Re: [PyMOL] Pymol visualization problem
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 -- 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 -- 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
Re: [PyMOL] Pymol visualization problem
Thomas and Martin I have tried both suggestions. Still it did not work out.RegardsAbida 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 -- 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
Re: [PyMOL] Pymol visualization problem
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-, 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-, 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
