Great! Looks like a good start. The session log is a good resource too.
Thanks again,
Paul
On Thu, May 6, 2010 at 11:32 PM, Jason Vertrees
<jason.vertr...@schrodinger.com> wrote:
> Paul,
>
> PyMOL is pretty good at this kind of thing and you can automate it at
> various levels (eg. bash/shell script level, inside PyMOL using Python
> commands, etc). Let's say you have 100 poses in your ouput directory;
> to do what you've asked, I'd try:
>
> python
> import glob
> inFiles = glob.glob("output/*.pdb")
> for f in inFiles:
> cmd.load(f, "current")
> cmd.zoom("org")
> cmd.zoom()
> cmd.show_as("surface", "poly")
> cmd.show_as("sticks", "org")
> cmd.png( f + ".png", f, ray=1, height=800, width=600)
> cmd.delete("current")
> python end
>
> This will write out 100 png files each just named with ".png" appended
> to the PDB name, ray traced, and at 800x600 image size.
>
> A couple other hints:
> (1) If it's the same protein over and over again, you can setup the
> best view by hand, just once, and then do
> get_view()
> and restore that view in all other proteins
> (2) PyMOL has a preset view for ligand binding sites; A > Preset >
> Ligand Sites > Transparent (better) is a good one.
>
> Good luck,
>
> -- Jason
>
> On Thu, May 6, 2010 at 1:00 AM, Paul Rigor (uci-ics) <pri...@ics.uci.edu>
> wrote:
>> Hi,
>>
>> Is there anyway to access the rendering engine of pymol through a
>> command line script?
>>
>> I'd like to take a snapshot of a ligand-bound protein, but automate
>> the view such that
>> 1) The protein is shown as a surface
>> 2) The view centers around the binding area
>> 3) The view zooms out enough to present the entire protein
>> 4) Produce a png or a brief video.
>>
>> Thanks in advance!
>> Paul
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
--
Paul Rigor
Pre-doctoral BIT Fellow and Graduate Student
Institute for Genomics and Bioinformatics
Donald Bren School of Information and Computer Sciences
University of California, Irvine
http://www.ics.uci.edu/~prigor
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