Dear PyMol users!
I have some structure.pdb from the md simulation wich consist of 1 chain
not defined in the pdb file explicitly ( missing chain id in the pdb file).
So the pymol recognise that chain as the ' ' . I need to rename this
chain to the desired name ( e.g to chain A ).
How I could do it?
James
1 апреля 2012 г. 15:04 пользователь James Starlight
<jmsstarli...@gmail.com>написал:
> Thomas,
>
>
> thank you I'll test your script with modeller after obtaining of this
> software on my workstation and post here results :)
>
>
> James
>
> 1 апреля 2012 г. 12:30 пользователь Thomas Holder <
> spel...@users.sourceforge.net> написал:
>
> Hi James,
>>
>> I use Modeller for exactly such tasks (build missing residues). It's free
>> for academic use.
>>
>> http://salilab.org/modeller/
>>
>> Using modeller is also not "comfortable" since it only has a python
>> scripting interface and thus requires you to write a script for each task.
>> But I wrote a general purpose automodel client which is quite convenient
>> for simple modelling tasks. See attachment.
>>
>> Usage:
>> python automodeller.py sequence.fasta template.pdb
>>
>> I provide this script "as is" without any warranty :) Let me know if it
>> works for you.
>>
>> Cheers,
>> Thomas
>>
>> James Starlight wrote, On 04/01/12 08:55:
>>
>> Hi Thomas!
>>>
>>> Thanks for help- this works good :)
>>>
>>>
>>> By the way I have some question not about pymol :)
>>> I've already looked for some software for processing of my PDB
>>> structure for a long time ( often I need to build missing residues and
>>> flexible LOOP fragments with some refining of the result ). For such
>>> purposes I've used amber tools software but I've found that this tools are
>>> not very comfortable for me :)
>>>
>>> Also I've found exactly what I need for in the MAESTRO's prime module
>>> but this tools avialable for the licensing only.
>>>
>>> Is there any other free software for structure processing with
>>> easy-to-use interface and free academical ussage ?
>>>
>>> Thanks again
>>>
>>> James
>>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>
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