defattr Attribute File recipient value molecules or structures

[ccaffalett@…]

Hello,
I am having difficulty with my *.defattr attribute file, and I am interested to know if there was a change in the value of recipient from "molecules" to "structures" at some point? I was using ChimeraX on two different machines, and one instance of ChimeraX refers to "molecules" and the other refers to "structures".

Best,
Chris Caffalette

[ccaffalett@…]

Hello,
I apologize, this was started because I thought I could use #1/A to define an attribute value for an ID/Chain. However, I realize now that I can only use the #1.1 nomenclature after splitting the molecule into each chain as sub IDs. Is there any way to refer to specific chains or only structure ID?

While I was having difficulty building attribute files for ChimeraX, I was reviewing https://www.cgl.ucsf.edu/chimerax/docs/user/formats/defattr.html where I saw the “molecules” recipient. I must have mistakenly thought I saw it in the ChimeraX Render by Attributes as well.

Thank you, and I apologize for the inconvenience.

Best,
Chris



On Apr 3, 2024, at 00:45, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

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#14880: defattr Attribute File recipient value molecules or structures
--------------------------+-----------------------------
Reporter:  ccaffalett@…  |                Type:  defect
  Status:  new           |            Priority:  normal
Component:  Unassigned    |          Blocked By:
Blocking:                |  Notify when closed:
--------------------------+-----------------------------
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[Eric Pettersen]

Hi Chris,

The defattr file uses "molecules" to be backwards compatible with files used with our previous Chimera program. With ChimeraX we prefer the nomenclature "structures", which is why you see that in the Render By Attribute interface. It would seem good to allow that same term in defattr files (along with backwards-compatible "molecules").
Though the setattr command allows setting chain attributes, the defattr file doesn't currently support it. It probably should. We don't currently show chain attributes in the Render By Attribute tool basically because there are no interesting chain attributes to render by. If there was some compelling use case, that could be changed.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[ccaffalett@…]

Hi Eric,
Thank you so much for this information. All of this stems from the desire to create a custom attribute, such as "pValue", and visualize an atomic model with a heat-map-like coloring of chains according to experimentally-determined numbers. In this particular case, the atomic models are of large complexes with many Chains representing the individual proteins of the complex. I originally, thought that I could use the atom-spec nomenclature to specify a range of Chains for molecule ID #1, such as #1/A-F, in a *.defattr attribute assignment file. However, since you mentioned that the setattr command will accept chains, I will instead create a complex setattr command delimited by semicolons to perform the same assignment of a custom attribute with "create true" e.g. the following setattr command and the cyan-grey-maroon palette in Render by Attribute.

setattr #1/A-G res pValue 0.001 create true; setattr #1/H-N res pValue 0.005 create true; setattr #1/O-U res pValue 0.009 create true

[cid:5e3d89e7-4222-4442-b903-0232a233b87b]
[cid:90075dcc-aac8-4398-a526-98a0f50da491][cid:0a263e08-bade-4f4c-8995-67750a89308e]
[cid:54b17d82-f808-490a-a7e4-30f50587b0a3]

Thank you again, Eric!

Best,
Chris Caffalette


________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, April 3, 2024 2:13 PM
To: Chris Caffalette <ccaffalett@rockefeller.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #14880: defattr Attribute File recipient value molecules or structures

Caution: External email

#14880: defattr Attribute File recipient value molecules or structures
----------------------------------------+----------------------
          Reporter:  ccaffalett@…       |      Owner:  pett
              Type:  enhancement        |     Status:  accepted
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------
Changes (by pett):

 * component:  Unassigned => Structure Editing
 * owner:  (none) => pett
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => accepted
 * type:  defect => enhancement

Comment:

 Hi Chris,
         The defattr file uses "molecules" to be backwards compatible with
 files used with our previous Chimera program.  With ChimeraX we prefer the
 nomenclature "structures", which is why you see that in the Render By
 Attribute interface.  It would seem good to allow that same term in
 defattr files (along with backwards-compatible "molecules").
         Though the setattr command allows setting chain attributes, the
 defattr file doesn't currently support it.  It probably should.  We don't
 currently show chain attributes in the Render By Attribute tool basically
 because there are no interesting chain attributes to render by.  If there
 was some compelling use case, that could be changed.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
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[Eric Pettersen]

Actually, the *code* already supports all the features I outlined, as well as allowing setting attributes for bonds and pseudobonds! It's just that the description in the help page needs updating.