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From: Whitford, Paul (p.whitford_at_northeastern.edu)
Date: Fri Feb 04 2022 - 10:28:32 CST

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VMD team,
When using VMD 1.9.4a55 rev11 (on OSX Monterey), I was trying to view a PDBx/mmCIF file (RCSB ID 7NWH),
https://urldefense.com/v3/__https://files.rcsb.org/download/7NWH.cif__;!!DZ3fjg!o2MX6pg7XHqkVmxfsWBs5nvZVvmDA0uP32ahrETO4uc1yXMd-dmXGR4fRRzX0v07WA$
and I encountered some unexpected behavior. When I look in the structure file with a text editor, I see there is chain "XB". But, when I used the selection "chain XB" in VMD, nothing is selected. This happens when using the Graphical Representation window, or the Tk console. However, if I give "chain XB1", the desired chain (XB) is selected. I checked in vmd 1.9.3, and the behavior was different. That is, in 1.9.3, "chain XB" works in the GUI and in the console, for the same .cif file. I am not very familiar with the mmCIF file format, so perhaps appending a digit to the chain ID is encoded in the file. Any suggestions about what I may be missing/overlooking would be greatly appreciated.

Thanks.

Paul Whitford

Associate Professor
Department of Physics

Center for Theoretical Biological Physics
Northeastern University

p.whitford_at_neu.edu

https://urldefense.com/v3/__http://www.northeastern.edu/whitford__;!!DZ3fjg!o2MX6pg7XHqkVmxfsWBs5nvZVvmDA0uP32ahrETO4uc1yXMd-dmXGR4fRRyBBbsSmQ$