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....@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. 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