VMD-L Mailing List

From: Jason Smith (jason_smith_18_at_sfu.ca)
Date: Sat Jan 22 2022 - 14:55:29 CST

I see that the first file is the newer file specification (mmCIF). Perhaps VMD is expecting the older file specification (CIF)?

Cheers,

-
Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6
Canada

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Andrew White <white.d.andrew_at_gmail.com>
Sent: Thursday, 20 January 2022 8:38:44 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: PDBx/CIF Problem on New PDBs

I've noticed a problem with some RCSB PDBx files. These two files:

https://urldefense.com/v3/__https://files.rcsb.org/download/7Q4B.cif__;!!DZ3fjg!qnz2Oco5sqAltDCZiF9UgnmYJjGtmkovVzjU6lLTL0PYMI9SI6ZDy-YGySx8chWFAw$ <https://urldefense.com/v3/__https://files.rcsb.org/download/7Q4B.cif__;!!DZ3fjg!s_HZVg6R9EydPCL1IHrN2CITDQkI1jJOHSme5aXzty3l_4dC-5G8RkVwaZJNCdvXHA$>
https://urldefense.com/v3/__https://files.rcsb.org/download/7Q4M.cif__;!!DZ3fjg!qnz2Oco5sqAltDCZiF9UgnmYJjGtmkovVzjU6lLTL0PYMI9SI6ZDy-YGySx8vbYs8A$ <https://urldefense.com/v3/__https://files.rcsb.org/download/7Q4M.cif__;!!DZ3fjg!s_HZVg6R9EydPCL1IHrN2CITDQkI1jJOHSme5aXzty3l_4dC-5G8RkVwaZIO2PADgA$>

have the following error when trying to load in VMD:

pdbxplugin) encountered 10 bad element indices!
pdbxplugin) Error while trying to parse pdbx structure
ERROR) molecule_structure: Unable to read structure for molecule 0
ERROR) molecule_structure: severe error indicated by plugin aborting loading of molecule 0

I cannot understand the meaning of the error (there is no field called element indices). I was hoping someone could help me understand how to fix this issue and/or if it's caused by the file or plugin.

Thanks,
Andrew