[PyMOL] 0.86 and MacOS X
I would like to report that 0.86 works fine under MacOS X 10.2.3 using Apples X11 version of xwindows. As far as I can tell it also has graphics acceleration (but I'm not sure as I haven't done any rigorous tests...seems dramatically faster than previous xwindows(fink) versions of pymol). I am using the latest fink package on a TiBook 800. Can anyone else comment about speed/features using 0.86 under X11 versus current/future MacOS X ports? It is nice to have the more full featured menus again. Y yuri...@mac.com
RE: [PyMOL] "Rolling your own" functions in PyMol
Stephen,
You're looking for the PyMOL API function "extend":
from pymol import cmd
cmd.extend("ramp_colors",ramp_chain.ramp_colors)
Would then permit the following:
ramp_colors chain A
See "help extend" for more info...
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
> -Original Message-
> From: Stephen Graham [mailto:steph...@usyd.edu.au]
> Sent: Tuesday, January 07, 2003 4:14 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] "Rolling your own" functions in PyMol
>
>
> Hi All,
>
> I am a recent subscriber to the list, so apologies if this
> question has
> been answered before. I am interested in finding out how you can add
> your own functions to PyMol such that they may be
> "transparently" called
> from inside PyMol's shell. The the basic question is "How do
> I register
> PyMol names for home-grown functions so that they can be used like the
> functions in the util module". A more detailed example of what I am
> after is below. Also, are there any warehouses or collections of
> home-grown functions to which I could submit functions I
> write and from
> which I could gain examples from other users?
>
> Cheers
>
> Stephen
>
> == More detailed description of my problem ==
>
> I have written a function to ramp coloring of a backbone
> between two or
> more arbitrary colors (it is really a generalization of the code in
> util.rainbow). I have imported the code using the general
> Python import
> command:
> import ramp_chain
> Now, let's say that I have a selection object defined as:
> select A,(chain A)
> Were I using the rainbow command I would be able to issue the command:
> util.rainbow A
> Which follows the general rules of command line parsing.
> Unfortunately,
> in my case issuing the command:
> ramp_chain.ramp_colors A
> gives the error:
> Syntax error: unexpected EOF (and there is an arrow under the letter
> A).
> I *can* call the command using the syntax:
> ramp_chain.ramp_colors( "chain A" )
> but this syntax is not optimal - I would like to be able to use my
> already defined selections.
>
> --
> Stephen Graham
> PhD candidate and nasty sysadmin
> Crystallography Group
> School of Molecular and Microbial Biosciences
> Building G08
> University of Sydney
> New South Wales, 2006
> Australia
> Ph: +61 2 9351 8197
> Fax: +61 2 9351 4726
>
>
> ---
> This SF.NET email is sponsored by:
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>
[PyMOL] "Rolling your own" functions in PyMol
Hi All, I am a recent subscriber to the list, so apologies if this question has been answered before. I am interested in finding out how you can add your own functions to PyMol such that they may be "transparently" called from inside PyMol's shell. The the basic question is "How do I register PyMol names for home-grown functions so that they can be used like the functions in the util module". A more detailed example of what I am after is below. Also, are there any warehouses or collections of home-grown functions to which I could submit functions I write and from which I could gain examples from other users? Cheers Stephen == More detailed description of my problem == I have written a function to ramp coloring of a backbone between two or more arbitrary colors (it is really a generalization of the code in util.rainbow). I have imported the code using the general Python import command: import ramp_chain Now, let's say that I have a selection object defined as: select A,(chain A) Were I using the rainbow command I would be able to issue the command: util.rainbow A Which follows the general rules of command line parsing. Unfortunately, in my case issuing the command: ramp_chain.ramp_colors A gives the error: Syntax error: unexpected EOF (and there is an arrow under the letter A). I *can* call the command using the syntax: ramp_chain.ramp_colors( "chain A" ) but this syntax is not optimal - I would like to be able to use my already defined selections. -- Stephen Graham PhD candidate and nasty sysadmin Crystallography Group School of Molecular and Microbial Biosciences Building G08 University of Sydney New South Wales, 2006 Australia Ph: +61 2 9351 8197 Fax: +61 2 9351 4726
[PyMOL] povray rendering in windows
Hi all, Has anyone sucessfully set up pymol so it can ray trace images using povray?
Re: [PyMOL] New PyMOL Release for Win/Linux/SGI
Has anybody managed to get ScriptBox working under Windows with v0.86?? I'm having trouble. I put ScriptBox.py in the appropriate placeplace and the following at the end of the createMain(self) procedure in PMGApp.py in the usual manner: ScriptBox.__init__(self) But get the following error on loading PyMol: NameError: global name 'ScriptBox' is not defined If anyone has any suggestions they'd be most appreciated. I like ScriptBox a lot so do you think there's any chance of incorporating this into PyMol either as a GUI window or as its own dropdown scripts menu that could also list all the scripts in a given directory?? Cheers, Chris. ___ Dr Chris Winfield Lab: N317/318 Post-Doctoral Researcher Tel: +44 (0)1179 546 324 School of Chemistry Fax: +44 (0)1179 298 611 University of Bristol Mob: +44 (0)7866 550 518 Cantocks Closechris.winfi...@bristol.ac.uk Bristol BS8 1TS ___
