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Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!
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From: Robert C. <rob...@qu...> - 2017-06-21 14:47:57
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Hi Leila, I responded too quickly without reading carefully! Adding those lines should have worked (but only the CRYST1 line is needed). Your model.pdb file that you linked to on Dropbox does not have the CRYST1 line. Adding that line works for me. Cheers, Rob On Wed, 2017-06-21 09:29 +0200, leila karami <kar...@gm...> wrote: > Dear PYMOL users, > > I have done a homology modelling using swiss model. Template pdb file > contain 3 chains (A, B, C). I used only chain A for homology > modelling as template. > > There is a symmetry operator in template pdb file (temp.pdb). I want > to use symexp to obtain dimeric structure for modeled pdb file > (model.pdb). > > I manually added following records (from temp.pdb) at the first of the > modeled pdb file: > =========================================================== > REMARK 290 > REMARK 290 CRYSTALLOGRAPHIC SYMMETRY > REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 > REMARK 290 > REMARK 290 SYMOP SYMMETRY > REMARK 290 NNNMMM OPERATOR > REMARK 290 1555 X,Y,Z > REMARK 290 2555 -X,Y,-Z > REMARK 290 3555 X+1/2,Y+1/2,Z > REMARK 290 4555 -X+1/2,Y+1/2,-Z > REMARK 290 > REMARK 290 WHERE NNN -> OPERATOR NUMBER > REMARK 290 MMM -> TRANSLATION VECTOR > REMARK 290 > REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS > REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM > REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY > REMARK 290 RELATED MOLECULES. > REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 > REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 > REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 > REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 > REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 > REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 > REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 88.99000 > REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.29500 > REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 > REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 88.99000 > REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.29500 > REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 > REMARK 290 > CRYST1 177.980 56.590 83.220 90.00 116.58 90.00 C 1 2 1 12 > ORIGX1 1.000000 0.000000 0.000000 0.00000 > ORIGX2 0.000000 1.000000 0.000000 0.00000 > ORIGX3 0.000000 0.000000 1.000000 0.00000 > SCALE1 0.005619 0.000000 0.002811 0.00000 > SCALE2 0.000000 0.017671 0.000000 0.00000 > SCALE3 0.000000 0.000000 0.013436 0.00000 > > =========================================================== > > After using symexp sym,model,(model),1 in command line, I encountered > with: > > ExecutivesSymexp-Error: No Symmetry loaded! > > temp.pdb and model.pdb files are in following links: > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Ft8m1nrkx2s69wi9%2Fmodel.pdb%3Fdl%3D0&data=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556&sdata=g6I122L2C0o%2FAObHdjC9xXwoiPUx8J9MfupIpPp07ZM%3D&reserved=0 > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fmt7toc0wtenr779%2Ftemp.pdb%3Fdl%3D0&data=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556&sdata=6U5D%2BZOPnIAx3X61eeK77XLW23mroFnaM8sxiX7n1Ow%3D&reserved=0 > > Any help will be highly appreciated. > > Best, > Leila -- Robert L. Campbell, Ph.D. Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |