PAE surf output problem

[kristen.browne@…]

Eric:
[cid:image001.png@01DAD6AB.AD606BA0]

When looking at the output from Q9Y6X6, we're seeing what looks like coloring by element in the PAE surf output, which isn't expected.  Compared to the pLDDT output, you can see this region aligns with a short low-confidence region.

Could you please take a look?

Thanks!

Kristen

[kristen.browne@…]

Added by email2trac

[mbopf@…]

Eric,
Here’s another example where this anomaly is really obvious: UniProt A0A0D3QKQ5


[cid:image002.png@01DAD6CD.A3EF4E20]


From: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>
Date: Monday, July 15, 2024 at 11:39
To: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu>
Cc: Piya, Bhinnata (NIH/NIAID) [C] <bhinnata.piya@nih.gov>, Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>, Bopf, Mike (NIH/NIAID) [C] <mbopf@mail.nih.gov>
Subject: PAE surf output problem
Eric:
[cid:image001.png@01DAD6AB.AD606BA0]

When looking at the output from Q9Y6X6, we’re seeing what looks like coloring by element in the PAE surf output, which isn’t expected.  Compared to the pLDDT output, you can see this region aligns with a short low-confidence region.

Could you please take a look?

Thanks!

Kristen

[mbopf@…]

Added by email2trac

[mbopf@…]

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[Eric Pettersen]

Hi Kristen,

The PAE domain-coloring command only colors domains that contain at least 10 residues. The "domain" that didn't get its own color is only 5 residues long. The options are to force the command to color shorter "domains" (via its "minSize" parameter) or to color such areas gray (or another neutral color). Which would you prefer?

--Eric

[phil.cruz@…]

Hi all,

Given our discussion yesterday about de-emphasizing/eliminating shorter segments, my vote would be to color these segments gray.  The rationale being these shorter “domains” aren’t really domains.

Phil

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, August 1, 2024 at 9:22 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] #15612: PAE surf output problem
#15612: PAE surf output problem
---------------------------------------+----------------------
          Reporter:  kristen.browne@…  |      Owner:  pett
              Type:  defect            |     Status:  feedback
          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)
 * status:  accepted => feedback

Comment:

 Hi Kristen,
         The PAE domain-coloring command only colors domains that contain
 at least 10 residues. The "domain" that didn't get its own color is only 5
 residues long.  The options are to force the command to color shorter
 "domains" (via its "minSize" parameter) or to color such areas gray (or
 another neutral color).  Which would you prefer?

 --Eric
--
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[Eric Pettersen]

The "non-domain" sections are now colored gray in the latest version of the bundle.