(hopefully) simple rendering question
Hello, 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@vanderbilt.edu<mailto:terry.p.lybrand@vanderbilt.edu> WWW: http://structbio.vanderbilt.edu/lybrand
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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html> 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. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValues> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> (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 ----- 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@vanderbilt.edu> wrote:
Hello,
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.
Elaine, 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, Terry On Dec 3, 2015, at 12:28 PM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html> 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. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValues> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> (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 ----- 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@vanderbilt.edu<mailto:terry.p.lybrand@vanderbilt.edu>> wrote: Hello, 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@vanderbilt.edu<mailto:terry.p.lybrand@vanderbilt.edu> WWW: http://structbio.vanderbilt.edu/lybrand
participants (2)
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Elaine Meng -
Lybrand, Terry P.