Proteopedia:Development: Difference between revisions

(25 intermediate revisions by 2 users not shown)

Line 2:

* [[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 ==

Line 55:

Line 173:

=== Template for ConSurf ===

A mediawiki template, [[Template:ConSurf|~~<nowiki>~~{{ConSurf}}~~</nowiki>~~]], 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.

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:

Proteopedia:Development: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 2: / Line 2: @@
 * [[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 ==
@@ Line 55: / Line 173: @@
 === Template for ConSurf ===
-A mediawiki template, [[Template:ConSurf|<nowiki>{{ConSurf}}</nowiki>]], 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.
+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: