From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Aug 26 2013 - 03:46:55 CDT

I asked that because I must have done a mistake with the "measure fit".
What I did:

set sel0 [atomselect 0 "name CA and resid 41 to 48"]
set sel1 [atomselect 1 a"name CA and resid 41 to 48"]
set M [measure fit $sel0 $sel1]
$sel0 move $M

set selaligned [atomselect 1 "segname P2I"]
$selaligned writepdb P2I_aligned.pdb

where model 0 (of segname P2) is a 450 residue polypeptide and model 1 (of
segname P2I) is a stretch of 48 residues that was isolated from model 0 and
subjected to simulations, while rmsd-colvars restraining CA atoms of
residues 41 to 48. Actually, P2I_aligned.pdb turned out to be laterally
displaced by a few angstroms from model 0 (i.e., the 41-48 helical portions
did not exactly superimpose)

Alternatively, I tried

set selaligned [atomselect 1 "name CA and resid 41 to 48"]
$selaligned writepdb P2I_41-48_aligned.pdb

which only saves the coordinates for the CA atoms. I observed exactly the
same lateral shift as with "segname' above.

There must be some silly error that I was unable to catch (obviously, when
corrected, a script to delete the redundant atoms (41-48 resids) and
recomposing the 450-resid peptide would help.

Thanks for advice
francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Aug 26, 2013 at 8:47 AM
Subject: vmd-l: matching part of two models
To: vmd-l_at_ks.uiuc.edu

Hello;
I am looking for a VMD plugin/script to match (superimpose) a portion (such
as a few alpha-helix turns) of a large polypeptide model 1 with a small
polypeptide model 2. All that in order to replace the model-2 part in model
1.

This means that model 2 was modeled separately while maintaining by
rmsd-colvars the conformation of the helical portion that I would like to
superimpose.

Thanks

francesco pietra