Proteopedia:Development - Revision history

Angel Herraez: image showing the colour legends according to reliability of predicted structures

2023-08-21T17:36:42Z

image showing the colour legends according to reliability of predicted structures

←Older revision		Revision as of 17:36, 21 August 2023
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	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 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.	+	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===		===Prediction of structure===

Angel Herraez: documenting developments in March 2023

2023-08-21T17:11:49Z

documenting developments in March 2023

←Older revision		Revision as of 17:11, 21 August 2023
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	* [[Proteopedia:Wishlist]]		* [[Proteopedia:Wishlist]]
	* [[Proteopedia:Problems]]		* [[Proteopedia:Problems]]
		+
		+	==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.
		+
		+	===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==		==Alcalá, Spain, March 2021==

Jaime Prilusky at 18:15, 14 March 2021

2021-03-14T18:15:41Z

←Older revision		Revision as of 18:15, 14 March 2021
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	* [[Proteopedia:Wishlist]]		* [[Proteopedia:Wishlist]]
	* [[Proteopedia:Problems]]		* [[Proteopedia:Problems]]
		+
		+	==Alcalá, Spain, March 2021==
		+	[[User:Angel_Herraez\|AH]] modified Html5mediator.php to allow embedding videos from [https://vimeo.com Vimeo]

	==Rehovot December 2020==		==Rehovot December 2020==

Jaime Prilusky at 07:18, 21 December 2020

2020-12-21T07:18:26Z

←Older revision		Revision as of 07:18, 21 December 2020
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	* [[Proteopedia:Wishlist]]		* [[Proteopedia:Wishlist]]
	* [[Proteopedia:Problems]]		* [[Proteopedia:Problems]]
		+
		+	==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==		==Rehovot October 2020==

Jaime Prilusky at 05:04, 1 November 2020

2020-11-01T05:04:53Z

←Older revision		Revision as of 05:04, 1 November 2020
Line 2:		Line 2:
	* [[Proteopedia:Wishlist]]		* [[Proteopedia:Wishlist]]
	* [[Proteopedia:Problems]]		* [[Proteopedia:Problems]]
		+
		+	==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==		==Rehovot, January 2019==

Jaime Prilusky at 10:51, 3 February 2019

2019-02-03T10:51:35Z

←Older revision		Revision as of 10:51, 3 February 2019
Line 2:		Line 2:
	* [[Proteopedia:Wishlist]]		* [[Proteopedia:Wishlist]]
	* [[Proteopedia:Problems]]		* [[Proteopedia:Problems]]
		+
		+	==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==		==Rehovot, October 2018==

Angel Herraez: /* Rehovot, October 2018 */

2018-10-29T12:43:18Z

Rehovot, October 2018

←Older revision		Revision as of 12:43, 29 October 2018
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	==Rehovot, October 2018==		==Rehovot, October 2018==
-	''[[User:Angel_Herraez\|AH]] and [[User:Jaime_Prilusky\|JP]] working ~~side by side~~ during AH's visit to Weizmann Institute, 12 to 19 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		* JSmol was upgraded to version 14.29.16
-	* A conflict was solved between display of PDB file information (~~like~~ resolution, nr.of ~~NRM~~ models) and display of caption.	+	* 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.		* 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.		* More work on connecting the Sequence display with the Structure.
-	* Use WebGL for rendering, enabled per user~~, based on each user's preferences~~. 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].	+	* 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 ==		== Rehovot, August 2018 ==

Angel Herraez: /* Rehovot, October 2018 */

2018-10-17T12:38:07Z

Rehovot, October 2018

←Older revision		Revision as of 12:38, 17 October 2018
Line 9:		Line 9:
	* 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.		* 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.		* More work on connecting the Sequence display with the Structure.
-	* Use WebGL for rendering, enabled per user, based on each user's preferences	+	* Use WebGL for rendering, enabled per user, based on each user's preferences. 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].

	== Rehovot, August 2018 ==		== Rehovot, August 2018 ==

Jaime Prilusky at 12:24, 17 October 2018

2018-10-17T12:24:41Z

←Older revision		Revision as of 12:24, 17 October 2018
Line 9:		Line 9:
	* 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.		* 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.		* More work on connecting the Sequence display with the Structure.
-	* ~~TODO Try~~ WebGL for ~~seeded pages~~	+	* Use WebGL for rendering, enabled per user, based on each user's preferences

	== Rehovot, August 2018 ==		== Rehovot, August 2018 ==

Angel Herraez: /* Rehovot, October 2018 */

2018-10-17T05:55:00Z

Rehovot, October 2018

←Older revision		Revision as of 05:55, 17 October 2018
Line 5:		Line 5:
	==Rehovot, October 2018==		==Rehovot, October 2018==
	''[[User:Angel_Herraez\|AH]] and [[User:Jaime_Prilusky\|JP]] working side by side during AH's visit to Weizmann Institute, 12 to 19 October 2018.''		''[[User:Angel_Herraez\|AH]] and [[User:Jaime_Prilusky\|JP]] working side by side during AH's visit to Weizmann Institute, 12 to 19 October 2018.''
-	* ~~upgrade~~ JSmol to 14.29.16	+	* JSmol was upgraded to version 14.29.16
-	* ~~connect Sequence-Structure~~	+	* A conflict was solved between display of PDB file information (like resolution, nr.of NRM models) and display of caption.
-	* fix caption ~~on human pages~~	+	* 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.
-	* SAT ~~load current caption,~~ description, spin and ~~other options~~	+	* More work on connecting the Sequence display with the Structure.
	* TODO Try WebGL for seeded pages		* TODO Try WebGL for seeded pages