[Chimera-users] RMSD

[Elaine Meng]

Hi John,
(1) First figure out which atoms you want to use for the calculation,  
by trying the "match" command.  (2) If you are showing the trajectory  
with MD Movie, you can have the RMSD calculated at multiple different  
frames by putting the same command in a per-frame script.

(1) Figuring out which atoms to use. Show the command line by choosing  
Favorites... Command Line  from the menu.  Now enter some test "match"  
commands.  The RMSD will be reported in the Reply Log (Favorites...  
Reply Log).  Say your crystal structure is #0 and the trajectory is  
#1.  If they had exactly the same residues, you could just do  
something like

match #0 at ca #1ca

or

match #0 at n,ca,c,o #1 at n,ca,c,o

to use just alpha-carbons or the whole backbone, respectively.   
However, maybe your crystal structure doesn't have the same residues  
as the trajectory (could be missing a loop or a few residues off the  
end), so you may need to specify just the residues they have in  
common, for example:

match #0:10-30,50-80 at ca #1:10-30,50-80 at ca

to use the alpha-carbons of those residues.  The numbering might even  
be different in the two structures, in which case you could use  
different residue numbers in the two specifications.

(2) Using a per-frame script.  In the MD Movie dialog, you can choose  
"Per-Frame... Define script..." and enter "Chimera commands" to be  
executed at each frame.  Click OK or Apply in the script dialog, then  
use the MD Movie controller to go to the first frame.  Show the Reply  
Log and clear its contents.  In MD Movie, turn off looping and play  
the whole trajectory.   You can enter step size in the MD Movie dialog  
to only calculate for every 2nd, 3rd, ... frame as you wish instead of  
every single frame.  All the values will now be in the Reply Log.  You  
can also echo frame number into the Reply Log, although it won't end  
up on the same line as the RMSD value.  For example, per-frame Chimera  
script:

echo <FRAME>
match #0:10-30,50-80 at ca #1:10-30,50-80 at ca

Using the match command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
Superimposing structures:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. I like your "hand" signature!


On Mar 26, 2010, at 4:26 AM, Beale, John wrote:

> What is the best way to use Chimera to compute the RMSd value of an  
> MD trajectory snapshot relative to the crystal structure of the  
> protein?
>
> Thanks!
>
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>
> John M. Beale, Jr., Ph,D.
> Professor of Medicinal Chemistry and Pharmacognosy
> St. Louis College of Pharmacy
> 4588 Parkview Place
> St. Louis, Missouri  63110
> (314)-446-8461
> Cell: (314)-315-0409
> FAX (314) 446-8460
> jbeale at stlcop.edu