Hello Jason,
Thank you very much for sharing the script with us!
It works perfectly!
Best Regards,
Anatoliy
________________________________________
From: Jason Vertrees [jason.vertr...@schrodinger.com]
Sent: Tuesday, March 06, 2012 6:28 AM
To: Anatoliy Volkov
Cc: pymol-users@lists.sourceforge.net; Chris L. Irwin
Subject: Re: [PyMOL] volume rendering in PyMOL 1.5
Hi Anatoliy,
> 1. We are able to create volume rendering sessions as shown in the videos
> posted on PyMOL website, but when we save a session as .pse file, and try
> to re-open it again, it does not actually render data until we press a
> 'Volume' button in the
> external GUI. The problem is that we need to render these images on our
> hyperwall production nodes, where mouse is not available. Is there any way
> to get PyMOL to automatically reproduce a volume rendering session
> from a .pse file ?
Use this terribly ugly code to initialize volumes without the Volume
Editor. We'll be sure to add this functionality to PyMOL soon:
python
import pymol
from pymol import cmd
from pmg_tk.skins.normal.ColorRampModel import ColorRamp
s = cmd.get_session()
c = None
obj_name = None
for x in range(1,len(s["names"])):
obj_name = s["names"][x][0]
if cmd.get_type(obj_name) == "object:volume":
c = s["names"][x][5][2][0][-1]
r = ColorRamp(360)
for x in range(len(c)/5):
r.addColor(int(c[x*5]),
(float(c[x*5+1]),float(c[x*5+2]),float(c[x*5+3]),float(c[x*5+4])))
ramp_colors = r.getRamp()
cmd.volume_color(obj_name, ramp_colors)
cmd.recolor()
python end
> 2. In ideal case, we would also like to run volume rendering from a .pml
> script.
> Could we possibly get a comprehensive list of all PyMOL commands and
> their usage instructions related to volume rendering?
> Specifically, we would like to have all (or as many as possible) volume
> rendering-related functions that are currently available through the
> external gui ('Volume' option) to be available via .pml scripts.
The main volume functions are:
volume_new -- create a new volume from a map just like isomesh.
volume_color -- assign colors to the volume data.
See the PyMOLWiki (http://pymolwiki.org) or the Incentive PyMOL
documentation (http://pymol.org/dsc/dokuwiki/doku.php) for more help.
You _must_ have an openGL context for saving images of volumes at this
point. Volumes require shaders which requires GLEW which requires a
context to be initialized.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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