Hi Carola For future reference, good to know it seems to be a version issue.
Best regards Martin Am 07.11.12 18:38, schrieb Carola Sophie Hengstenberg: > Hi Martin, > > thanks for your reply. Yes, I played with these settings, but it did not > work for me. I ended up with installing the pymol version 1.5 now. Here > the problem did not appear anymore, but the real cause of the problem I > could not find out... > > Carola > > Am Mittwoch, den 07.11.2012, 11:24 +0100 schrieb Martin Hediger: >> Hi Carola >> What did you try? Does it work when you use these commands right after >> starting up PyMOL and before you do any of the steps you take: >> >> set retain_order, 0 >> set pdb_retain_ids >> >> Martin >> >> >> >> >> >> >> >> On 31.10.12 14:03, Carola Sophie Hengstenberg wrote: >>> Dear all, >>> >>> I recently upgraded to Ubuntu 12.04 (pymol version 1.4.1-3). Since I did >>> the upgrade, mutations done with the mutagenesis wizard lead to >>> incorrect atom numbering in the saved pdb file. Before, the problem >>> definitely did not exist. I read the recent post in this forum >>> concerning this, but the pymol version 1.4 seems to lead to this >>> problem, too. >>> >>> Here an example: >>> >>> ATOM 1 N MET A 7 72.739 -17.539 8.852 1.00 36.46 >>> N >>> TER 2 MET A 7 >>> ATOM 0 N ALA A 12 77.920 -8.244 14.624 1.00 0.00 >>> N >>> TER 1 ALA A 12 >>> ATOM 2 CA MET A 7 73.836 -17.058 9.739 1.00 35.87 >>> C >>> TER 3 MET A 7 >>> ATOM 1 CA ALA A 12 77.603 -6.935 15.187 1.00 0.00 >>> C >>> TER 2 ALA A 12 >>> ATOM 3 C MET A 7 74.382 -18.171 10.623 1.00 36.04 >>> C >>> TER 4 MET A 7 >>> ATOM 2 CB ALA A 12 78.933 -6.222 15.489 1.00 0.00 >>> C >>> TER 3 ALA A 12 >>> ATOM 4 O MET A 7 73.676 -18.689 11.489 1.00 36.57 >>> O >>> TER 5 MET A 7 >>> ATOM 3 C ALA A 12 76.716 -6.146 14.255 1.00 0.00 >>> C >>> TER 4 ALA A 12 >>> ATOM 5 CB MET A 7 73.338 -15.921 10.634 1.00 34.58 >>> C >>> TER 6 MET A 7 >>> ATOM 4 O ALA A 12 77.070 -6.025 13.073 1.00 0.00 >>> O >>> TER 5 ALA A 12 >>> ATOM 6 CG MET A 7 72.989 -14.645 9.899 1.00 33.55 >>> C >>> ATOM 7 SD MET A 7 72.558 -13.328 11.053 1.00 30.82 >>> S >>> ATOM 8 CE MET A 7 74.184 -12.785 11.572 1.00 31.08 >>> C >>> ATOM 9 N THR A 8 75.645 -18.528 10.413 1.00 36.23 >>> N >>> ATOM 10 CA THR A 8 76.278 -19.573 11.207 1.00 35.81 >>> C >>> ATOM 11 C THR A 8 76.461 -19.071 12.633 1.00 34.75 >>> C >>> ATOM 12 O THR A 8 76.529 -19.861 13.578 1.00 35.68 >>> O >>> ATOM 13 CB THR A 8 77.662 -19.947 10.646 1.00 37.30 >>> C >>> ATOM 14 OG1 THR A 8 78.530 -18.810 10.723 1.00 38.49 >>> O >>> ATOM 15 CG2 THR A 8 77.544 -20.390 9.196 1.00 38.06 >>> C >>> ATOM 16 N GLY A 9 76.539 -17.750 12.779 1.00 32.20 >>> N >>> ATOM 17 CA GLY A 9 76.713 -17.161 14.096 1.00 27.95 >>> C >>> ATOM 18 C GLY A 9 76.334 -15.690 14.126 1.00 24.78 >>> C >>> ATOM 19 O GLY A 9 76.080 -15.092 13.083 1.00 24.20 >>> O >>> >>> [...] >>> >>> Can somebody help me out? >>> >>> Thanks in advance, >>> >>> Caro >>> >>> >>> ------------------------------------------------------------------------------ >>> Everyone hates slow websites. So do we. >>> Make your web apps faster with AppDynamics >>> Download AppDynamics Lite for free today: >>> http://p.sf.net/sfu/appdyn_sfd2d_oct >>> _______________________________________________ >>> 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 >>> > > ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_nov _______________________________________________ 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
