Hi Leila, You need the "CRYST1" line from the template pdb file. That is where PyMOL gets the symmetry information from.
Cheers, Rob On Wed, 2017-06-21 09:29 +0200, leila karami <karami.lei...@gmail.com> 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 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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
