From: Smith, Harper E. (smith.12510_at_buckeyemail.osu.edu)
Date: Thu Mar 04 2021 - 18:18:26 CST

Hi all,

According to the dynamic network analysis tutorial, I can define clusters of atoms associated with each node -- this is used when calculating distances between nodes. However, clustering always fails when I do this (e.g. "can't read "nodeMap(7)": no such element in array"). The offending line is "set localSel [atomselect $molId $localSelString]" in adjacencyMatrix.tcl (part of networkview1.41), but I can't figure out what causes it.

This issue was reported here in 2019: https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/30977.html . The definitions used here give me the error. I tried even simpler definitions, which still fail:

>SystemSelection
not hydrogen

>NodeSelection
name CA

>Clusters
CA SER name CA
CA LEU name CA
CA GLU name CA
CA CYS name CA
CA ASP name CA
CA PRO name CA
CA ALA name CA
CA VAL name CA
CA ILE name CA
CA GLY name CA
CA THR name CA
CA LYS name CA
CA HSE name CA
CA TYR name CA
CA TRP name CA
CA ASN name CA
CA ARG name CA
CA MET name CA
CA GLN name CA
CA PHE name CA

>Restrictions
notSameResidue
notNeighboringCAlpha

This time, the error is "can't read "nodeMap(0)": no such element in array"

Any ideas?

Best,
Harper