Re: [PyMOL] Missing residues in PDB

[Thomas H. <sp...@us...>]

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