Hi Martin, > Could you point me out to the Python module where the "reader" is > implemented? > I would be interested in seeing how PyMOL handles this because I > recently had to write something similar.
See pymol/modules/pymol/importing.py Look for "def load". Cheers, -- Jason > On 23.07.12 18:19, Jason Vertrees wrote: >> Hi Malai, >> >> Thanks for bringing this to our attention. The file you sent does have >> a TER record (which separates chains) but it went ahead and >> re-declared chain A. This confused PyMOL. You can easily correct this >> by forcing PyMOL to start a new model. Just insert, >> >> ENDMDL >> >> on line 4379 of your file. >> >> While not technically PyMOL's fault, we'll update the reader to handle >> this more robustly in the future. >> >> Cheers, >> >> -- Jason >> >> >> On Fri, Jul 20, 2012 at 5:44 PM, Jason Vertrees >> <jason.vertr...@schrodinger.com> wrote: >>> Hi Malai, >>> >>> What structure? Can we see it? (Feel free to send it to me if you can share >>> it.) >>> >>> Cheers, >>> >>> -- Jason >>> >>> On Fri, Jul 20, 2012 at 3:09 PM, Malai <winterho...@gmail.com> wrote: >>>> Hi Pymol users, >>>> >>>> I am using Pymol 1.5.0.0. I tried to cartoon for the complex but Pymol can >>>> not assign the cartoon for some parts of complex. When I use some >>>> commercial >>>> visualizer like MOE and Discovery Studio. It works well. Could you help me >>>> what is the problem in the structure or pymol? >>>> >>>> Many thanks in advance. >>>> >>>> With regards, >>>> Malai >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. Discussions >>>> will include endpoint security, mobile security and the latest in malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> 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 >>> >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrödinger, LLC >>> >>> (e) jason.vertr...@schrodinger.com >>> (o) +1 (603) 374-7120 >> >> > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
