Hi Robert, On 2004-05-24 13:46 you wrote: > > I probably have a very stupid question. > How do I run the color_b.py script using the latest PYMOL on windows? > Just clicking on it does not work, I also tried to run it by calling it from > within pymol but this did not work either.
Sorry if the instructions aren't clear. I don't often work with windows, so I forget that windows users may not think the way we UNIX-types do. I type more than I click! In general, *many* python scripts for use with PyMOL are used in a two-step process. You "run" the script from the PyMOL command line (i.e. in the external GUI window, or within the OpenGL window, it doesn't matter), by issuing the "run" command (hmmm, confusing nomenclature here!): run color_b.py This just loads the color_b function into PyMOL. The "run" command is running the python script, but in the case of most of my scripts, that just defines a function that can be called repeatedly in PyMOL. Then you can use it like a standard PyMOL command, again typing in the PyMOL command line: color_b object or with optional parameters such as: color_b object, grad=bwr, b0=5, b1=10 Let me know if this still isn't clear. This is typical of external python scripts that are to be run from PyMOL; unless the script does something you are only likely to do once it should be written as a function that can be called multiple times after loading it. You can even get help after doing "run color_b.py" by typing "help color_b". You should see a description of what it does and how to use it. In fact, for the scripts that I use often, I include the "run scriptname.py" commands in my .pymolrc file so that they are included automatically. Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 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
