From: John Stone (
Date: Mon Mar 28 2005 - 11:58:17 CST

  The atom selection keyword "alpha" depends on the secondary structure.
VMD gets the secondary structure for a molecule by running the STRIDE
program, which calculates it heuristically, based on the 3-D structure.
It is quite possible that the reason you're having trouble is because
STRIDE is assigning a differing number of atoms as alpha helices in the
various structures you've got. You can see that's what's going on by
comparing the atom counts as you did below. Given this result, I'd
suggest changing your alignment script to use a selection such as
"name CA" or something of that sort. Otherwise, another way to solve
the problem is to extract the list of atom indices from the "alpha"
selection for your zeroth molecule, make a new atom selection macro
from that list of indices, and then use the macro to select the same
set of atoms for all molecules, and that will solve your problem.
The issue here is just that when you used the "alpha" selection, you're
relying on STRIDE to make exactly the same secondary structure prediction
for all of your molecules, which as you can see it won't necessarily do.

  John Stone

On Thu, Mar 24, 2005 at 04:49:44PM -0500, Josh Ward wrote:
> 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"]
> atomselect0
> >Main< 38 % set a1 [atomselect 1 "alpha"]
> atomselect1
> >Main< 39 % set a2 [atomselect 2 "alpha"]
> atomselect2
> >Main< 40 % set a3 [atomselect 3 "alpha"]
> atomselect3
> >Main< 41 % set a4 [atomselect 4 "alpha"]
> atomselect4
> >Main< 42 % llength [$a0 get index]
> 106
> >Main< 43 % llength [$a1 get index]
> 106
> >Main< 44 % llength [$a2 get index]
> 43
> >Main< 45 % llength [$a3 get index]
> 106
> >Main< 46 % llength [$a4 get index]
> 43
> >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
> either.
> Thanks in advance,
> Josh
> --
> Josh Ward
> Graduate Research Assistant
> Purdue University
> Department of Medicinal Chemistry and Molecular Pharmacology
> Lily Hall of Life Sciences
> Phone: (765) 494-2191

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