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 > ------------------------------------------------------------------------------ LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d _______________________________________________ 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
