Re: [PyMOL] Selection of chains based on PDB header

[John B. <jm...@eb...>]

Dear Julian

You can also try the PDB plugin which places each chain into a selection 
automatically for you.

https://pymolwiki.org/index.php/PDB_plugin


Regards

John
PDBe


On 12/06/2017 17:10, Thomas Holder wrote:
> Hi Julian,
>
> A one-liner to create chain selections looks like this:
>
> for c in cmd.get_chains(): cmd.select("chain_" + c, "chain " + c)
>
> PyMOL doesn't provide access to the PDB header fields. In principle PyMOL provides a way to access everything inside mmCIF files, see:
>
> https://pymolwiki.org/index.php/Cif_keepinmemory
>
> However, instead of doing this, I recommend to use the PDBe web API which provides the data in a friendly JSON data structure. I've attached a Python script which creates molecule (or chain) selections for 5n61 as an example. I recommend to load PDB structures from mmCIF or MMTF format, which not only have chain identifiers, but also molecule identifiers ("segi" field in PyMOL).
>
> Hope that helps.
>
> Cheers,
>    Thomas
>
>> On Jun 12, 2017, at 12:21 PM, Julian Reitz <jul...@gm...> wrote:
>>
>> Dear all,
>>
>> I have a pdb-file with multiple chains (5N61).
>>
>> Is there an easy way to create selections for all the chains that are defined in the pdb-header (A to U) without doing it manually for every chain (select A, chain A)?
>> Is it also possible to use the MOLECULE information from the header to name the selections?
>>
>> Thank you in advance,
>>
>> Julian
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
>
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-- 
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
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