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] pymol launching problems from python???
Dear PyMol Experts, I am quite new in pymol. I have just installed python 2.3.2 and pymol-0.93 using python setup.py (i.e. pymol was installed in site-packages of python). I am using RedHat 8.0 on a dual Xeon system. Here's the problems that I am getting: (1) Case 1: import pymol pymol.finish_launching() Segmentation fault (core dumped) (2) Case 2: from pymol import cmd after couple of seconds, it crashes again with the following error: Fatal Python error: GC object already tracked Abort Interestingly after from pymol import cmd, I can use the external gui, run demos, etc. However as soon as I move my mouse over the python shell, the program aborts and gives the Fatal Python error: GC object already tracked??? I have a feeling that this error is related to the external GUI application. Is it possible to disable the external gui when I lounch pymol from python? I really appreciate any help you can provide me. At first I was very excited about using pymol in my research but now I am getting a little bit frustrated. I need to find a way to launch pymol from python without segmentation fault... thanks alot, best Taner Dr. Taner Yildirim, Ph.D. Physicist, Condensed Matter Science Group, ta...@nist.gov NIST Center for Neutron Research, PHONE: 301-975-6228 National Institute of Standards Technology FAX : 301-921-9847 Gaithersburg, MD 20899-8562 Web : http://webster.ncnr.nist.gov/staff/taner
