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#15428 closed defect (fixed)

problem with viruses bychain outputs in flows

Reported by:	kristen.browne@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Depiction	Version:
Keywords:		Cc:	Tom Goddard, phil.cruz@…, Bhinnata.piya@…
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

Hey all!

I just stumbled into this one today.  I was looking at PDB 6WDT and there is an inconsistency between how the preset comes out in ChimeraX vs NIH 3D:
ChimeraX:
[cid:image001.png@01DABD93.19087DC0]
The ChimeraX preset is how I would expect it to look with each chain of the sym units a different color.  But when this comes out of NIH 3D using our current prod and our most up-to-date testing environment it looks like the below where each sym unit seems to be colored differently instead of by-chain.  I checked with Phil and this isn't what we would expect, so was hoping that Eric could look into it?

Thanks!
Kristen

Attachments (1)

image001.png (432.1 KB ) - added by kristen.browne@… 16 months ago.: Added by email2trac

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Change History (7)

by kristen.browne@…, 16 months ago

Attachment:	image001.png added

Added by email2trac

comment:1 by pett, 16 months ago

Cc:	Tom Goddard phil.cruz@… added
Component:	Unassigned → Depiction
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted

Hi Kristen,

The issue is that the pipeline script opens the structure with "open pdbe_bio:6wdt maxassemblies 1", which produces chain IDs of A, AA, AAA, through ABG for the 60 copies of chain A from the original asymmetric unit. Similarly for chains B-F of the asymmetric unit. Whereas if you simply open 6wdt and click on the first entry of its assembly table, you get 60 chain As, 60 chain Bs, etc. These 2 sets of chain IDs color differently when you "rainbow chains" on them (which is what the preset is doing).
If you look at the pipeline "color bypolymer" output for 6wdt you will see that the color arrangement is the same as the "by chain" you did by hand (though the colors themselves will be different).
So the question is what do we want to do about this. There seems to be metadata in the pdbe_bio file indicating that it is an assembly, so it's possible that the by-chains preset could do something different/smarter if it detects that.

--Eric

comment:2 by kristen.browne@…, 16 months ago

This is definitely a Phil question so I’ll let him rely.

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________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, June 13, 2024 6:30:53 PM
To: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #15428: problem with viruses bychain outputs in flows

#15428: problem with viruses bychain outputs in flows
---------------------------------------+----------------------
          Reporter:  kristen.browne@…  |      Owner:  pett
              Type:  defect            |     Status:  accepted
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------
Changes (by pett):

 * cc: Tom Goddard, phil.cruz@… (added)
 * component:  Unassigned => Depiction
 * owner:  (none) => pett
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => accepted

Comment:

 Hi Kristen,
         The issue is that the pipeline script opens the structure with
 "open pdbe_bio:6wdt maxassemblies 1", which produces chain IDs of A, AA,
 AAA, through ABG for the 60 copies of chain A from the original asymmetric
 unit.  Similarly for chains B-F of the asymmetric unit.  Whereas if you
 simply open 6wdt and click on the first entry of its assembly table, you
 get 60 chain As, 60 chain Bs, etc.  These 2 sets of chain IDs color
 differently when you "rainbow chains" on them (which is what the preset is
 doing).
         If you look at the pipeline "color bypolymer" output for 6wdt you
 will see that the color arrangement is the same as the "by chain" you did
 by hand (though the colors themselves will be different).
         So the question is what do we want to do about this.  There seems
 to be metadata in the pdbe_bio file indicating that it is an assembly, so
 it's possible that the by-chains preset could do something
 different/smarter if it detects that.

 --Eric
--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15428%23comment%3A1&data=05%7C02%7Ckristen.browne%40nih.gov%7Cfbef6798674d41076f1208dc8bf881f1%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638539146661168344%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=66sQ8jCUQtXL3BHFrjqhk1TmaKFRMNC1rbWixJpQ5Tk%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15428#comment:1>>
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comment:3 by kristen.browne@…, 16 months ago

Let’s also add bhinnata to this thread so she can track the issue.  Bhinnata.piya@nih.gov

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________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, June 13, 2024 6:54:48 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #15428: problem with viruses bychain outputs in flows

#15428: problem with viruses bychain outputs in flows
---------------------------------------+----------------------
          Reporter:  kristen.browne@…  |      Owner:  pett
              Type:  defect            |     Status:  accepted
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------
Comment (by kristen.browne@…):

 {{{
 This is definitely a Phil question so I’ll let him rely.

 Get Outlook for iOS<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=05%7C02%7Ckristen.browne%40nih.gov%7C22ff71f196094e8e42c008dc8bfbd683%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638539160969551214%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=oGmBC7t0qV%2FXTkZQkvJttt5x2yqAQOwuisazqzYsfIU%3D&reserved=0<https://aka.ms/o0ukef>>
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: Thursday, June 13, 2024 6:30:53 PM
 To: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>;
 pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
 Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Cruz, Phil (NIH/NIAID)
 [C] <phil.cruz@nih.gov>
 Subject: [EXTERNAL] Re: [ChimeraX] #15428: problem with viruses bychain
 outputs in flows

 #15428: problem with viruses bychain outputs in flows
 ---------------------------------------+----------------------
           Reporter:  kristen.browne@…  |      Owner:  pett
               Type:  defect            |     Status:  accepted
           Priority:  normal            |  Milestone:
          Component:  Depiction         |    Version:
         Resolution:                    |   Keywords:
         Blocked By:                    |   Blocking:
 Notify when closed:                    |   Platform:  all
            Project:  ChimeraX          |
 ---------------------------------------+----------------------
 Changes (by pett):

  * cc: Tom Goddard, phil.cruz@… (added)
  * component:  Unassigned => Depiction
  * owner:  (none) => pett
  * platform:   => all
  * project:   => ChimeraX
  * status:  new => accepted

 Comment:

  Hi Kristen,
          The issue is that the pipeline script opens the structure with
  "open pdbe_bio:6wdt maxassemblies 1", which produces chain IDs of A, AA,
  AAA, through ABG for the 60 copies of chain A from the original
 asymmetric
  unit.  Similarly for chains B-F of the asymmetric unit.  Whereas if you
  simply open 6wdt and click on the first entry of its assembly table, you
  get 60 chain As, 60 chain Bs, etc.  These 2 sets of chain IDs color
  differently when you "rainbow chains" on them (which is what the preset
 is
  doing).
          If you look at the pipeline "color bypolymer" output for 6wdt you
  will see that the color arrangement is the same as the "by chain" you did
  by hand (though the colors themselves will be different).
          So the question is what do we want to do about this.  There seems
  to be metadata in the pdbe_bio file indicating that it is an assembly, so
  it's possible that the by-chains preset could do something
  different/smarter if it detects that.

  --Eric
 --
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comment:4 by pett, 16 months ago

Cc:	Bhinnata.piya@… added

comment:5 by pett, 16 months ago

I have updated the presets bundle to look at the PDBE mmCIF table that maps final chain IDs to the original asymmetric unit IDs. I'll send an updated version of the bundle once the daily build is working again, since the change depends on a fix that will be in the next daily build.

comment:6 by pett, 16 months ago

Resolution:	→ fixed
Status:	accepted → closed

The updated bundle is on the toolshed, and the pipeline script has been updated.

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