[Chimera-users] (hopefully) simple rendering question

Lybrand, Terry P. terry.p.lybrand at Vanderbilt.Edu
Thu Dec 3 11:22:58 PST 2015


Its good to hear from you as well.

Thanks for the suggestions. I will try them as soon as I finish grading
hour exams. I’ll have to refresh my memory as it has been ages since
I did anything with BILD. I’ll let you know how this goes.

Please give my best regards to Patsy,


On Dec 3, 2015, at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Terry,
Always nice to hear from you!

If you don’t need transparency, one possibility is to process these coordinates into a BILD-format file.  This is a simple text format that generates 3D objects in Chimera, described here including examples:

Other than reformatting coordinates, it might be annoying to color each arrow the way you want. If they are all one color it is trivial.  If they are individually colored by ESP or something like that you’d need to figure out the values and value->color mapping you want separately and then insert “.color R G B” type lines in the BILD file as described in link above.

If you have a PDB file of “atoms” at the points of interest and a map of values both open in Chimera (here are the known map formats: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>)  you can color the atoms by interpolated map values by using Values at Atom Positions and then Render by Attribute (or commands “measure mapValues” and “rangecolor”, respectively) but unfortunately this approach does not work on the objects read in from BILD files.


(command “measure fieldLines” is the thing you didn’t want :-)  <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#fieldLines> )

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

On Dec 3, 2015, at 7:18 AM, Lybrand, Terry P. <terry.p.lybrand at vanderbilt.edu<mailto:terry.p.lybrand at vanderbilt.edu>> wrote:


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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