I found a solution! With openbabel a pdb without residue names and numbers can be easily fixed: 1. babel file.pdb file.mol 2. babel file.mol file.pdb
Et voila! Now you have a pdb with repaired residue names! 2012/1/31 Андрей Гончар <gontc...@gmail.com>: > Thanks! > > 2012/1/31 Thomas Holder <spel...@users.sourceforge.net>: >> I put a script on the PyMOLWiki that does renumbering based connectivity: >> >> http://pymolwiki.org/index.php/Renumber >> >> Cheers, >> Thomas >> >> >> On 01/30/2012 02:52 PM, Thomas Holder wrote: >>> >>> On 01/30/2012 02:24 PM, gontchar andrey wrote: >>>> >>>> Thanks a lot! >>>> A very useful script, but not exactly that I need... >>>> In my pdb file residues are not numbered. I think that I have to >>>> determine amino acids only by atom sequence and connetcions... This >>>> problem is a little more complicated than assigning names to numbered >>>> residues, I think... >>>> Do you think, is it possible? >>> >>> >>> this is indeed more complicated. A simple heuristic would be to assume >>> that the first atom in a residue is always "N". I added a >>> "set_numbering" function to the script, maybe this works for you? >>> >>> Example: >>> >>> set_numbering myobj >>> set_sequence CDEFGHIKL, myobj >>> >>> Cheers, >>> Thomas >>> >>>> On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote: >>>>> >>>>> Hi Andrey, >>>>> >>>>> I have a script that updates the sequence based on residue numbering >>>>> (resi). See attachment. >>>>> >>>>> Usage: set_sequence sequence [, selection [, start ]] >>>>> >>>>> Example: >>>>> >>>>> # import script >>>>> run setseq.py >>>>> >>>>> # create a poly-ala peptide >>>>> fab AAAAAAAAA, myobj >>>>> >>>>> # set new sequence >>>>> set_sequence CDEFGHIKL, myobj >>>>> >>>>> # update sequence viewer >>>>> rebuild >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>> On 01/30/2012 01:38 PM, gontchar andrey wrote: >>>>>> >>>>>> Hi. >>>>>> We have a pdb-file of a small sequence of aminoacids. In this file >>>>>> there are atom names, atom coordinates, connects etc. except residue >>>>>> names records. Sure we can try to write them manually, but I'd like >>>>>> to know if there is some tool to do this automatically? >>>>>> >>>>>> -- >>>>>> >>>>>> Andrey >> >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen > > > > -- > > Андрей Гончар -- Андрей Гончар ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ 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
