VMD-L Mailing List

From: Loison Claire (cloison_at_lasim.univ-lyon1.fr)
Date: Tue Jul 29 2008 - 09:16:36 CDT

Hi VMD users!

There are several messages on alignement in the mailing-list already,
but to my knwoledge my question was not answered yet.

*) Just to set the background :
I would like to use vmd to align the peptide bond of a small model amide
molecule (NMA = CH3-CONH-CH3)
on a given peptide bond of a protein (here, i have just chosen a di-NMA
molecule,
with 2 peptide bonds, for testing : CH3-CONH-CH2-CONH-CH3).
My idea is to select the CNO atoms of the NMA and align them with the
one of the CNO bonds of di-NMA

*) Now to the tcl-script problem:
If the di-NMA.pdb molecule is numbered 0 and the NMA.pdb molecule is
numbered 1, my tcl script look like :

set selatoms [atomselect 1 " (residue 0 and name C) or (residue 0 and
name O) or (residue 1 and name N)"]
puts "NMA selection = [$selatoms get {name residue index}] "

set refatoms [atomselect 0 "(residue 0 and name C) or (residue 0 and
name O) or (residue 1 and name N) "]
puts "di-NMA selection = [$refatoms get {name residue index}]"

set tm [measure fit $selatoms $refatoms order {0 1 2 }]
set all [atomselect 1 "all"]
$all move $tm

The problem appears because of the atomselect command : it seems to
reorder the atoms
with increasing index, which is *NOT* the order of my selection text.
So the order of the two selection is more or less random, depending on
how the indexes are in two pdb files.
Then the measure fit does not complain, but of course the molecule are
not aligned as expected.

Is there any option for atomselect to impose the order of the atoms ?
If not, how can I get the right order for the fit procedure ?

Thanks in advance for your help,
Claire

ps : here are the two (faked) pdb files
NMA.pdb :
ATOM 1 CA ALA 0 1.125 1.534 0.000 0.00 0.00
0 C
ATOM 2 C ALA 0 0.000 0.514 0.000 0.00 0.00
0 C
ATOM 3 O ALA 0 -1.173 0.853 0.000 0.00 0.00
0 O
ATOM 4 N ALA 1 0.394 -0.796 0.000 0.00 0.00
0 N
ATOM 5 CA ALA 1 -0.546 -1.905 0.000 0.00 0.00
0 C
ATOM 6 H1 ALA 1 1.017 2.171 0.880 0.00 0.00
0 H
ATOM 7 H2 ALA 1 1.017 2.171 -0.880 0.00 0.00
0 H
ATOM 8 H3 ALA 1 1.381 -0.999 0.000 0.00 0.00
0 H
ATOM 9 H4 ALA 1 -1.551 -1.486 0.000 0.00 0.00
0 H
ATOM 10 H5 ALA 1 -0.420 -2.528 -0.890 0.00 0.00
0 H
ATOM 11 H6 ALA 1 2.123 1.091 0.000 0.00 0.00
0 H
ATOM 12 H7 ALA 1 -0.420 -2.528 0.890 0.00 0.00
0 H

di-NMA.pdb
ATOM 1 HA1 GLY X 1 4.097 2.626 -0.889
1.00300.00 H
ATOM 2 O GLY X 1 1.492 4.135 0.000
1.00300.00 O
ATOM 3 H GLY X 1 4.097 4.166 0.000
1.00300.00 H
ATOM 4 C GLY X 1 2.211 3.139 0.000
1.00300.00 C
ATOM 5 CA GLY X 1 3.733 3.139 0.000
1.00300.00 C
ATOM 6 HA2 GLY X 1 4.097 2.626 0.889
1.00300.00 H
ATOM 7 N GLY X 2 1.680 1.769 0.000
1.00300.00 N
ATOM 8 CA GLY X 2 0.256 1.500 0.000
1.00300.00 C
ATOM 9 H GLY X 2 2.315 0.984 0.000
1.00300.00 H
ATOM 10 C GLY X 2 0.000 0.000 0.000
1.00300.00 C
ATOM 11 O GLY X 2 0.860 -0.877 -0.000
1.00300.00 O
ATOM 12 HA2 GLY X 2 -0.183 1.932 -0.889
1.00300.00 H
ATOM 13 HA1 GLY X 2 -0.183 1.932 0.889
1.00300.00 H
ATOM 14 HA1 GLY X 3 -1.591 -2.170 -0.889
1.00300.00 H
ATOM 15 H GLY X 3 -3.036 -1.633 0.000
1.00300.00 H
ATOM 16 H GLY X 3 -2.107 0.465 0.000
1.00300.00 H
ATOM 17 N GLY X 3 -1.441 -0.293 0.000
1.00300.00 N
ATOM 18 CA GLY X 3 -1.946 -1.651 0.000
1.00300.00 C
ATOM 19 HA2 GLY X 3 -1.591 -2.170 0.889
1.00300.00 H 

-- 
----------------------------------------------------
Claire LOISON
Theoretical Physical-Chemistry Group in LASIM
tel      : 00 33 4 72 43 12 57
cellular : 00 33 6 31 30 11 72 
----------------------------------------------------
Laboratoire de Spectrométrie Ionique et Moléculaire 
UMR 5579
Domaine Scientifique de la Doua
Université Claude Bernard Lyon 1 
Bâtiment Alfred Kastler
43, bd du 11 Novembre 1918
69622 Villeurbanne cedex
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