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 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 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > 10 Tips for Better Web Security > Learn 10 ways to better secure your business today. Topics covered include: > Web security, SSL, hacker attacks & Denial of Service (DoS), private keys, > security Microsoft Exchange, secure Instant Messaging, and much more. > http://www.accelacomm.com/jaw/sfnl/114/51426210/ > ------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ------------------------ Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 ------------------------------------------------------------------------------ 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks & Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
