[PyMOL] RMSD calculation sans alignment

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

Re: [PyMOL] RMSD calculation sans alignment

Tom- Try ProFit http://www.bioinf.org.uk/software/profit/ Jed Thomas Grant 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

Re: [PyMOL] RMSD calculation sans alignment

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)

Re: [PyMOL] RMSD calculation sans alignment

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