Hi, On Tue, 16 Mar 2010 09:23:50 -0400 David Hall <li...@cowsandmilk.net> wrote:
> See http://www.pymolwiki.org/index.php/Intra_Rms#USER_EXAMPLES.2FCOMMENTS > comments that start with "Fit, Rms, Rms_Cur are finicky and only > work..." as that likely explains your problem and a possible solution. > > But I agree that pymol's behavior with this command can be extremely > annoying. I should have added to my previous e-mail that I wrote a script to take care of this problem. It will calculate the RMS for a pair of selections by converting one to match the other (residue names, numbers, atom names etc. -- obviously only matching the backbone atoms). It creates a new object in order to do this. The script is called fitting.py and can be found at my pymol scripts site: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol and a description of the problems of fitting and an example of the use of the fitting.py script can be found here: http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
