[Chimera-users] Batch Processing of Molecular Attributes

Benjamin Feinsilver benjamin.feinsilver at gmail.com
Thu Nov 1 07:47:23 PDT 2018

Dr. Meng,

Thank you for getting back. I did some more research and came across a tool
called "Mordred" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801138/)
that seems better suited for my application.


On Wed, Oct 31, 2018 at 6:32 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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):
> <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
> Some relevant Chimera commands: surface, measure area, measure volume
> For individual command manual pages see links here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
> 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
> -----
> 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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