Hi Martin, It does an alignment, finding matching pairs of atoms, removing outliers and calculating the RMSD over the remaining matches.
Cheers, Tsjerk On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger <ma....@bluewin.ch> wrote: > How does PyMOL calculate the RMSD between two structures where the > number of atoms is different? > Martin > > > > > > > Am 11.11.11 14:59, schrieb Thomas Holder: >> Hi Martin, >> >> is it the transform=0 argument what you are looking for? >> >> http://pymolwiki.org/index.php/Align#PYMOL_API >> >> x = cmd.align('foo', 'bar', transform=0) >> print 'RMSD:', x[0] >> >> About the "some kind of refinement": There are arguments "cutoff" and >> "cycles" that control this behaviour. >> >> Cheers, >> Thomas >> >> On 11/11/2011 02:46 PM, Martin Hediger wrote: >>> Dear List. >>> When aligning two structures using the PyMOL align command, one gets a >>> final RMS value indicating some kind of "convergence" i would say. Can I >>> somehow access the function for calculating this value directly from the >>> pymol prompt without aligning? >>> >>> Thanks for hints >>> Martin >> > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ 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
