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 ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! 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-d2d _______________________________________________ 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
