Hi Martin, As you've found, the mutagenesis wizard destroys the ordering in some cases. I'll look into it.
Cheers, -- Jason On Tue, Dec 7, 2010 at 11:34 AM, Martin Hediger <ma....@bluewin.ch> wrote: > Good day > I use PyMOL to introduce mutations into a structure. It occured to me that > when saving the modified structure, atom sequence was not preserved. Using > > set retain_order > set pdb_retain_ids > > is supposed to control this. It seems now, as if mutating a structure does a > really weired thing: > Once the mutation is introduced, the sequence becomes completely disordered > in a sense that the atoms of the "new" residue are placed in between the > atoms of the very first residue, in terms of sequence (not geometry). > This results in a PDB file like this (PRO is the first residue, PHE is the > residue to which the mutation is being carried out): > > ATOM 1 N PRO A 1 53.611 -4.470 40.679 1.00 0.00 PROT > N > TER 2 PRO A 1 > ATOM 0 N PHE D 14 55.428 -5.717 38.365 1.00 0.00 PROT > N > TER 1 PHE D 14 > ATOM 2 CA PRO A 1 52.399 -3.722 40.197 1.00 0.00 PROT > C > TER 3 PRO A 1 > ATOM 1 CA PHE D 14 55.821 -4.897 37.223 1.00 0.00 PROT > C > TER 2 PHE D 14 > ATOM 3 C PRO A 1 52.805 -2.296 39.783 1.00 0.00 PROT > C > TER 4 PRO A 1 > ATOM 2 CB PHE D 14 54.681 -4.879 36.160 1.00 0.00 PROT > C > TER 3 PHE D 14 > ATOM 4 O PRO A 1 53.381 -1.530 40.550 1.00 0.00 PROT > O > TER 5 PRO A 1 > ATOM 3 CG PHE D 14 54.928 -4.027 34.905 1.00 0.00 PROT > C > TER 4 PHE D 14 > ATOM 5 CB PRO A 1 51.360 -3.675 41.342 1.00 0.00 PROT > C > TER 6 PRO A 1 > ATOM 4 CD1 PHE D 14 56.116 -4.189 34.183 1.00 0.00 PROT > C > TER 5 PHE D 14 > ATOM 6 CG PRO A 1 52.019 -4.362 42.549 1.00 0.00 PROT > C > TER 7 PRO A 1 > ATOM 5 CD2 PHE D 14 54.011 -3.049 34.512 1.00 0.00 PROT > C > TER 6 PHE D 14 > ATOM 7 CD PRO A 1 53.253 -5.096 41.996 1.00 0.00 PROT > C > TER 8 PRO A 1 > ATOM 6 CE1 PHE D 14 56.391 -3.370 33.093 1.00 0.00 PROT > C > TER 7 PHE D 14 > ATOM 8 HA PRO A 1 51.990 -4.297 39.323 1.00 0.00 PROT > H > TER 9 PRO A 1 > ATOM 7 CE2 PHE D 14 54.282 -2.238 33.413 1.00 0.00 PROT > C > TER 8 PHE D 14 > ATOM 9 1HB PRO A 1 50.434 -4.192 41.043 1.00 0.00 PROT > H > TER 10 PRO A 1 > ATOM 8 CZ PHE D 14 55.473 -2.397 32.707 1.00 0.00 PROT > C > TER 9 PHE D 14 > ATOM 10 2HB PRO A 1 51.070 -2.637 41.594 1.00 0.00 PROT > H > TER 11 PRO A 1 > ATOM 9 C PHE D 14 56.113 -3.478 37.649 1.00 0.00 PROT > C > TER 10 PHE D 14 > ATOM 11 1HG PRO A 1 51.327 -5.056 43.052 1.00 0.00 PROT > H > TER 12 PRO A 1 > ATOM 10 O PHE D 14 55.357 -2.867 38.421 1.00 0.00 PROT > O > TER 11 PHE D 14 > ATOM 12 2HG PRO A 1 52.313 -3.615 43.311 1.00 0.00 PROT > H > TER 13 PRO A 1 > ATOM 11 1HD PHE D 14 56.847 -4.922 34.497 1.00 0.00 PROT > H > TER 12 PHE D 14 > ATOM 13 1HD PRO A 1 54.110 -5.062 42.704 1.00 0.00 PROT > H > > > Can this be explained somehow? > > Thanks for your answers. > Martin > > > > > > > > > On 09.11.10 13:26, Jason Vertrees wrote: >> >> Hi Martin, >> >> set retain_order >> set pdb_retain_ids >> >> Cheers, >> >> -- Jason >> >> On Tue, Nov 9, 2010 at 4:30 AM, Martin Hediger<ma....@bluewin.ch> wrote: >>> >>> Dear all >>> It occured to me that PyMOL is resequencing a structure when saving. I >>> am trying to interpolate between two structures where it is critical to >>> have identical sequence in both structures. Is it possible submit a >>> <DO_NOT_RESEQUENCE>-option to the save command? >>> >>> Thanks for your help >>> Martin >>> >>> >>> ------------------------------------------------------------------------------ >>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper >>> David G. Thomson, author of the best-selling book "Blueprint to a >>> Billion" shares his insights and actions to help propel your >>> business during the next growth cycle. Listen Now! >>> http://p.sf.net/sfu/SAP-dev2dev >>> _______________________________________________ >>> 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 >>> >> >> > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev _______________________________________________ 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
