[Chimera-users] Batch Processing of Molecular Attributes

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 31 15:32:22 PDT 2018

Hi Ben,
Chimera may not be the best tool for what you want to do.  I’ll try to briefly explain what it can do and limitations related to your question.

Although in principal some of those measurables could be calculated in Chimera, you’d have to figure out Chimera commands or python, make a script to work on a single SMILES input, and then adapt to looping through a list of multiple SMILES.  Chimera does not read csv files.  Information on scripts and looping, and saving the log (which contains results messages):

Some relevant Chimera commands: surface, measure area, measure volume

For individual command manual pages see links here:

Chimera’s electrostatic potential-related features are meant mainly for proteins and not a panoply of small molecules.  Although you could try to calculate ESP for the small molecules (relevant commands: addh, addcharge, coulombic  or  vina ) the charge calculation would be run via antechamber/sqm and is only effective/intended for smallish small molecules without high charge density, metals, uncommon elements or other unusual features.

Chimera has a “mimimize” command that reports total energy but it is mainly meant for getting reasonable conformations, not reporting conformational energies. It also requires parametrization of the molecule beforehand with addh and addcharge, just like ESP calculations.

There is no command to report number of surface points with positive electrostatic potential, so you’d have to figure out python to do that, which would take fairly advanced understanding of Chimera code.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 31, 2018, at 9:15 AM, Benjamin Feinsilver <benjamin.feinsilver at gmail.com> wrote:
> Hello,
> Is it possible to pass a CSV file to Chimera containing a list of SMILEs, then output their molecular attributes in a new CSV file? For example, volume, surface area, the number of surface points with positive electrostatic potential, and the energy of the molecule's current 3D conformation. If so, would you please let me know how I would accomplish this?
> Thanks,
> Ben

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