[PyMOL] Multiple Structure Superposition
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
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 biobud...@gmail.com 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
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 Ravindranbiobud...@gmail.com 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
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
