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Re: [PyMOL] Dont resequence atoms when saving
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From: Jason V. <jas...@sc...> - 2012-05-02 12:54:22
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Hi Martin, I don't think there's a fix for this. Please file a bug report on the open-source tracker. Cheers, -- Jason On Mon, Apr 30, 2012 at 10:09 AM, Martin Hediger <ma...@bl...> wrote: > Dear Pymol users > We are trying to generate a number of mutated structures using the > mutagenesis wizard. However, after mutating a position and saving to a new > PDB file, the mutated residue ends up being "mixed" into the coordinate > lines of the first residue. Some two coordinate lines are separated by TER > statements. At the position, where the residue should sit, there is a TER > statement, and the residue is skipped (e.g Res ID 139, TER, Res ID 141). > We also observe this using > > set retain_order > set pdb_retain_ids > > Is there a fix for this? > > Any help is appreciated. > > Thanks, > Martin > > > > > > > > > > On 13.12.10 16:52, Jason Vertrees wrote: >> >> 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...@bl...> 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...@bl...> >>>> 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 (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>>> >>>> >> >> > -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... 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