Re: [PyMOL] restoring default surface coloring
On Tuesday 02 March 2004 07:56, Matt Franklin wrote: [...snip...] I then realized that I had absolutely no idea how to restore the default surface coloring! (Except by quitting and restarting...) set surface_color, default didn't work, nor did set surface_color, atom_color. All I could get was solid colors. I'm guessing there's some special color name I should be using, but what is it? You can use something like color white,object to set an object to a fixed color, or the utility command util.cbag(object) (note the parentheses and quotes) to color the object by atom type and set the carbon atoms to green. There's cbag for color by atom type, carbons green, cbaw for white carbons, cbay for yellow carbons and so on. Alternatively, you can use the color menu in the internal GUI. Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] restoring default surface coloring
* Lieven Buts lie...@ultr.vub.ac.be [2004-03-02 09:03] wrote: On Tuesday 02 March 2004 07:56, Matt Franklin wrote: [...snip...] I then realized that I had absolutely no idea how to restore the default surface coloring! (Except by quitting and restarting...) set surface_color, default didn't work, nor did set surface_color, atom_color. All I could get was solid colors. I'm guessing there's some special color name I should be using, but what is it? You can use something like color white,object to set an object to a fixed color, or the utility command util.cbag(object) (note the parentheses and quotes) to color the object by atom type and set the carbon atoms to green. There's cbag for color by atom type, carbons green, cbaw for white carbons, cbay for yellow carbons and so on. Alternatively, you can use the color menu in the internal GUI. Or you could type: set surface_color, -1 or if you had set the surface_color for a particular object, then you would type: set surface_color, -1, objectname where -1 is the way of resetting to the default. This also works for other settings that show up as default in the Settings - Edit All... GUI. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
[PyMOL] restoring default surface coloring
I was recently making a figure of a ligand nestled in its binding pocket, where I wanted the surface of the binding protein colored by electrostatic potential, and the surface of the ligand colored by atom type. So I read in a DelPhi map from Grasp, used ramp_new to set up the color ramp, then set the surface color to the ramp color. Unfortunately, I forgot to specify an object at this point, so the ligand surface was also colored by potential. I then realized that I had absolutely no idea how to restore the default surface coloring! (Except by quitting and restarting...) set surface_color, default didn't work, nor did set surface_color, atom_color. All I could get was solid colors. I'm guessing there's some special color name I should be using, but what is it? Thanks for the help, Matt -- Matthew FranklinPhone:(650)225-4596 Postdoctoral Researcher Fax:(650)225-3734 Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080
