Re: [PyMOL] Writing a script yo pymol

[Yotam A. <yo...@gm...>]

Great, thank you.

On Mon, Sep 12, 2011 at 10:05 AM, Thomas Holder <
sp...@us...> wrote:

> Hi Yotam,
>
>
>  I'm sorry but this is too complected. Currently, I can't afford the time
>> to learn another scripting  languish. Consider gnuplot script files, which
>> are simply a list of gnuplot commands.
>>
>
> PyMOL understands two languages. The "PyMOL language" is indeed similar to
> gnuplot commands, that's what you usually type into the PyMOL command prompt
> or put into .pml script files.
>
> The other language is pure python (PyMOL API) and can be used to write more
> complicated routines (.py script files).
>
> http://pymolwiki.org/index.**php/Running_Scripts<http://pymolwiki.org/index.php/Running_Scripts>
>
>
>  Sure you can do some sophisticated stuff but you don't have to. All my
>> files will be simple atom list in xyz format (name \t x \t y \t z), and all
>> I want to do is select all the atoms of a certain name, color them and then
>> rotate the system.
>>
>
> by "rotate the system" do you mean a movie-like 360° rotation? Then your
> simple list of PyMOL commands will be something like:
>
> # color everything gray and histidines blue
> color gray, all
> color blue, resn HIS
>
> # make 100 movie frames and do full rotation about Y-axis
> mset 1 x100
> util.mroll
> mplay
>
> For documentation and more examples see:
> http://pymolwiki.org/index.**php/Color<http://pymolwiki.org/index.php/Color>
> http://pymolwiki.org/index.**php/Util.mroll<http://pymolwiki.org/index.php/Util.mroll>
> http://pymolwiki.org/index.**php/Property_Selectors<http://pymolwiki.org/index.php/Property_Selectors>
> http://pymolwiki.org/index.**php/Selection_Algebra<http://pymolwiki.org/index.php/Selection_Algebra>
>
> Cheers,
>  Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>



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