VMD extended PDB format

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-6.8.0-65-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
I don't know how much (if any) effort you want to put into supporting these old MD hacks to the legacy PDB format, but I just ran into this so figured I'd report it. The attached PDB file fails to load all coordinates (and hence can't be used for the associated DCD) because it's taking the VMD approach to residue numbering: just like with atom serial numbers, if a chain has more than 9999 residudes it switches to using hexadecimal numbering for that chain. 

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open trek1_minispadin_in_membrane.pdb

Summary of feedback from opening trek1_minispadin_in_membrane.pdb  
---  
warnings | Ignored bad PDB record found on line 298382  
HETATMD06EC O HOH M 1A 30.576 7.638 -63.694 1.00 0.00 O  
  
Ignored bad PDB record found on line 298383  
HETATMD06ED H1 HOH M 1A 30.253 8.493 -63.979 1.00 0.00 H  
  
Ignored bad PDB record found on line 298384  
HETATMD06EE H2 HOH M 1A 31.460 7.810 -63.372 1.00 0.00 H  
  
Ignored bad PDB record found on line 298385  
HETATMD06EF O HOH M 1B 28.843 1.502 -51.944 1.00 0.00 O  
  
Ignored bad PDB record found on line 298386  
HETATMD06F0 H1 HOH M 1B 29.562 1.180 -52.486 1.00 0.00 H  
  
34267 messages similar to the above omitted  
  
Chain information for trek1_minispadin_in_membrane.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
  




OpenGL version: 3.3.0 NVIDIA 570.172.08
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.UTF-8
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Qt runtime version: 6.8.2
Qt platform: xcb

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Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04
Architecture: 64bit ELF
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File attachment: trek1_minispadin_in_membrane.pdb

trek1_minispadin_in_membrane.pdb​

[Tristan Croll]

Added by email2trac

[Tristan Croll]

Hmm... turns out there's an easy workaround, so personally I wouldn't
bother changing ChimeraX. I didn't find it on first look, but OpenMM does
have a mmCIF reader/writer (`openmm.app.PDBxFile`), the output of which
appears compliant enough to be accepted by ChimeraX. In case it ever comes
up with other users, to rescue my existing simulation trajectory:

from openmm.app import PDBFile, PDBxFile
pdb = PDBFile('trek1_minispadin_in_membrane.pdb')

with open('trek1_minispadin_in_membrane.cif', 'wt') as out:
    PDBxFile.writeFile(pdb.topology, pdb.positions, out)

Opening the resulting mmCIF followed by the DCD seems perfectly
well-behaved.

On Tue, Aug 5, 2025 at 9:42 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

[Eric Pettersen]

I'm glad there's a workaround. The library that reads individual lines of a PDB file is not stateful, but would need to stateful in order to know that it had previously seen hexadecimal serial numbers. Not excited about jury rigging state into that library...