Dear all, I wonder if someone has written and would share a script to sequentially read a pdb file, show its molecular surface and color it by the electrostatic potential from an appropriate .dx file. Cheers, Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens
Hi Miguel, Unfortunately we do not yet have a Chimera command equivalent of the Surface Color dialog which does the coloring by electrostatic potential. So it requires a Python script to do that step. I've attached a Python script that opens a PDB, makes the molecular surface, opens the electrostatic potential map and colors the surface. I hope to add the Chimera command that does the coloring soon which will make this much simpler. Tom
Hi Miguel, Guess it would help if I really attached the script. You open the script with File/Open... to run it. The paths to the files appear in the script and you'll need to edit those. Tom # ----------------------------------------------------------------------------- # Tested in Chimera version 1.2510, May 13, 2008. # Will not work with earlier Chimera versions. # def color_surface(surf, volume): from SurfaceColor import color_surface, Volume_Color, Color_Map vc = Volume_Color() vc.set_volume(volume) data_values = (-10, 0, 10) colors = [(1,0,0,0.9), # Red,green,blue,opacity (1,1,1,0.5), (0,0,1,.9)] vc.set_colormap(Color_Map(data_values, colors)) color_surface(surf, vc, caps_only = False, auto_update = False) # ----------------------------------------------------------------------------- # Open PDB, make surface, open volume # pdb_path = '/tmp/1sx3_chainA.pdb' es_path = '/tmp/1sx3_chainA.dx' from chimera import runCommand runCommand('open #0 %s' % pdb_path) runCommand('surf #0') runCommand('open #1 %s' % es_path) # Color surface from chimera import openModels as om, MSMSModel surf = om.list(id = 0, modelTypes = [MSMSModel])[0] vol = om.list(id = 1)[0] color_surface(surf, vol)
participants (2)
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Miguel Ortiz-Lombardía -
Thomas Goddard