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#17112 assigned enhancement

Add alphafold error plot menu entry to select residues when dragging box

Reported by:	matthias.vorlaender@…	Owned by:	Tom Goddard
Priority:	moderate	Milestone:
Component:	Structure Prediction	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

Matthias asked how to select residues when dragging a box on a PAE plot. Would be helpful if there were separate color and select menu entries.

Hi Matthias,

Right click on the ChimeraX PAE plot to show a menu and turn off "Dragging box colors structure". Then dragging a box will instead select the parts of the structure. Not obvious. Probably there shoudl be two menu entries to separately control coloring and selecting. I made a ChimeraX request for that.

By the way the ChimeraX daily build handles PAE from Boltz and Chai (variants of AlphaFold 3) better (recognizes numpy PAE files and the file names used by those programs).

Tom

On Mar 17, 2025, at 10:16 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@…> wrote:

Dear ChimeraX team,

I love the alphafold tools in ChimeraX, and have a small suggestion to make it even better. Currently, when associating a PAE plot from a JSON file, you can drag the mouse in the PAE plot to color the corresponding residues (magenta and lime), but the residues do not become selected (although the color command gets printed in the log). I think it would be helpful if there was an option (or default behavior) to return a selection in addition, so that the selected region could be saved as a named selection, the display style changed ect…

Or am I missing anything?

Many thanks in advance,
Matthias

Change History (3)

comment:1 by matthias.vorlaender@…, 7 months ago

Hi Tom,

Amazing, thanks a lot, that’s very helpful!

Best wishes,
Matthias
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, March 17, 2025 at 18:28
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [ChimeraX] #17112: Add alphafold error plot menu entry to select residues when dragging box
#17112: Add alphafold error plot menu entry to select residues when dragging box
-----------------------------------+----------------------------------
 Reporter:  matthias.vorlaender@…  |               Owner:  Tom Goddard
     Type:  enhancement            |              Status:  assigned
 Priority:  moderate               |           Milestone:
Component:  Structure Prediction   |             Version:
 Keywords:                         |          Blocked By:
 Blocking:                         |  Notify when closed:
 Platform:  all                    |             Project:  ChimeraX
-----------------------------------+----------------------------------
 Matthias asked how to select residues when dragging a box on a PAE plot.
 Would be helpful if there were separate color and select menu entries.

 Hi Matthias,

   Right click on the ChimeraX PAE plot to show a menu and turn off
 "Dragging box colors structure".  Then dragging a box will instead select
 the parts of the structure.  Not obvious.  Probably there shoudl be two
 menu entries to separately control coloring and selecting.  I made a
 ChimeraX request for that.

   By the way the ChimeraX daily build handles PAE from Boltz and Chai
 (variants of AlphaFold 3) better (recognizes numpy PAE files and the file
 names used by those programs).

         Tom

 On Mar 17, 2025, at 10:16 AM, Vorländer,Matthias Kopano via ChimeraX-users
 <chimerax-users@cgl.ucsf.edu> wrote:

 Dear ChimeraX team,

 I love the alphafold tools in ChimeraX, and have a small suggestion to
 make it even better. Currently, when associating a PAE plot from a JSON
 file, you can drag the mouse in the PAE plot to color the corresponding
 residues (magenta and lime), but the residues do not become selected
 (although the color command gets printed in the log). I think it would be
 helpful if there was an option (or default behavior) to return a selection
 in addition, so that the selected region could be saved as a named
 selection, the display style changed ect…

 Or am I missing anything?

 Many thanks in advance,
 Matthias
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17112>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by matthias.vorlaender@…, 7 months ago

Hi Tom and Eric,

Related to this ticket, would it be possible to enable selection syncing from the structure to the PAE plot? Currently only syncing from the PAE to the structure appears to be supported, from what I can tell, but it would be cool to have a way to highlight the current atom selection on the plot too.

What do you think?
Thanks a lot,
Matthias

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, March 17, 2025 at 18:31
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>
Subject: Re: [ChimeraX] #17112: Add alphafold error plot menu entry to select residues when dragging box
#17112: Add alphafold error plot menu entry to select residues when dragging box
--------------------------------------------+-------------------------
          Reporter:  matthias.vorlaender@…  |      Owner:  Tom Goddard
              Type:  enhancement            |     Status:  assigned
          Priority:  moderate               |  Milestone:
         Component:  Structure Prediction   |    Version:
        Resolution:                         |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+-------------------------
Comment (by matthias.vorlaender@…):

 {{{
 Hi Tom,

 Amazing, thanks a lot, that’s very helpful!


 Best wishes,
 Matthias
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Date: Monday, March 17, 2025 at 18:28
 To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Vorländer,Matthias Kopano
 <matthias.vorlaender@imp.ac.at>
 Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
 Subject: [ChimeraX] #17112: Add alphafold error plot menu entry to select
 residues when dragging box
 #17112: Add alphafold error plot menu entry to select residues when
 dragging box
 -----------------------------------+----------------------------------
  Reporter:  matthias.vorlaender@…  |               Owner:  Tom Goddard
      Type:  enhancement            |              Status:  assigned
  Priority:  moderate               |           Milestone:
 Component:  Structure Prediction   |             Version:
  Keywords:                         |          Blocked By:
  Blocking:                         |  Notify when closed:
  Platform:  all                    |             Project:  ChimeraX
 -----------------------------------+----------------------------------
  Matthias asked how to select residues when dragging a box on a PAE plot.
  Would be helpful if there were separate color and select menu entries.

  Hi Matthias,

    Right click on the ChimeraX PAE plot to show a menu and turn off
  "Dragging box colors structure".  Then dragging a box will instead select
  the parts of the structure.  Not obvious.  Probably there shoudl be two
  menu entries to separately control coloring and selecting.  I made a
  ChimeraX request for that.

    By the way the ChimeraX daily build handles PAE from Boltz and Chai
  (variants of AlphaFold 3) better (recognizes numpy PAE files and the file
  names used by those programs).

          Tom

  On Mar 17, 2025, at 10:16 AM, Vorländer,Matthias Kopano via ChimeraX-
 users
  <chimerax-users@cgl.ucsf.edu> wrote:

  Dear ChimeraX team,

  I love the alphafold tools in ChimeraX, and have a small suggestion to
  make it even better. Currently, when associating a PAE plot from a JSON
  file, you can drag the mouse in the PAE plot to color the corresponding
  residues (magenta and lime), but the residues do not become selected
  (although the color command gets printed in the log). I think it would be
  helpful if there was an option (or default behavior) to return a
 selection
  in addition, so that the selected region could be saved as a named
  selection, the display style changed ect…

  Or am I missing anything?

  Many thanks in advance,
  Matthias
 --
 Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17112>
 ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
 ChimeraX Issue Tracker
 }}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17112#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:3 by goddard@…, 7 months ago

Hi Matthias,

  That is a nice idea. I think trying to outline the parts of the PAE plot for selected residues and atoms would cover the pae colors. But maybe it could dim all the non-selected plot pixels. 

   Tom

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