Hi Shyamala, You would specify the atoms in the rmsd command instead of using a separate selection step. This could be a list of all the atom names, or if the residues you are comparing have the same number of atoms with the same names, you could just supply the residue names or numbers. There are many ways to specify atoms in commands... # means model, : means residue, @ means atom, :45.a means residue 45 in chain A, etc. Some examples are shown below, but here is the full documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html

If atom order is not specified in the rmsd (or match) command, for example, rmsd #1:3@C1,C2,P,O2 #2:5@C1,C2,P,O2 rmsd #1:3 #2:5 rmsd #4:hem #0:hem the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number. Repeated use of the @ symbol specifies atoms in order: rmsd #1:3@C1@C2@P@O2 #2:5@C1@C2@P@O2 Since the atoms being paired in the example above have the same names, commas instead of @ symbols would also work. You would have to use @ repeatedly, however, if you wanted to pair atoms with different names: rmsd #1:3@ca@cb@cg@cd #2:5@c1@c2@c3@c4 Now, about scripting: You could just use a Chimera command script, simply a text file with the same commands you would enter at the command line. First test the commands by entering them in the Command Line, and then when you figure out what works, put a series of analogous commands into the file, name it something.cmd or something.com, and then simply open the file in Chimera to execute its contents. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile

However, if you already know how to do shell scripting, that might allow a more elegant approach with looping through structures combined with a short generic Chimera command file, rather than repeating the rmsd command many times in a long Chimera command file. This previous post on how to get RMSD results in nogui mode may also be relevant: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003064.html

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 7, 2008, at 10:05 AM, shyamala wrote:

Hi, I am fairly new to Chimera. I am trying to calculate the RMSD of the heavy atoms across two different ligand (small molecule) coordinate files. I don't need a least square fit performed, hence using rmsd as opposed to match.

I have to do this comparison for around 200 docked conformations against the native ligand conformation, hence I am thinking shell script that can call chimera to execute this command is the way to go.

I am not sure how to first select the two small molecules and then use the rmsd command when I start chimera in nogui mode. Any help, examples, pointers will be very much appreciated.

Thanks a lot,

Shyamala