Hi Abida, if the PDB has multible models, you can also enable the "all_states" setting instead of modifying the file.
PyMOL> set all_states If this doesn't solve the issue, I guess it's a chain naming conflict with duplicate chain identifiers. Feel free to send me the PDB file off-list and I'll have a look at it. Cheers, Thomas Martin Hediger wrote, On 01/08/13 09:08: > Hi Abida > Is it possible that you have multiple states in your PDB file? Try > clicking the ">" arrow in the bottom right corner of PyMOL and see if > you can display the other protein. If so, you probably need to delete > the "MODEL" and "END" from your PDB file. Then all should appear at once. > > Martin > > On 08.01.13 06:12, Abida Siddiqa wrote: >> Hello, >> >> I have docked one protein named 'L1'( 450 amino acid) with another protein >> named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to >> visualize >> the complex. my system is windows 7 , 64 bit. The problem is, i am unable >> to see the sequence of 'E2' protein and so as its structure. In order to >> confirm, if it is docking problem or visualization problem, i have used >> swiss pdb viewer. it has shown me sequence and structure of both proteins. i >> wonder why can not i see it in pymol. >> secondly, i docked L1 and E2 ( this time used chain A and B of it), and >> visualized the complex in pymol. i was only able to see L1, and chain A of >> E2 (both chain A and B are alike). Then in order to see if it is docking >> error or visualization error, i rendered the complex in swiss pdb viwer and >> saw the L1 and E2 (both chain A and B). >> Thirdly, i changed the docking software and generated a complex using >> another software, this time i still was unable to visualize complete complex >> in pymol. >> Any help will be much appreciated. >> Kind regards >> Abida -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 _______________________________________________ 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
