VMD-L Mailing List

From: Christopher MacDermaid (chris.macdermaid_at_gmail.com)
Date: Wed Aug 26 2009 - 17:17:34 CDT

Hi Mark,

Check out the "measure fit" command:

http://www.ks.uiuc.edu/Research/vmd/current/ug/node133.html

Idealy, you'd create two atom selections for your proteins, say 1 and 2 and
you may want to align their backbones,
off the top of my head:

## Define atomselections

set sel1_bb [atomselect 1 "backbone"]
set sel2_bb [atomselect 2 "backbone"]
set sel1_all [atomselect 1 "all"]

## Calculate best fit matrix

set R [measure fit $sel1_bb $sel2_bb]

##Move the first molecule
$sel1_all move $R

Should work. Something to note though. When calculating the RMSD in VMD,
you need to make sure that the indices for the atoms in your selections are
ordered the same. Thus if you have 1 pdb formatted like this:

ATOM 1 N
ATOM 2 CA
ATOM 3 C
ATOM 4 O
ATOM 5 CB
ATOM 6 CG

and another like this:

ATOM 1 N
ATOM 2 CA
ATOM 3 CB
ATOM 4 CG
ATOM 5 C
ATOM 6 O

and you try to calculate their RMSD, VMD will calculate the dist between N/N
CA/CA C/CB O/CG CB/C CG/O, which is obviously incorrect. the measure fit
command does have an "order" option that allows you to fix this via VMD, or
you can just edit the PDB files to make sure things behave.

Chris

On Wed, Aug 26, 2009 at 5:17 PM, Mark M Huntress <markmh_at_bgsu.edu> wrote:

> thank you for the responses to my previous question. Here is a new one: I
> have two very similar proteins, and I want to look at side chain position
> differences between them, but their coordinates are so different that when I
> open both files in VMD that the two proteins appear on different sides of
> the screen. Is there a way that I can superimpose one on the other without
> changing its internal geometric structure?
> Thanks
> 

-- 
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Christopher M. MacDermaid  chris.macdermaid_at_gmail.com  (215) 898-5742
Saven Group -- University of Pennsylvania -- http://saven.chem.upenn.edu
Department of Chemistry, 231 South 34th Street, Philadelphia, PA 19104-3803
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