Hi Abida, thanks for the PDB file that you sent me off-list.
It is a naming conflict, you have more than one chain A which have overlapping residue numbers and even IDs. You can still load them like this: PyMOL> set retain_order PyMOL> load complex.1.pdb PyMOL> as cartoon I also suggest to fix the chain identifier: PyMOL> alter complex.1 and rank 3578-9999, chain="B" PyMOL> util.cbc And for the second file: PyMOL> set retain_order PyMOL> load complex.5.pdb PyMOL> as cartoon PyMOL> alter complex.5 and chain A and rank 1322-9999, chain="C" PyMOL> util.cbc Hope that helps. Cheers, Thomas Abida Siddiqa wrote, On 01/08/13 16:58: > > Thomas and Martin I have tried both suggestions. Still it did not work out. > Regards > Abida > ------------------------------------------------------------------------ > From: abida_sidd...@hotmail.com > To: pymol-users@lists.sourceforge.net > Subject: Pymol visualization problem > Date: Tue, 8 Jan 2013 10:12:46 +0500 > > 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
