[Chimera-users] How to load PDB data inline in Chimera script/command files

[Eric Pettersen]

On Sep 29, 2014, at 8:08 AM, Tony Lewis <t.lewis at ucl.ac.uk> wrote:

> Dear Chimera people,
> 
> Many thanks to all Chimera contributors.
> 
> Please can anyone tell me if there's a way to include PDB data *inline* in Chimera script / command / Chimerax files?
> 
> PyMOL's read_pdbstr() command loads PDB data from an inline string, which means one file can contain both the structural data and the associated commands. That's rather convenient.
> 
> I would much appreciate any help on how to do the same with Chimera. Apologies if the answer is obvious.

Hi Tony,
	I wouldn't say the answer is obvious, but Chimera can read streams and therefore you can use a StringIO buffer to open PDB data in Chimera.  Here is an example that open a histidine residue:

from StringIO import StringIO
buf = StringIO("""ATOM      1  N   HIS A   1      49.668  24.248  10.436  1.00 25.00           N  
ATOM      2  CA  HIS A   1      50.197  25.578  10.784  1.00 16.00           C  
ATOM      3  C   HIS A   1      49.169  26.701  10.917  1.00 16.00           C  
ATOM      4  O   HIS A   1      48.241  26.524  11.749  1.00 16.00           O  
ATOM      5  CB  HIS A   1      51.312  26.048   9.843  1.00 16.00           C  
ATOM      6  CG  HIS A   1      50.958  26.068   8.340  1.00 16.00           C  
ATOM      7  ND1 HIS A   1      49.636  26.144   7.860  1.00 16.00           N  
ATOM      8  CD2 HIS A   1      51.797  26.043   7.286  1.00 16.00           C  
ATOM      9  CE1 HIS A   1      49.691  26.152   6.454  1.00 17.00           C  
ATOM     10  NE2 HIS A   1      51.046  26.090   6.098  1.00 17.00           N  """)
from chimera import openModels
models = openModels.open(buf, type="PDB", identifyAs="his")

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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