On Sep 29, 2014, at 8:08 AM, Tony Lewis <t.lewis@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.

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