[PyMOL] Subject: Re: Hi all...

[Jason V. <jv...@cs...>]

PyMOLers,

This example was just too cool not to be made into a script.  See

  http://www.pymolwiki.org/index.php/FindSurfaceResidues

-- Jason

> Message: 3
> Date: Mon, 8 Jun 2009 19:01:01 -0700
> From: "Warren DeLano" <wa...@de...>
> Subject: Re: [PyMOL] Hi all...
> To: "Yasser Almeida Hernandez" <ped...@fe...>,
> 	<pym...@li...>
> Message-ID:
> 	<896...@pl...lsci.local>
> Content-Type: text/plain;	charset="US-ASCII"
> 
> As for the your general question:  can you "import pymol; from pymol
> import cmd; pymol.finish_launching(); etc"?
> 
> Answer 1: Yes, if you manually compile PyMOL open-source code into an
> existing Python interpreter. 
> 
> Or 
> 
> Answer 2: Yes, if you run your Python script using PyMOL's built-in
> Python interpreter (launch PyMOL as follows):
> 
> ./pymol your-script.py      # with full 3D GUI
>   
> ./pymol -qc your-script.py  # command-line only (in a terminal)
> 
> Or 
> 
> Answer 3: Yes, if you call your Python script from a PyMOL script via
> the "run" or "spawn" commands inside PyMOL.
> 
> However,
> 
> Answer 4: No, if you want precompiled PyMOL build to work with an
> external precompiled Python build.  This approach has proved impractical
> due unavoidable application binary interface (ABI) version mismatches
> between PyMOL, Python, and the host environment.
>  
> As for your specific question, this is something you could do with a
> plain old script without even introducing the complexity of Python:
> 
> 
> load $TUT/1hpv.pdb, query
> 
> remove not polymer
> 
> create tmp, query
> 
> set dot_solvent
> 
> get_area tmp, load_b=1
> 
> # threshold on what one considers an "exposed" atom (in A**2):
> 
> remove tmp and b<2.5
> 
> tmp_dict = {}
> 
> iterate tmp, tmp_dict[(chain,resv)]=1
> 
> select exposed 
> 
> exposed = tmp_dict.keys()
> 
> exposed.sort()
> 
> print "Solvent exposed residues (chain,residue):"
> 
> for res in exposed: print res
> 
> select exposed, query in tmp
> 
> dele tmp
> 
> 
> # visual confirmation
> 
> color white
> 
> color red, byres exposed
> 
> set sphere_solvent
> 
> as spheres
> 
> orient
> 
> 
> Cheers,
> Warren


-- 

Jason Vertrees, PhD

Dartmouth College : jv...@cs...
Boston University : ja...@bu...

PyMOLWiki : http://www.pymolwiki.org/