Re: [PyMOL] Multiple Structure Superposition
Dear Suda, cealign can be used to do structure based superposition PyMOL> cealign target, mobile However, it's a pair-wise based alignment. You have to align two structures each time. Hope this helps. Zhijian Xu Suda Ravindran wrote: > Hi, > > I would like to know how to do structure based superposition using > PyMol for 3 or more structures. Please help me out. > > Thanks, > > -Suda > > > -- > EMC VNX: the world's simplest storage, starting under $10K > The only unified storage solution that offers unified management > Up to 160% more powerful than alternatives and 25% more efficient. > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev > > > ___ > 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 -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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
Re: [PyMOL] Multiple Structure Superposition
Hi Suda and Tsjerk, there is "alignto" which used cealign. There is also in the menu "Action > align > all to this" which uses cmd.util.mass_align (and that uses cmd.align). On Robert Campbell's site there is the "align_all.py" script: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ On my PyMOLWiki user page there is a "extra_fit" script. http://pymolwiki.org/index.php/User:Speleo3 All those align to a reference object (or state, in case of intra_fit) instead of an all-against-all best fit. Cheers, Thomas On 08/29/2011 08:52 AM, Tsjerk Wassenaar wrote: > Hi Suda, > > Do you mean different structures of the same molecule or different > molecules? For a multistate object, there is intra_fit. for selections > comprising multiple objects it's not currently possible. But it's > being worked on. > > Cheers, > > Tsjerk > > On Mon, Aug 29, 2011 at 8:43 AM, Suda Ravindran wrote: >> Hi, >> >> I would like to know how to do structure based superposition using PyMol for >> 3 or more structures. Please help me out. >> >> Thanks, >> >> -Suda -- Thomas Holder MPI for Developmental Biology -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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
Re: [PyMOL] Multiple Structure Superposition
Hi Suda, Do you mean different structures of the same molecule or different molecules? For a multistate object, there is intra_fit. for selections comprising multiple objects it's not currently possible. But it's being worked on. Cheers, Tsjerk On Mon, Aug 29, 2011 at 8:43 AM, Suda Ravindran wrote: > Hi, > > I would like to know how to do structure based superposition using PyMol for > 3 or more structures. Please help me out. > > Thanks, > > -Suda > > -- > EMC VNX: the world's simplest storage, starting under $10K > The only unified storage solution that offers unified management > Up to 160% more powerful than alternatives and 25% more efficient. > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev > ___ > 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 -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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
