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Re: [PyMOL] Dont resequence atoms when saving
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From: Martin H. <ma...@bl...> - 2010-12-07 16:35:03
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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... >> > > |