From: Paul R. (uci-ics) <pr...@ic...> - 2010-05-07 09:16:49
|
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 <jas...@sc...> 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) <pr...@ic...> 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 >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (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 |