chimerax.build_structure.bond.CreateBondError: Must specify two or more atoms

[kristen.browne@…]

Since switching to the new presets have started seeing this error come up.  This was for PDB 2JTN.  I just extracted the part of the logs around the error, let me know if you would like more.

Opened 1 biological assemblies for 2JTN
STATUS:
Opened 1 biological assemblies for 2JTN
NIH3D INFO: HEAVY ATOM MASS: 0.1 kDa
INFO:
Executing: ~bond #1
INFO:
Executing: bond #1

ERROR:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/build_structure/cmd.py", line 20, in cmd_bondcreated = create_bonds(*args, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/build_structure/bond.py", line 27, in create_bonds
raise CreateBondError("Must specify two or more atoms")
chimerax.build_structure.bond.CreateBondError: Must specify two or more atoms


Kristen Browne, MSc, MscBMC
Contractor - MSC, Inc. | A Guidehouse Company
3D Modeling and Biovisualization Specialist
Bioinformatics and Computational Biosciences Branch (BCBB)<https://www.niaid.nih.gov/research/bioinformatics-computational-biosciences-branch>
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, Room 4A60
Rockville, MD 20852
Office 202-253-5228

[kristen.browne@…]

Just adding  a note that this is impacting a lot of entries now and is the error of highest concern at this point.

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Thursday, December 15, 2022 4:49 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8194: chimerax.build_structure.bond.CreateBondError: Must specify two or more atoms

#8194: chimerax.build_structure.bond.CreateBondError: Must specify two or more atoms
---------------------------------------+----------------------
          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):

 * owner:  (none) => pett
 * platform:   => all
 * status:  new => accepted
 * component:  Unassigned => Depiction
 * project:   => ChimeraX


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[Eric Pettersen]

Okay, I have submitted a pull request that "fixes" this problem. I use quotes because the underlying problem is that the entry/structure has either zero or 1 atoms -- so you will undoubtedly be submitting other bug reports!

[kristen.browne@…]

Oh well that's strange.  A lot of these are quicksubmits directly from the PDB and definitely have atoms, so I guess we'll see what the error is once it gets past this problem!

K

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Friday, December 16, 2022 1:47 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; Stolarczyk, Michal (NIH/NIAID) [C] <michal.stolarczyk@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8194: chimerax.build_structure.bond.CreateBondError: Must specify two or more atoms

#8194: chimerax.build_structure.bond.CreateBondError: Must specify two or more atoms
---------------------------------------+--------------------
          Reporter:  kristen.browne@...  |      Owner:  pett
              Type:  defect            |     Status:  closed
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:  fixed             |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+--------------------
Changes (by pett):

 * cc: michal.stolarczyk@... (added)
 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 Okay, I have submitted a pull request that "fixes" this problem.  I use  quotes because the underlying problem is that the entry/structure has  either zero or 1 atoms -- so you will undoubtedly be submitting other bug  reports!

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[Eric Pettersen]

I am going to open a separate ticket for 2JTN, since the bio assembly file has protein in it as well as 80 zinc atoms, and the only thing ChimeraX produces from it is 20 zinc atoms!