[Chimera-users] Write a PDB with Python API

Jaime Rodríguez-Guerra Pedregal Jaime.RodriguezGuerra at uab.cat
Tue Dec 1 09:11:07 PST 2015

Hi again!

So in my quest to use OpenMM from Chimera, my first proof-of-concept attempts consist of using a PDB file as intermediate to convert chimera.Molecule objects to OpenMM Topologies (using openmm.app.PDBFile loader).

While not ideal yet, it'd be convenient to use StringIO() as a memory file, and I have been more or less successful. This is my strategy:

memfile = StringIO()

m = chimera.openModels.list()

chimera.pdbWrite(m, m[0].openState.xform, memfile)


# pass memfile to openmm.app.PDBFile and do OpenMM stuff


It works, but some residues are not properly recognised... I dumped the converted PDB to an actual file and saw that the problematic residue (an ARG) is totally messed up! I've attached the results: original file is the mol2, the converted one is the pdb, and also a Chimera session with both superimposed.

What's the recommended method to convert a chimera.Molecule to a PDB file (if possible, in-memory) with Chimera Python API?

Thanks a lot!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151201/0461c6d3/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: streptavidin.mol2
Type: chemical/x-mol2
Size: 91889 bytes
Desc: streptavidin.mol2
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151201/0461c6d3/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: streptavidin.pdb
Type: chemical/x-pdb
Size: 75320 bytes
Desc: streptavidin.pdb
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151201/0461c6d3/attachment-0001.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pdbwritebug.py.zip
Type: application/zip
Size: 71107 bytes
Desc: pdbwritebug.py.zip
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151201/0461c6d3/attachment.zip>

More information about the Chimera-users mailing list