VMD-L Mailing List

From: Andrew White (white.d.andrew_at_gmail.com)
Date: Thu Jan 20 2022 - 10:38:44 CST

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!s_HZVg6R9EydPCL1IHrN2CITDQkI1jJOHSme5aXzty3l_4dC-5G8RkVwaZJNCdvXHA$
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