From: Josh Ward (
Date: Thu Mar 24 2005 - 15:49:44 CST

I think I have found a MOLID-dependent bug in atomselection using TCL.
I'm running VMD 1.8.3 on Debian Sarge Linux with TCL 8.4.1 / TK8.4.1

I have three structures of the same protein in charmm crd format that I
am trying to align. Each loaded seperately - result = molids 0, 1, and
2 are used. When I tried to align, molid 0 and molid 1 align without
problem, but tcl complains that the number of selected atoms differes
between 0 and 2.

After double checking the integrety of the crd file, I loaded a single
file multiple times and tried to realign, getting the same error
result. Loading the same file 5 times and trying to align, I got the
following output in the TK console:

Main console display active (Tcl8.4.1 / Tk8.4.1)
37 % set a0 [atomselect 0 "alpha"]
>Main< 38 % set a1 [atomselect 1 "alpha"]
>Main< 39 % set a2 [atomselect 2 "alpha"]
>Main< 40 % set a3 [atomselect 3 "alpha"]
>Main< 41 % set a4 [atomselect 4 "alpha"]
>Main< 42 % llength [$a0 get index]
>Main< 43 % llength [$a1 get index]
>Main< 44 % llength [$a2 get index]
>Main< 45 % llength [$a3 get index]
>Main< 46 % llength [$a4 get index]
>Main< 47 %

This alignment procedure worked until we upgraded to 1.8.3 I'm not sure
if the bug might be in TCL. It won't align when I downgrade to 1.8.2

Thanks in advance,

Josh Ward
Graduate Research Assistant
Purdue University
Department of Medicinal Chemistry and Molecular Pharmacology
Lily Hall of Life Sciences
Phone: (765) 494-2191