Proteopedia:Development: Difference between revisions

Line 48:

** 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|<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.

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.

* Implement also the “rocking” motion as an alternative animated display.

=== 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 {{file|initialview02v3.spt}} 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]]

=== Tutorial: Ramachandran Plot Inspection ===

Interactive page displaying dihedral angles (ϕ and ψ) in a JSmol model of proteins and the Ramachandran plot. Both displays are linked.

This is a highly customised page that uses Javascript, css, and html tags not allowed by the regular mediawiki editor.

A special procedure allowed to include it in [[Tutorial:Ramachandran_Plot_Inspection]]

The page is protected, non-editable.

Pending:

* A few bugs in the page controls remain to be fixed.

=== 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

* 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)

==== 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.

==== Category:Pyrho ====

[[Category:Pyrho]] which is very frequent, inserts a bad link to Wikipedia

==== Localisation ====

* When a page is written in a non-English language, the language of the JSmol interface could be changed to match.

Proteopedia:Development: Difference between revisions

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@@ Line 48: / Line 48: @@
 ** 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|<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.
+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.
+* Implement also the “rocking” motion as an alternative animated display.
+=== 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 {{file|initialview02v3.spt}} 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]]
+=== Tutorial: Ramachandran Plot Inspection ===
+Interactive page displaying dihedral angles (ϕ and ψ) in a JSmol model of proteins and the Ramachandran plot. Both displays are linked.
+This is a highly customised page that uses Javascript, css, and html tags not allowed by the regular mediawiki editor.
+A special procedure allowed to include it in [[Tutorial:Ramachandran_Plot_Inspection]]
+The page is protected, non-editable.
+Pending:
+* A few bugs in the page controls remain to be fixed.
+=== 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
+* 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)
+==== 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.
+==== Category:Pyrho ====
+[[Category:Pyrho]]  which is very frequent, inserts a bad link to Wikipedia
+==== Localisation ====
+* When a page is written in a non-English language, the language of the JSmol interface could be changed to match.