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

[Thomas H. <tho...@sc...>]

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.