VMD-L Mailing List

From: Whitford, Paul (p.whitford_at_northeastern.edu)
Date: Thu Jun 23 2022 - 22:29:17 CDT

VMD Team,
  Now that rev12 is available for 1.9.4, I wanted to follow up on this issue. I just tried rev12 on OSX Monterey with a CIF file. It appears that I still can not select a chain based on its chain ID, if the chain ID is two characters. In the example, I'm using 7nwh.cif.

# one-character IDs works
>set sel [atomselect 0 "chain K"]
>$sel num
3617

# two-character IDs fail
vmd>set sel [atomselect 0 "chain NB"]
vmd>$sel num
0

#appending a "1" works
vmd>set sel [atomselect 0 "chain NB1"]
vmd>$sel num
1752

I checked the CIF file, and "NB1" does not appear anywhere in the file. "NB" does appear. I was able to reproduce the issue for any two-character chain ID. Appending a "1" to any two-character chain ID works.

As noted in the earlier message, this is a 1.9.4 issue. The behavior is different with 1.9.3:
Here is what I get with 1.9.3 on linux, using the same file:

vmd > set sel [atomselect 0 "chain NB"]

vmd > $sel num

1752

If there is any additional information that can be helpful, let me know.

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!_kHfKmTHoqOBT8PD1uNYge9v3jHM1RPIyJkKPK3CwFr5dLMGVxrlX6MdZg7WXarMEXcWKF4jC1vNlDzdQJP8Bp8BTrLb$

________________________________
From: Whitford, Paul
Sent: Friday, February 4, 2022 11:28 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: PDBx and chain IDs in VMD 1.9.4a55

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!_kHfKmTHoqOBT8PD1uNYge9v3jHM1RPIyJkKPK3CwFr5dLMGVxrlX6MdZg7WXarMEXcWKF4jC1vNlDzdQJP8Bn1T9C3c$
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!_kHfKmTHoqOBT8PD1uNYge9v3jHM1RPIyJkKPK3CwFr5dLMGVxrlX6MdZg7WXarMEXcWKF4jC1vNlDzdQJP8Bp8BTrLb$