Re: [PyMOL] Pair_fit syntax
First off, when the documentation includes square brackets in the command it indicates optional arguments. You don't include them in the command itself. In this case, pair_fit takes alternating selections from obj1 and obj 2. It also requires that the number of atoms in each selection be equal. I usually use CA atoms. >From you example it seems like you want to align two structures in chunks of 254 residues, but in a permuted order. I would do it as follows. I'm going to use the shorter "/obj1///1-255/CA" syntax to stand for "obj1 and resi 1-255 and name CA"). pair_fit /obj2///256-510/CA, /obj1///1-255/CA, /obj2///1-255/CA, /obj1///256-510/CA, /obj2///766-1020/CA, /obj1///511-765/CA, /obj2///511-765/CA, /obj1///766-1020/CA Note that if you have any missing residues you might get an error 'Atom counts between selection sets don't match'. In this case you should make sure that the obj2 selections have the same number of atoms as the obj1 selection. -Spencer On Fri, Oct 21, 2016 at 12:10 AM Subha K wrote: > Hi there, > > Could somebody please help me with the correct syntax for pair fit? > > I tried this, but this doesn't work. > > pairfit (obj2 and resi 256-510), (onj1 and resi 1-255), [(obj2 and resi > 1-255), (obj1 and resi 256-510), [(obj2 and resi 766-1020), (obj1 and resi > 511-765), [(obj2 and resi 511-765), (obj1 and resi 766-1020)]]] > > Thanks, > Subha > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > ___ > 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 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik___ 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] Pair_fit syntax
Hi Spencer, Thanks a lot for that very useful information. Regards, Subha On Tue, Oct 25, 2016 at 4:48 AM, Spencer Bliven wrote: > First off, when the documentation includes square brackets in the command > it indicates optional arguments. You don't include them in the command > itself. In this case, pair_fit takes alternating selections from obj1 and > obj 2. It also requires that the number of atoms in each selection be > equal. I usually use CA atoms. > > From you example it seems like you want to align two structures in chunks > of 254 residues, but in a permuted order. I would do it as follows. I'm > going to use the shorter "/obj1///1-255/CA" syntax to stand for "obj1 and > resi 1-255 and name CA"). > > pair_fit /obj2///256-510/CA, /obj1///1-255/CA, /obj2///1-255/CA, > /obj1///256-510/CA, /obj2///766-1020/CA, /obj1///511-765/CA, > /obj2///511-765/CA, /obj1///766-1020/CA > > Note that if you have any missing residues you might get an error 'Atom > counts between selection sets don't match'. In this case you should make > sure that the obj2 selections have the same number of atoms as the obj1 > selection. > > -Spencer > > On Fri, Oct 21, 2016 at 12:10 AM Subha K wrote: > >> Hi there, >> >> Could somebody please help me with the correct syntax for pair fit? >> >> I tried this, but this doesn't work. >> >> pairfit (obj2 and resi 256-510), (onj1 and resi 1-255), [(obj2 and resi >> 1-255), (obj1 and resi 256-510), [(obj2 and resi 766-1020), (obj1 and resi >> 511-765), [(obj2 and resi 511-765), (obj1 and resi 766-1020)]]] >> >> Thanks, >> Subha >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot__ >> _ >> 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 > > -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik___ 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] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
Hi everyone, Can someone please assist me opening this pdb file? I am trying to open EmrE protein (pdb: 3B5D) in Pymol a and show it as cartoon representation, but it opens up as many little cross signs seem to be corresponding to CA atoms. When I try to preset it pretty or any other preset options, it disappears. The command "show cartoon" is not doing anything on it. Cheers Mohsen -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik___ 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] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
Hi Mohsen, The PDB file of 3B5D only contains CA atoms, so most rendering like cartoon fails. You could try to visualize it by "set ribbon_trace_atoms, 1" and then show it as ribbon. Yuxing -Original Message- From: pymol-users-requ...@lists.sourceforge.net [mailto:pymol-users-requ...@lists.sourceforge.net] Sent: Tuesday, October 25, 2016 4:50 PM To: pymol-users@lists.sourceforge.net Subject: PyMOL-users Digest, Vol 125, Issue 14 Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." -- Message: 4 Date: Tue, 25 Oct 2016 21:34:01 + From: Mohsen Chitsaz Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol To: "pymol-users@lists.sourceforge.net" Message-ID: Content-Type: text/plain; charset="us-ascii" Hi everyone, Can someone please assist me opening this pdb file? I am trying to open EmrE protein (pdb: 3B5D) in Pymol a and show it as cartoon representation, but it opens up as many little cross signs seem to be corresponding to CA atoms. When I try to preset it pretty or any other preset options, it disappears. The command "show cartoon" is not doing anything on it. Cheers Mohsen -- next part -- An HTML attachment was scrubbed... -- -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest, Vol 125, Issue 14 UT Southwestern Medical Center The future of medicine, today. -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ 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
