[Chimera-users] Visualizing Electrostatic Potential of *.grd format?
Dear All, I would like to ask you a question regarding the visualization of electrostatic potential on msms. For this purpose, of course, I need a readable format for Potential Map. In the past I used to work with DelPhi for potential calculations and then visualize the outputted *.14 file by Chimera. Today I calculate potentials by using UHBD program, while output files are saved in /phi/ format with .grd extension (could be written either in binary or ascii form). Unfortunately, the Chimera doesn't recognize this format. Dear Chimera users, do you know the way to convert the *.grd files to the *.phi ones readable by Chimera, or any other trick? I can't recalculate the potentials by DelPhiController, because I have only one dat-file for both radii sizes and charges (it also doesn't work in the simple way). I'd very appreciate any help of yours! Yours sincerely, Anna.
Hi Anna, Actually, Chimera does read UHBD grids, the binary version. The older approach to displaying potential on a surface, DelPhiViewer, is being phased out in favor of the newer and more general tool, Surface Color (Tools... Surface/Binding Analysis... Electrostatic Surface Coloring or Tools... Volume Data... Surface Color both open this tool). Surface Color can color surfaces based on any of the volume data (3D grid) formats that can be read by Volume Viewer (which include UHBD binary): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ volumeviewer.html#formats Surface Color is relatively new. It is available in the snapshots 1.2154 (linux, mac) and 1.2143 (windows). It is also available in 1.2105, but I don't recommend using that one because we have made it easier to use in the more recent snapshots. Here is the man page for Surface Color in version 1.2154: http://www.cgl.ucsf.edu/chimera/1.2154/docs/ContributedSoftware/ surfcolor/surfcolor.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Sep 7, 2005, at 4:14 AM, Anna Feldman-Salit wrote:
Dear All,
I would like to ask you a question regarding the visualization of electrostatic potential on msms. For this purpose, of course, I need a readable format for Potential Map. In the past I used to work with DelPhi for potential calculations and then visualize the outputted *.14 file by Chimera. Today I calculate potentials by using UHBD program, while output files are saved in /phi/ format with .grd extension (could be written either in binary or ascii form). Unfortunately, the Chimera doesn't recognize this format.
Dear Chimera users, do you know the way to convert the *.grd files to the *.phi ones readable by Chimera, or any other trick? I can't recalculate the potentials by DelPhiController, because I have only one dat-file for both radii sizes and charges (it also doesn't work in the simple way).
I'd very appreciate any help of yours!
Yours sincerely,
Anna. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Anna Feldman-Salit -
Elaine Meng