non-printable surface missing coulombic coloring

[kristen.browne@…]

The attached file (8VEL) came out of the most recent flows where I'm testing outputs for our 2.0 workflows.  The file was renamed, but this is the surf coulombic output (non-printable).  For some reason, it is coming out completely white.  The printable version is fine with the expected red-white-blue.  This doesn't happen for all files as 8SYJ (attached too) is just fine.  I'm not sure if it has to do with it being a single chain.  When I just open the PDB entry in ChimeraX and run the preset 8VEL is fine, so I suspect it might have to do with the sequence of events that occur prior.

Any ideas what might be happening?

Thanks,

K

8vel-mol-surf-lowres-coulombic.glb​

8syj-mol-surf-lowres-coulombic-nih3d.glb​

[kristen.browne@…]

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[kristen.browne@…]

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[Eric Pettersen]

The cx_unified.py script on the AlphaFold branch was changed the day after this report because the "printable" surface outputs weren't actually using the printable version of the corresponding preset. AFAIK, there are no "non-printable" surface outputs.

Maybe try again?

[kristen.browne@…]

I think we can close this for now.  I was using our Testing environment which included some of the surf-vis outputs that you had done way back when.  Since I ran this test, Mike has replaced what was there with the AlphaFold changes and wiped some of this out.  We'll just revisit when we "officially" start work on Workflows 2.0.

Mike doesn't see a pull request for these changes, did you submit one?

Thanks!

Kristen

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, July 15, 2024 3:03 PM
To: pett@cgl.ucsf.edu; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #15577: non-printable surface missing coulombic coloring

#15577: non-printable surface missing coulombic coloring
---------------------------------------+----------------------
          Reporter:  kristen.browne@...  |      Owner:  pett
              Type:  defect            |     Status:  accepted
          Priority:  normal            |  Milestone:
         Component:  Third Party       |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------
Comment (by pett):

 The cx_unified.py script on the AlphaFold branch was changed the day after  this report because the "printable" surface outputs weren't actually using  the printable version of the corresponding preset. AFAIK, there are no  "non-printable" surface outputs.

 Maybe try again?
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[Eric Pettersen]

Okay! :-)