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@ca #1ca

or

match #0@n,ca,c,o #1@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@ca #1:10-30,50-80@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@ca #1:10-30,50-80@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!

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@stlcop.edu