VMD-L Mailing List
From: Diego Gomes (diego.enry_at_gmail.com)
Date: Mon Jun 23 2025 - 10:24:04 CDT
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Hi Finley,
I wrote you a minimal mmCIF reader in Tcl.
Make sure to load the PSF topology first, this only reads the atoms.
Let me know if that works for you.
On Fri, Jun 20, 2025 at 2:42 PM Finley Clark <fc36_at_rice.edu> wrote:
> Hello all,
>
> I find that VMD (trying v. 1.9.3 and v2.0.0a5) can load CIF files
> downloaded directly from the PDB, such as 1r69.cif, but cannot load CIF
> files written by the OpenMM Python API's pdbxfile.PDBxFile.writeFile.
>
> This happens even when I create the OpenMM CIF file by first loading the
> PDB-sourced file into OpenMM, then writing it immediately without making
> any changes to the topology or coordinates.
>
> In VMD 1.9.3, the specific error message that I get is:
> Info) File loading in progress, please wait.
> pdbxplugin) Could not get atom number
> Segmentation fault (core dumped)
>
> And in 2.0.0.a5:
> Info) File loading in progress, please wait.
> pdbxplugin) Could not get atom number
> pdbxplugin) error opening file.
> ERROR) Could not read file 1r69_openmm.cif
> ERROR) Loading of startup molecule files aborted.
>
> In general, I'd like to be able to load systems that cannot be easily
> represented in PDB format, so converting CIF files to PDB format before
> loading in VMD is not a great workaround.
>
> Any advice from the community would be appreciated!
>
>
>
-- Diego Enry B. Gomes, PhD Department of Physics at Auburn University & NIH Center for Macromolecular Modeling and Visualization Leach Science Center - Ste. 3182 - Auburn, AL dgomes_at_auburn.edu
- application/x-tcl attachment: parse_mmcif_atoms.tcl
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