VMD-L Mailing List

From: Jim Pfaendtner (jpfaendt_at_hec.utah.edu)
Date: Fri Aug 24 2007 - 17:58:51 CDT

Dear VMD-list,

I am trying to align two molecules using "measure fit" on two
selections and then the move command on the operator defined by
"measure fit"

I am selecting 3 alpha carbons from one molecule and 3 alpha carbons
from another molecule and I would like to align the two molecules
based on the selection of these 6 atoms.

set sel1 [atomselect 0 "(selction 1) or (selection 2) or (selection 3)"]
set sel2 [atomselect 1 "(selction 4) or (selection 5) or (selection 6)"]
# note the (selection X) is just a placeholder for my specific
selection syntax
# each selection looks like this (segid X and name CA and resid 123)
with proper segid/resid in place
set M [measure fit $sel1 $sel2]
set mol0 [atomselect 0 all]
$mol0 move $M

What I expect is that $sel1 is going to give me the atom numbers for
1 2 and 3 and $sel2 is going to give me the atom numbers for 4, 5 and
6 in that order. Unfortunately the selections are being reordered so
that:

$sel1 = [atom 1, atom3, atom2]
$sel2 = [atom 6, atom 5, atom 4]

this is causing the calculation of M to get messed up and
consequently the alignment is not working.

When I look at the resids in each of my selections, the selection is
ordered from highest resid to lowest. I guess this has something to
do with the way the atoms are searched in the pdb during atomselect,
i.e., the order that I specify (selection 1), (selection 2),
(selection 3) does not matter...

I think frequently the alignment procedure is used on two identical
proteins, so this is probably not an issue because the residue
numbers are all the same.

One idea I had was to perform all six atom selections separately and
then form a concatenated atom selection in the order I want. Is this
possible?

Does anyone else have a suggestion how to do this alignment?

Thank you in advance for your help,
Jim