </script>

User:Angel Herraez/Sandbox Rama

2026-08-23T17:48:52Z

Angel Herraez: Created page with "test <script> a = 3; b = a+10; </script>"

test
<script> a = 3; b = a+10; </script>

2026-07-11T10:55:18Z

Angel Herraez: /* RNase A multiple conformations (2AAS) */

2026-07-09T13:54:45Z

Angel Herraez: Created page with "<StructureSection load='3kg2' size='300' scene ='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1' caption='Glutamate Receptor Structure (PDB code 3kg2)' name='main2NDwindow' >. </StructureSection>"

Glutamate receptor (GluA2)

2026-07-09T13:41:23Z

Angel Herraez: The structure panel is not displayed for lack of closing tag. Returning to last version by Wayne Decatur (16 December 2013) plus 3 new extra links at the end

[[Image:3KG2-snapshot-900x900-14724.jpg|left|270px]]
The glutamate receptor is the ion channel opened by glutamate that keeps neurons in touch by mediating fast cell-to-cell information transfer in the nervous system. Several studies have revealed structures for portions of the glutamate receptor <ref name="r80">PMID: 19461580</ref><ref name="r14">PMID: 19465914</ref><ref name="r22">PMID: 19910922</ref><ref>PMID: 9804426</ref>. Groundbreaking work elucidated the structure of a complete functional, homomeric glutamate receptor<ref name="main">PMID:19946266</ref><ref>PMID: 20010675</ref> and that structure, [[3kg2]], is the subject of this page.
<div style="clear:none !important; display:inline-block;">__TOC__</div>

<br style="clear:both;">

==Structure of the Glutamate Receptor (GluA2)==
<table><tr>
<td><div style="height:600px!important; overflow:auto;">
===Overview===
The homomeric rat GluA2 receptor <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1' target='main1STwindow'> has four subunits</scene> arranged in a 'Y'-shape with the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Meas3kg2/1' target='main1STwindow'>'top' being about three times the width of the 'bottom'</scene><ref name="main" />. This structure is a functional homotetramer of the AMPA-subtype; native ionotropic glutamate receptors are almost exclusively heterotetramers. {{Link Toggle FancyCartoonHighQualityView}}.

===Domains===
The subunits themselves are modular <ref>PMID: 7539962</ref>and the major domains are found in layers in the tetrameric structure.

*The 'top' layer is composed of the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atd_domain/4' target='main1STwindow'>amino-terminal domain(ATD)</scene>
::This <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atd_gly/2' target='main1STwindow'>extracellular domain is glycosylated</scene>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Lbd_domain/4' target='main1STwindow'>The ligand-binding domain (LBD)</scene> participates directly in agonist/competitive antagonist binding, affects activation gating, and is the portion that forms the 'middle' layer.
::<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Lbd_zk1/2' target='main1STwindow'>The competitive antagonist ZK200775 is bound to the LBD</scene> in the structure.
::The small molecule <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Zk1_zoom/1' target='main1STwindow'>ZK200775, a phosphonate quinoxalinedione AMPA antagonist</scene><ref>PMID: 9724812</ref>, was studied as a treatment for stroke because it had demonstrated neuroprotective efficacy in experimental models of stroke and tolerability in healthy volunteers; however, in a multicenter, double-blind, randomized, placebo-controlled phase II trial, it was found to have significant sedative effects in patients with acute stroke which precludes its further development as a neuroprotective agent<ref>PMID: 16131799</ref>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmd_domain/2' target='main1STwindow'>The transmembrane domain (TMD)</scene> is the portion that forms the membrane-spanning on the 'bottom' of the solved structure.
::To help give a better idea of how the glutamate receptor is oriented on the cell surface in the membrane lipid bilayer, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/3kg2opm_mem/11' target='main1STwindow'>a slab representative of hydrophobic core of the lipid bilayer</scene> as calculated by the [http://opm.phar.umich.edu/protein.php?pdbid=3kg2 Orientations of Proteins in Membranes database] (University of Michigan, USA) is shown with the red patch of spheres indicating the boundary of the hydrophobic core closet to the outside of the cell and the dark blue patch of spheres indicating the boundary closest to the inside of the cell.
::[[Image:Opm_periplasmic_topology.gif]]
* The carboxy-terminal domain that plays a role in both receptor localization and regulation is not seen in the structure but would be below the transmembrane domain as it is cytoplasmic.

===Domain swapping between the subunits and symmetry mismatch between the domains===
*Unanticipated is the domain swapping and crossover that occurs between the subunits interactions. In order to discuss the remarkable swapping, it is best to <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2letter/4' target='main1STwindow'>designate each subunit with a letter</scene>: <br>    '''<span style="color:forestgreen">A</span>'''       '''<span style="color:red">B</span>'''       '''<span style="color:cornflowerblue">C</span>'''        '''D'''

*Considering each chain, there is crossover as the pairs of subunits seen in the ATD are swapped in the LBD.
::In the ATD domain -
::*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ab_in_atd/1' target='main1STwindow'>Portions of the A and B subunits pair up</scene>.
::*And the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Cd_in_atd/2' target='main1STwindow'>Portions of the C and D subunits form a pair</scene>.
::*While that is going on, in the ATD there is also inter-pair interactions mediated between <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_atd/2' target='main1STwindow'>subunits B and D</scene>. Note this view really highlights the two-fold symmetry between the A-B and C-D pairs at the level of the ATD.
::In the LBD domain -
::*Whereas in the ATD domain A and B paired up, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ad_in_lbd/3' target='main1STwindow'>portions of the A and D subunits pair up</scene> in the LBD.
::*And the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Bc_in_lbd/1' target='main1STwindow'>Portions of the B and C subunits form a pair</scene>.
::*While that is going on, in the LBD there is also extensive inter-pair interactions mediated between <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_lbd/6' target='main1STwindow'>subunits A and C</scene>. Note this view highlights the two-fold symmetry between the A-D and B-C pairs at the level of the LBD. <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_lbdside/1' target='main1STwindow'>Looking from the side helps in seeing the inter-pair interactions between A and C</scene>.
:The domain swapping can be observed from the side following the backbone of each chain as well: <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/1' target='main1STwindow'>A chain</scene>, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/2' target='main1STwindow'>B chain</scene>, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/3' target='main1STwindow'>C chain</scene>, and <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/5' target='main1STwindow'>D chain</scene>. And <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2letter/4' target='main1STwindow'>all for comparison</scene>.

*As explored further in [[#Transmembrane domain architecture and the occluded pore|a later section below]] , the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmd_domain_4fold/2' target='main1STwindow'>symmetry is an overall four-fold for the TMD</scene>. Thus, remarkably, the symmetry switches from an overall two-fold symmetry for the ATD and LBD to four-fold for the TMD.
</div>
</td>
<td>
<StructureSection load='3kg2' size='500' side='left' scene='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1' caption='The rat glycosylated glutamate receptor in complex with a competitive antagonist ([[3kg2]])' name='main1STwindow'>
</StructureSection>

</td>
</tr></table>

<br style="clear:both;">
===Subunit Non-Equivalence, Transmembrane Domain Architecture and the Occluded Pore===
<div style="float:left;">
<StructureSection load='3kg2' size='500' scene ='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1' caption='Glutamate Receptor Structure (PDB code [[3kg2]])' name='main2NDwindow' >
</StructureSection>

<table cellpadding='2' style='width:300px; margin-right:1.3em;'>
<tr>
<td bgcolor='#eeeeee'>
<applet load='3kg2' size='190' frame='true' align='left' scene='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ac3kg2letter/1' caption='A is equivalent to C'/>
</td>
<td bgcolor='#eeeeee'>
<applet load='3kg2' size='190' frame='true' align='left' scene='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Bd3kg2letter/2' caption='B is equivalent to D'/>
</td>
</tr>
</table>

</div>

===Subunit non-equivalence===
As a result of the swapping and symmetry mismatch, there is subunit non-equivalence; even though all the chains are the same chemically, there are two distinct conformations of the subunits. This means there are two matching pairs of subunits. The pairs are illustrated below and the morphs referred to below will show in the main window on the left:

* <span style="color:forestgreen">Subunit '''A'''</span> is equivalent to <span style="color:cornflowerblue">Subunit '''C'''</span> (in the small structure window in this section). In the main window, a <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atocmorph/5' target='main2NDwindow'>morph showing the equivalency of the two subunits by rotating around the axis of their symmetry</scene>.
* <span style="color:red">Subunit '''B</span>''' is equivalent to Subunit '''D''' (in the small structure window in this section).  In the main window, a <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Btodmorph/5' target='main2NDwindow'>morph showing the equivalency of the two subunits by rotating around the axis of their symmetry</scene>.

However, each of the subunit '''<span style="color:forestgreen">A</span>'''/<span style="color:cornflowerblue">'''C'''</span> group though is distinct from those of the <span style="color:red">'''B</span>'''/'''D''' group. Having established the two equivalent groups we can simplify the discussion of the relationship between the two pairs by focusing solely on comparing <span style="color:forestgreen">Subunit '''A'</span>''' and <span style="color:red">Subunit '''B</span>'''.<br>
The domains themselves stay relatively static between the two conformational forms, with the linkers in between and the resulting arrangement changing. This is best illustrated by superposition of the individual domains of <span style="color:forestgreen">Subunit '''A</span>''' and <span style="color:red">Subunit '''B</span>''':
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atdatobsuper/4' target='main2NDwindow'>Superposition of the ATD</scene>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Lbdatobsuper/2' target='main2NDwindow'>Superposition of the LBD</scene>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmdatobsuper/1' target='main2NDwindow'>Superposition of the TMD</scene>.

<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atobmorph/2' target='main2NDwindow'>Subunit A morphing into Subunit B best illustrates how portions, especially the linkers, of the protein change</scene> between the two conformational forms.<br>
{{Button Toggle AnimationOnPause}}
:The linkers are key; besides playing roles in domain swapping and resolving the symmetry mismatch, they are also responsible for relaying the modulation signals from the ATD to the other domains and signaling the conformational change of the LBD to control the opening and closing of the pore. Beyond the two conformations seen here though this particular structure ([[3kg2]]) of the receptor does not shed light on the transduction process.

===Transmembrane domain architecture and the occluded pore===
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmemlabeled/1' target='main2NDwindow'>Transmembrane segments M1 to M4 depicted in different colors to show the approximate 4-fold rotational symmetry of the entire ion channel domain.</scene>
::* '''<span style="color:coral">M1</span>'''
::* '''<span style="color:lightgreen">M2</span>'''
::* '''<span style="color:violet">M3</span>'''
::* '''<span style="color:lightskyblue">M4</span>'''

*The segments shown again, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmem/4' target='main2NDwindow'>this time parallel to the four-fold axis</scene>.
::There is <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmemclosed/1'>no pore visible in the center</scene> consistent with the channel being in a closed state with the antagonist (ZK200775) bound to the LBD.
::It is <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/M3_closed/3' target='main2NDwindow'>the tight helix crossing of specifically the M3 helices</scene> that occludes the channel. [BE PATIENT as a small surface is generated.]
::Note <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/M3_closed_top/1' target='main2NDwindow'>the differences between the conformations of the carboxy-termini ('top') of the subunit A/C and B/D M3 segments</scene>. This is in part is why the symmetry is only approximately four-fold and is one of the several intriguing observations in regard to symmetry for this macromolecule. In fact, the location of two-fold symmetry at the ends of M3 is just above the portion that spans the membrane and is close to the last region of the structure that doesn't show four-fold symmetry as abruptly below this point everything is four-fold symmetric.

*To better observe the contributions of each of the membrane segments to the subunit-subunit interactions, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Trans_surf/4' target='main2NDwindow'>the transmembrane domains of three subunits are shown in a surface representation with the segments M1-M4 of the fourth subunit shown as green cylinders</scene>. <nowiki>[</nowiki>Note: this scene generates a substantial surface which may take about a minute to calculate. Be patient.<nowiki>]</nowiki>
::Note that the M4 segment associates with the ion-channel core of an adjacent subunit.
:{{Link Toggle FancyCartoonHighQualityView}}.
*The TMD domain of the GluA2 receptor shares structural and sequence similarity with the pore region of the potassium (K+), as hinted at by earlier work<ref name ="pot1">PMID: 7539962</ref><ref name ="pot2">PMID: 7761417</ref><ref name ="pot3">PMID: 9525859</ref>. Here the pore region of ''Streptomyces lividans'' potassium channel ([[1bl8]])<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmd/4' target='main2NDwindow'> superposed with the TMD domain of GluA2</scene>, specifically the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm3/1' target='main2NDwindow'>inner helix of the K+ channel aligned with the M3 segment</scene>. The <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm1/2' target='main2NDwindow'>M1 segment of GluA2 also overlays well with the outer helix</scene> of the K+ channel even though these portions weren't even included in the calculation of the alignment seen here.

==Details of Structure Featured==
[[3kg2]] is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KG2 OCA]. Although it is billed as the first structure of a full-length glutamate receptor, the carboxy-terminal domain is not present in the structure.

==Reference for the structure==
<ref group="xtra">PMID:19946266</ref><references group="xtra"/>

==3D structures of glutamate receptors==

[[Ionotropic Glutamate Receptors]]

==See Also==

* [[1iiw]] and [[1iit]] and [[1ii5]] – Prokaryotic glutamte receptor (Glur0) Apo structure and with various ligands bound, including glutmate <ref>PMID: 10617203</ref>. This helped cement the notion the glutamate and potassium receptors share structural similarity and possibly evolutionary ancestry <ref name="pot1" /><ref name="pot2" />.
* [[1bl8]] and [[1jq1]] and [[1jq2]] – ''Streptomyces lividans'' KcsA potassium channel<ref name="pot3" /><ref>PMID:11573095</ref>: The M1, M2 and M3 segments of GluA2's ion channel overlap remarkably well with the structurally equivalent portions KcsA.
* [[Molecular Playground/Glutamate Receptor]]
* [[Ligand Binding N-Terminal of Metabotropic Glutamate Receptors]]
* [[Receptor]]
* [[Transmembrane (cell surface) receptors]]
* [[Ionotropic receptors]]

==References==
{{Reflist}}

==Additional Literature and Resources==
* For additional information, see: [[Alzheimer's Disease]]
* For additional information, see: [[Membrane Channels & Pumps]]
* [http://www.nature.com/nature/journal/v462/n7274/covers/ Glutamate Receptor on the cover] of [http://www.nature.com/ Nature]
* [http://en.wikipedia.org/wiki/Glutamate_receptor Glutamate receptor Wikipedia entry]
* [http://www.bristol.ac.uk/synaptic/receptors/#ionotropic Glutamate Receptors page] at the [http://www.bristol.ac.uk/synaptic/ MRC Centre for Synaptic Plasticity at the University of Bristol]

''Page started with original page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 16 11:24:54 2009 for [[3kg2]].''

[[Category: Rattus norvegicus]]
[[Category: Gouaux, E.]]
[[Category: Rosconi, M P.]]
[[Category: Sobolevsky, A I.]]
[[Category: Alternative splicing]]
[[Category: Cell membrane]]
[[Category: Glycoprotein]]
[[Category: Ion channel]]
[[Category: Ion transport]]
[[Category: Membrane]]
[[Category: Membrane protein]]
[[Category: Postsynaptic cell membrane]]
[[Category: Receptor]]
[[Category: Rna editing]]
[[Category: Synapse]]
[[Category: Tetramer]]
[[Category: Transmembrane]]
[[Category: Transport]]
[[Category: Neuron]]
[[Category: Neurotransmitter]]
[[Category: Potassium Channels]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Streptomyces lividans]]
[[Category: Cabral, J M.]]
[[Category: Chait, B T.]]
[[Category: Cohen, S L.]]
[[Category: Doyle, D A.]]
[[Category: Gulbis, J M.]]
[[Category: Kuo, A.]]
[[Category: Mackinnon, R.]]
[[Category: Pfuetzner, R A.]]
[[Category: Integral membrane protein]]
[[Category: Potassium channel]]
[[Category:Topic Page]]

Glutamate receptor (GluA2)

2026-07-08T15:49:19Z

Angel Herraez: The structure panel is not displayed for lack of closing tag. Returning to last version by Wayne Decatur (16 December 2013) plus 3 new extra links at the end

[[Image:3KG2-snapshot-900x900-14724.jpg|left|270px]]
The glutamate receptor is the ion channel opened by glutamate that keeps neurons in touch by mediating fast cell-to-cell information transfer in the nervous system. Several studies have revealed structures for portions of the glutamate receptor <ref name="r80">PMID: 19461580</ref><ref name="r14">PMID: 19465914</ref><ref name="r22">PMID: 19910922</ref><ref>PMID: 9804426</ref>. Groundbreaking work elucidated the structure of a complete functional, homomeric glutamate receptor<ref name="main">PMID:19946266</ref><ref>PMID: 20010675</ref> and that structure, [[3kg2]], is the subject of this page.
<div style="clear:none !important; display:inline-block;">__TOC__</div>

<br style="clear:both;">

==Structure of the Glutamate Receptor (GluA2)==
<table><tr>
<td><div style="height:600px!important; overflow:auto;">
===Overview===
The homomeric rat GluA2 receptor <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1'>has four subunits</scene> arranged in a 'Y'-shape with the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Meas3kg2/1'>'top' being about three times the width of the 'bottom'</scene><ref name="main" />. This structure is a functional homotetramer of the AMPA-subtype; native ionotropic glutamate receptors are almost exclusively heterotetramers. {{Link Toggle FancyCartoonHighQualityView}}.

===Domains===
The subunits themselves are modular <ref>PMID: 7539962</ref>and the major domains are found in layers in the tetrameric structure.

*The 'top' layer is composed of the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atd_domain/4'>amino-terminal domain(ATD)</scene>
::This <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atd_gly/2'>extracellular domain is glycosylated</scene>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Lbd_domain/4'>The ligand-binding domain (LBD)</scene> participates directly in agonist/competitive antagonist binding, affects activation gating, and is the portion that forms the 'middle' layer.
::<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Lbd_zk1/2'>The competitive antagonist ZK200775 is bound to the LBD</scene> in the structure.
::The small molecule <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Zk1_zoom/1'>ZK200775, a phosphonate quinoxalinedione AMPA antagonist</scene><ref>PMID: 9724812</ref>, was studied as a treatment for stroke because it had demonstrated neuroprotective efficacy in experimental models of stroke and tolerability in healthy volunteers; however, in a multicenter, double-blind, randomized, placebo-controlled phase II trial, it was found to have significant sedative effects in patients with acute stroke which precludes its further development as a neuroprotective agent<ref>PMID: 16131799</ref>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmd_domain/2'>The transmembrane domain (TMD)</scene> is the portion that forms the membrane-spanning on the 'bottom' of the solved structure.
::To help give a better idea of how the glutamate receptor is oriented on the cell surface in the membrane lipid bilayer, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/3kg2opm_mem/11'>a slab representative of hydrophobic core of the lipid bilayer</scene> as calculated by the [http://opm.phar.umich.edu/protein.php?pdbid=3kg2 Orientations of Proteins in Membranes database] (University of Michigan, USA) is shown with the red patch of spheres indicating the boundary of the hydrophobic core closet to the outside of the cell and the dark blue patch of spheres indicating the boundary closest to the inside of the cell.
::[[Image:Opm_periplasmic_topology.gif]]
* The carboxy-terminal domain that plays a role in both receptor localization and regulation is not seen in the structure but would be below the transmembrane domain as it is cytoplasmic.

===Domain swapping between the subunits and symmetry mismatch between the domains===
*Unanticipated is the domain swapping and crossover that occurs between the subunits interactions. In order to discuss the remarkable swapping, it is best to <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2letter/4'>designate each subunit with a letter</scene>: <br>    '''<span style="color:forestgreen">A</span>'''       '''<span style="color:red">B</span>'''       '''<span style="color:cornflowerblue">C</span>'''        '''D'''

*Considering each chain, there is crossover as the pairs of subunits seen in the ATD are swapped in the LBD.
::In the ATD domain -
::*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ab_in_atd/1'>Portions of the A and B subunits pair up</scene>.
::*And the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Cd_in_atd/2'>Portions of the C and D subunits form a pair</scene>.
::*While that is going on, in the ATD there is also inter-pair interactions mediated between <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_atd/2'>subunits B and D</scene>. Note this view really highlights the two-fold symmetry between the A-B and C-D pairs at the level of the ATD.
::In the LBD domain -
::*Whereas in the ATD domain A and B paired up, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ad_in_lbd/3'>portions of the A and D subunits pair up</scene> in the LBD.
::*And the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Bc_in_lbd/1'>Portions of the B and C subunits form a pair</scene>.
::*While that is going on, in the LBD there is also extensive inter-pair interactions mediated between <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_lbd/6'>subunits A and C</scene>. Note this view highlights the two-fold symmetry between the A-D and B-C pairs at the level of the LBD. <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Abcd_in_lbdside/1'>Looking from the side helps in seeing the inter-pair interactions between A and C</scene>.
:The domain swapping can be observed from the side following the backbone of each chain as well: <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/1'>A chain</scene>, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/2'>B chain</scene>, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/3'>C chain</scene>, and <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Swap_full_side/5'>D chain</scene>. And <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2letter/4'>all for comparison</scene>.

*As explored further in [[#Transmembrane domain architecture and the occluded pore|a later section below]] , the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmd_domain_4fold/2'>symmetry is an overall four-fold for the TMD</scene>. Thus, remarkably, the symmetry switches from an overall two-fold symmetry for the ATD and LBD to four-fold for the TMD.
</div>
</td>
<td>
<Structure load='3kg2' size='500' side='right' scene='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1' caption='The rat glycosylated glutamate receptor in complex with a competitive antagonist ([[3kg2]])' />

</td>
</tr></table>

<br style="clear:both;">
===Subunit Non-Equivalence, Transmembrane Domain Architecture and the Occluded Pore===
<div style="float:left;">
<StructureSection load='3kg2' size='500' scene ='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1' caption='Glutamate Receptor Structure (PDB code [[3kg2]])' name='main2NDwindow' >
</StructureSection>

<table cellpadding='2' style='width:300px; margin-right:1.3em;'>
<tr>
<td bgcolor='#eeeeee'>
<applet load='3kg2' size='190' frame='true' align='left' scene='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ac3kg2letter/1' caption='A is equivalent to C'/>
</td>
<td bgcolor='#eeeeee'>
<applet load='3kg2' size='190' frame='true' align='left' scene='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Bd3kg2letter/2' caption='B is equivalent to D'/>
</td>
</tr>
</table>

</div>

===Subunit non-equivalence===
As a result of the swapping and symmetry mismatch, there is subunit non-equivalence; even though all the chains are the same chemically, there are two distinct conformations of the subunits. This means there are two matching pairs of subunits. The pairs are illustrated below and the morphs referred to below will show in the main window on the left:

* <span style="color:forestgreen">Subunit '''A'''</span> is equivalent to <span style="color:cornflowerblue">Subunit '''C'''</span> (in the small structure window in this section). In the main window, a <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atocmorph/5' target='main2NDwindow'>morph showing the equivalency of the two subunits by rotating around the axis of their symmetry</scene>.
* <span style="color:red">Subunit '''B</span>''' is equivalent to Subunit '''D''' (in the small structure window in this section).  In the main window, a <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Btodmorph/5' target='main2NDwindow'>morph showing the equivalency of the two subunits by rotating around the axis of their symmetry</scene>.

However, each of the subunit '''<span style="color:forestgreen">A</span>'''/<span style="color:cornflowerblue">'''C'''</span> group though is distinct from those of the <span style="color:red">'''B</span>'''/'''D''' group. Having established the two equivalent groups we can simplify the discussion of the relationship between the two pairs by focusing solely on comparing <span style="color:forestgreen">Subunit '''A'</span>''' and <span style="color:red">Subunit '''B</span>'''.<br>
The domains themselves stay relatively static between the two conformational forms, with the linkers in between and the resulting arrangement changing. This is best illustrated by superposition of the individual domains of <span style="color:forestgreen">Subunit '''A</span>''' and <span style="color:red">Subunit '''B</span>''':
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atdatobsuper/4' target='main2NDwindow'>Superposition of the ATD</scene>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Lbdatobsuper/2' target='main2NDwindow'>Superposition of the LBD</scene>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmdatobsuper/1' target='main2NDwindow'>Superposition of the TMD</scene>.

<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atobmorph/2' target='main2NDwindow'>Subunit A morphing into Subunit B best illustrates how portions, especially the linkers, of the protein change</scene> between the two conformational forms.<br>
{{Button Toggle AnimationOnPause}}
:The linkers are key; besides playing roles in domain swapping and resolving the symmetry mismatch, they are also responsible for relaying the modulation signals from the ATD to the other domains and signaling the conformational change of the LBD to control the opening and closing of the pore. Beyond the two conformations seen here though this particular structure ([[3kg2]]) of the receptor does not shed light on the transduction process.

===Transmembrane domain architecture and the occluded pore===
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmemlabeled/1' target='main2NDwindow'>Transmembrane segments M1 to M4 depicted in different colors to show the approximate 4-fold rotational symmetry of the entire ion channel domain.</scene>
::* '''<span style="color:coral">M1</span>'''
::* '''<span style="color:lightgreen">M2</span>'''
::* '''<span style="color:violet">M3</span>'''
::* '''<span style="color:lightskyblue">M4</span>'''

*The segments shown again, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmem/4' target='main2NDwindow'>this time parallel to the four-fold axis</scene>.
::There is <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmemclosed/1'>no pore visible in the center</scene> consistent with the channel being in a closed state with the antagonist (ZK200775) bound to the LBD.
::It is <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/M3_closed/3' target='main2NDwindow'>the tight helix crossing of specifically the M3 helices</scene> that occludes the channel. [BE PATIENT as a small surface is generated.]
::Note <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/M3_closed_top/1' target='main2NDwindow'>the differences between the conformations of the carboxy-termini ('top') of the subunit A/C and B/D M3 segments</scene>. This is in part is why the symmetry is only approximately four-fold and is one of the several intriguing observations in regard to symmetry for this macromolecule. In fact, the location of two-fold symmetry at the ends of M3 is just above the portion that spans the membrane and is close to the last region of the structure that doesn't show four-fold symmetry as abruptly below this point everything is four-fold symmetric.

*To better observe the contributions of each of the membrane segments to the subunit-subunit interactions, <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Trans_surf/4' target='main2NDwindow'>the transmembrane domains of three subunits are shown in a surface representation with the segments M1-M4 of the fourth subunit shown as green cylinders</scene>. <nowiki>[</nowiki>Note: this scene generates a substantial surface which may take about a minute to calculate. Be patient.<nowiki>]</nowiki>
::Note that the M4 segment associates with the ion-channel core of an adjacent subunit.
:{{Link Toggle FancyCartoonHighQualityView}}.
*The TMD domain of the GluA2 receptor shares structural and sequence similarity with the pore region of the potassium (K+), as hinted at by earlier work<ref name ="pot1">PMID: 7539962</ref><ref name ="pot2">PMID: 7761417</ref><ref name ="pot3">PMID: 9525859</ref>. Here the pore region of ''Streptomyces lividans'' potassium channel ([[1bl8]])<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmd/4' target='main2NDwindow'> superposed with the TMD domain of GluA2</scene>, specifically the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm3/1' target='main2NDwindow'>inner helix of the K+ channel aligned with the M3 segment</scene>. The <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm1/2' target='main2NDwindow'>M1 segment of GluA2 also overlays well with the outer helix</scene> of the K+ channel even though these portions weren't even included in the calculation of the alignment seen here.

==Details of Structure Featured==
[[3kg2]] is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KG2 OCA]. Although it is billed as the first structure of a full-length glutamate receptor, the carboxy-terminal domain is not present in the structure.

==Reference for the structure==
<ref group="xtra">PMID:19946266</ref><references group="xtra"/>

==3D structures of glutamate receptors==

[[Ionotropic Glutamate Receptors]]

==See Also==

* [[1iiw]] and [[1iit]] and [[1ii5]] – Prokaryotic glutamte receptor (Glur0) Apo structure and with various ligands bound, including glutmate <ref>PMID: 10617203</ref>. This helped cement the notion the glutamate and potassium receptors share structural similarity and possibly evolutionary ancestry <ref name="pot1" /><ref name="pot2" />.
* [[1bl8]] and [[1jq1]] and [[1jq2]] – ''Streptomyces lividans'' KcsA potassium channel<ref name="pot3" /><ref>PMID:11573095</ref>: The M1, M2 and M3 segments of GluA2's ion channel overlap remarkably well with the structurally equivalent portions KcsA.
* [[Molecular Playground/Glutamate Receptor]]
* [[Ligand Binding N-Terminal of Metabotropic Glutamate Receptors]]
* [[Receptor]]
* [[Transmembrane (cell surface) receptors]]
* [[Ionotropic receptors]]

==References==
{{Reflist}}

==Additional Literature and Resources==
* For additional information, see: [[Alzheimer's Disease]]
* For additional information, see: [[Membrane Channels & Pumps]]
* [http://www.nature.com/nature/journal/v462/n7274/covers/ Glutamate Receptor on the cover] of [http://www.nature.com/ Nature]
* [http://en.wikipedia.org/wiki/Glutamate_receptor Glutamate receptor Wikipedia entry]
* [http://www.bristol.ac.uk/synaptic/receptors/#ionotropic Glutamate Receptors page] at the [http://www.bristol.ac.uk/synaptic/ MRC Centre for Synaptic Plasticity at the University of Bristol]

''Page started with original page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 16 11:24:54 2009 for [[3kg2]].''

[[Category: Rattus norvegicus]]
[[Category: Gouaux, E.]]
[[Category: Rosconi, M P.]]
[[Category: Sobolevsky, A I.]]
[[Category: Alternative splicing]]
[[Category: Cell membrane]]
[[Category: Glycoprotein]]
[[Category: Ion channel]]
[[Category: Ion transport]]
[[Category: Membrane]]
[[Category: Membrane protein]]
[[Category: Postsynaptic cell membrane]]
[[Category: Receptor]]
[[Category: Rna editing]]
[[Category: Synapse]]
[[Category: Tetramer]]
[[Category: Transmembrane]]
[[Category: Transport]]
[[Category: Neuron]]
[[Category: Neurotransmitter]]
[[Category: Potassium Channels]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Streptomyces lividans]]
[[Category: Cabral, J M.]]
[[Category: Chait, B T.]]
[[Category: Cohen, S L.]]
[[Category: Doyle, D A.]]
[[Category: Gulbis, J M.]]
[[Category: Kuo, A.]]
[[Category: Mackinnon, R.]]
[[Category: Pfuetzner, R A.]]
[[Category: Integral membrane protein]]
[[Category: Potassium channel]]
[[Category:Topic Page]]