Re: [PyMOL] (no subject)
Hi Aliya, yes, likely there is a clash. But that's hard to tell without seeing your data. Cheers, Thomas On 01 Jul 2014, at 11:34, Aliya Holland wrote: > Hello, > > I just created an animation of a conformational change of a specific domain > on a molecule. During the animation the domain rotates just as it should, > however other parts of the molecule moves with the conformation change. I was > wondering if that was part of the PyMOL programming or if there was a clash > between the end domain and the rotating section. Why would there be movement > in the entire molecule when only one section of it is morphing. > > Thank you > > A -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ 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] Aligning multiple residue sets in two or more proteins
Monica, Try: align PDB1//A/80-120+160-220/, PDB2//A/80-120+160-220/ or if you want to align using the alpha carbons, align PDB1//A/80-120+160-220/CA, PDB2//A/80-120+160-220/CA Cheers, -Rajintha On Wed, Jul 2, 2014 at 7:22 AM, Monica Mittal wrote: > Dear all > I need to align lets say resi 80-120 and 160-220 from one protein to resi > 80-120 and 160-220 in second protein. How can i do this. > I tried following: > align PDB1 and resi 80-120, PDB2 and resi 80-120 > this is for one set but how to do for two sets 80-120 as well as 160-220 > simultaneously. > Thank you > Monica > > > -- > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > ___ > 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 > -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ 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] Aligning multiple residue sets in two or more proteins
Hi Monica, I haven't tested, but maybe you could try: align PDB1 and (resi 80-120 or resi 160-220), PDB2 and (resi 80-120 or resi 160-220) I.e. expanding the selection to both streches. Running sequential alignments will replace existing ones. How this may help. /Andreas On Jul 2, 2014 1:24 PM, "Monica Mittal" wrote: > Dear all > I need to align lets say resi 80-120 and 160-220 from one protein to resi > 80-120 and 160-220 in second protein. How can i do this. > I tried following: > align PDB1 and resi 80-120, PDB2 and resi 80-120 > this is for one set but how to do for two sets 80-120 as well as 160-220 > simultaneously. > Thank you > Monica > > > -- > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > ___ > 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 > -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ 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
[PyMOL] Aligning multiple residue sets in two or more proteins
Dear all I need to align lets say resi 80-120 and 160-220 from one protein to resi 80-120 and 160-220 in second protein. How can i do this. I tried following: align PDB1 and resi 80-120, PDB2 and resi 80-120 this is for one set but how to do for two sets 80-120 as well as 160-220 simultaneously. Thank you Monica -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ 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
