Thank you all for your help. Looks like both ProFit and rms_cur will do just what I needed.
PyMOL's rms_cur command will do what you want. E.g.fetch 1rx1fetch 1ra1# reports "Executive: RMS = 34.329 (159 to 159 atoms)"# because the structures still need to be translated and rotatedrms_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 moleculesrms (1rx1 and name CA), (1ra1 and name CA)# reports "Executive: RMS = 0.391 (1026 to 1026 atoms)"# standard PyMOL align, which also translates and rotatesalign 1rx1, 1ra1# both of these report "Executive: RMS = 0.862 (159 to 159 atoms)"# because the structures have now been translated and rotatedrms_cur (1rx1 and name CA), (1ra1 and name CA)rms (1rx1 and name CA), (1ra1 and name CA)Cheers,-MichaelOn Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant <email@example.com> wrote:
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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