Re: [PyMOL] electrostatic

[Yu C. <ch...@hh...>]

> I have tried getting the electrostatic in pymol using the following commands:
> load molecule.pdb, mol-object
> load grasp-map.phi, map-object
> ramp_new ramp-name, map-object
> show surface, mol-object
> set surface_color, ramp-name, mol-object
> The problem is getting the phi map in grasp. Can somebody explain me how to do it? 
> 

This is what we did and worked (we now using Delphi), try it. 
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*On the SGI computers:
 1) Start up the computer, log in and in a command line prompt, change the 
directory to where the .pdb fi
le, .siz file and .crg files are located.
 2) Run grasp (command: /hhmi/software/grasp/grasp)
 3) Open up the menu by right-clicking on the window
 4) With the menu open, right-click on the Read option.
 5) Right-click on the PDB File option and load the .pdb file.
 6) Open the read menu again (steps 3-4), and select the Radius/Charge 
File option, then load the raidus
file.  Repeat again, loading the charge file.
 7) Open the main menu, click on display, show, molecular surface.
 8) Open the main menu, click on calculate, new potential map.
 9) Open the main menu, click on calculate, Pot. via map at surface/atoms
10) Open the main menu, click on write, potential map, internal map, let 
me enter it.  In the command lin
e prompt, type in the name of the file (namefile.phi)



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Yu Chen
Howard Hughes Medical Institute
Chemistry Building, Rm 182
University of Maryland at Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250

phone: 	(410)455-6347 (primary)
	(410)455-2718 (secondary)
fax: 	(410)455-1174
email: 	ch...@hh...
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