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
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