Thank you all for your help.  Looks like both ProFit and rms_cur will do just what I needed. 

Thanks!

Tom


--
Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203



On Fri, Jul 22, 2011 at 10:59 AM, Michael Lerner <mglerner@gmail.com> wrote:
PyMOL's rms_cur command will do what you want. E.g.

fetch 1rx1
fetch 1ra1

# reports "Executive: RMS =   34.329 (159 to 159 atoms)"
# because the structures still need to be translated and rotated
rms_cur (1rx1 and name CA), (1ra1 and name CA)

# reports "Executive: RMS =    0.862 (159 to 159 atoms)"
# because it calculates translated/rotated value, but does now
# apply the translation/rotation to the molecules
rms (1rx1 and name CA), (1ra1 and name CA)


# reports "Executive: RMS =    0.391 (1026 to 1026 atoms)"
# standard PyMOL align, which also translates and rotates
align 1rx1, 1ra1

# both of these report "Executive: RMS =    0.862 (159 to 159 atoms)"
# because the structures have now been translated and rotated
rms_cur (1rx1 and name CA), (1ra1 and name CA)
rms (1rx1 and name CA), (1ra1 and name CA)

Cheers,

-Michael


On Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant <tgrant@hwi.buffalo.edu> wrote:
Dear all,

I'm attempting to align a series of structures using the CEAlign plug-in in PyMOL due to a lack of any detectable sequence homology.  CEAlign does a good job of aligning and the fits are very reasonable.  However, the RMSD that is calculated is based only on the c-alphas that were actually aligned, not based on the total number of c-alphas in the structure.  After searching online I have been unable to find any software or servers that will simply calculate the RMSD of two structures as is, without aligning them first.  I would think this would be a relatively straightforward thing to do, just to calculate RMSD from two existing structures without translation or rotation for alignment.

Does anyone know of a way either in PyMOL or in general to simply calculate the RMSD between all c-alphas of two structures?  Obviously it won't necessarily be a one-to-one ratio of c-alphas, but I can manually curate the pdb to include only the equivalent and "aligned" residues, even if not used in the CEAlign algorithm, so that there are the same number of c-alphas in both structures.

Thank you for any help and suggestions,

Tom

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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
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as of August 15th:

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