[Chimera-users] (hopefully) simple rendering question

Lybrand, Terry P. terry.p.lybrand at Vanderbilt.Edu
Thu Dec 3 07:18:28 PST 2015


I am looking for suggestions from the CHIMERA developers
and users’ community to address a rendering problem I have.

I have computed electric field data for protein ligand binding
sites (wt and related mutants) and would like to render this
field data as a collection of vectors, superimposed over a
nice rendering of the binding site structures. The field results
are from a series of QM/MM calculations we have performed,
and are in a simple ASCII format: cartesian coordinates for
N grid points, followed by cartesian coordinates of the N
field vectors that originate from the corresponding grid
points. I’ve debated whether I might be able to subvert the
PseudoBond reader to somehow process these data, but
still don’t have an easy option to display each field vector
as a short arrow.

Note that I don’t want to render the electric field data as a
set of continuous color-coded field lines. That is easy in any
number of molecular graphics programs. I know that rendering
fields as a collection of vectors (arrows) is “old-fashioned”,
but in this case we are convinced the old-fashioned render
is a more effective way to communicate our results.

Thanks in advance for any suggestions.

Terry L.

P.S. Greetings to all my former colleagues at UCSF.


Terry P. Lybrand
Prof. of Chemistry - College of Arts & Science
Professor of Pharmacology - School of Medicine
Vanderbilt University
Center for Structural Biology
5-154C BioSciences/MRB III
Nashville, TN 37232-8725

Telephone: 615-343-1247

Fax: 615-936-2211

e-mail: terry.p.lybrand at vanderbilt.edu<mailto:terry.p.lybrand at vanderbilt.edu>

WWW: http://structbio.vanderbilt.edu/lybrand

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