From: Jason Smith (
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)?


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

From: <> on behalf of Andrew White <>
Sent: Thursday, 20 January 2022 8:38:44 AM
Subject: vmd-l: PDBx/CIF Problem on New PDBs

I've noticed a problem with some RCSB PDBx files. These two files:;!!DZ3fjg!qnz2Oco5sqAltDCZiF9UgnmYJjGtmkovVzjU6lLTL0PYMI9SI6ZDy-YGySx8chWFAw$ <;!!DZ3fjg!s_HZVg6R9EydPCL1IHrN2CITDQkI1jJOHSme5aXzty3l_4dC-5G8RkVwaZJNCdvXHA$>;!!DZ3fjg!qnz2Oco5sqAltDCZiF9UgnmYJjGtmkovVzjU6lLTL0PYMI9SI6ZDy-YGySx8vbYs8A$ <;!!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.