Re: [PyMOL] sulfated tyrosine's losing connection
Hi Jordan, A quick look shows that there is no bond between the adjacent phosphotyrosines. Apparently they are too far apart for Pymol's bond check. Cheers, Tsjerk On Tue, Dec 23, 2014 at 6:20 AM, Jordan Willis jwillis0...@gmail.com wrote: Does anyone know why PyMoL renders the PDBs 3U2S and 3U4E without connecting backbone atoms at residue 100G and 100H? Are the bond distances for these two residue types not within the right parameters? SimpleViewer and JalView both bridge this connection. Thanks, Jordan -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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. -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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] sulfated tyrosine's losing connection
my experience shows that when you have two HETATM residues one after another, pymol never shows this bond because the crystallographer never put a CONECT record for it, which pymol wants. eg for 1674, there is not CONECT showing 1676 as being bonded and since they are HETATM , pymol decides to use the CONECT records. -David On Dec 23, 2014, at 12:20 AM, Jordan Willis jwillis0...@gmail.com wrote: Does anyone know why PyMoL renders the PDBs 3U2S and 3U4E without connecting backbone atoms at residue 100G and 100H? Are the bond distances for these two residue types not within the right parameters? SimpleViewer and JalView both bridge this connection. Thanks, Jordan -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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] sulfated tyrosine's losing connection
This unusual file has all the backbone bonds indicated with CONECT records -- except the missing links you note. I'm guessing that PyMOL is respecting that, and that it could be an RCSB file error. CONECT 9606 9593 9607 CONECT 9607 9606 CONECT 9608 9609 ... CONECT 1674 1661 1675 CONECT 1675 1674 CONECT 1676 1677 What are missing there are CONECT 9606 9608 CONECT 9608 9606 CONECT 1674 1676 CONECT 1676 1674 Jmol has the same missing links. (forwarding to Andreas Prlic at RCSB) -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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] sulfated tyrosine's losing connection
actually -- I see there are just CONECT records for all the HETATMs, as usual. Nothing odd about that. But, nonetheless, in this case those CONECT records are not there. The point is that it has nothing to do with PyMOL. -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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] sulfated tyrosine's losing connection
Does anyone know why PyMoL renders the PDBs 3U2S and 3U4E without connecting backbone atoms at residue 100G and 100H? Are the bond distances for these two residue types not within the right parameters? SimpleViewer and JalView both bridge this connection. Thanks, Jordan -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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
