Re: [PyMOL] Missing residues in PDB

[Андрей Г. <gon...@gm...>]

Thanks!

2012/1/31 Thomas Holder <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



-- 

Андрей Гончар