hey, just wanted to ask if you could find something on why the mutagenesis wizard is destroying the ordering of atoms?
Is this perhaps fixed in the latest versions? Then a download would make sense. Thanks, Martin Am 13.12.10 16:52, schrieb Jason Vertrees: > 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 >>>> >>> > > ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ 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
