Dear all,
I've written a .pml script to render volumes and save png files. The script
works fine when running it from the GUI, but for some reason when I run in
command line mode with pymol -cqr myscript.pml the image saved is blank.
It appears that when running from the command line it automatically ray
traces the image, even when I set ray = 0 in the png command, and since
volumes don't work well with ray tracing, the images end up blank.
I tried setting ray_volume=1, but that still doesn't fix the problem.
My script is below, as is the output from the command line and from the
GUI. Notice that when running from the command line there is a "Ray:
render time:" line that doesn't appear when running from the GUI.
Thanks for any insight.
Tom
*myscript.pml:*
$>cat myscript.pml:
bg white
fetch 1oky, type=2fofc, async=0
volume 1okyVol, 1oky_2fofc
set ray_volume, 1
png volume.png, ray=0
*command line output (doesn't work):*
$>pymol -cqr myscript.pml:
PyMOL>bg white
PyMOL>fetch 1oky, type=2fofc, async=0
ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'.
BRIXStrToMap: Map Size 102 x 99 x 92
BRIXStrToMap: Range = -0.906629 to 2.095844
BRIXStrToMap: Calculated Mean = -0.006, Sigma = 0.251
BRIXStrToMap: Normalizing...
Crystal: Unit Cell 124.162 124.162 47.300
Crystal: Alpha Beta Gamma 90.000 90.000 120.000
Crystal: RealToFrac Matrix
Crystal: 0.0081 0.0046 -0.0000
Crystal: 0.0000 0.0093 -0.0000
Crystal: 0.0000 0.0000 0.0211
Crystal: FracToReal Matrix
Crystal: 124.1625 -62.0812 0.0000
Crystal: 0.0000 107.5279 0.0000
Crystal: 0.0000 0.0000 47.3000
Crystal: Unit Cell Volume 631499.
CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc".
PyMOL>volume 1okyVol, 1oky_2fofc
Executive: object "1okyVol" created.
Volume: created "1okyVol"
PyMOL>set ray_volume, 1
Setting: ray_volume set to on.
PyMOL>png volume.png, ray=0
Ray: render time: 0.01 sec. = 242165.4 frames/hour (0.01 sec. accum.).
ScenePNG: wrote 640x480 pixel image to file "volume.png".
*GUI output (works):*
$>pymol -qr myscript.pml:
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 1.20.
PyMOL>bg white
PyMOL>fetch 1oky, type=2fofc, async=0
ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'.
BRIXStrToMap: Map Size 102 x 99 x 92
BRIXStrToMap: Range = -0.906629 to 2.095844
BRIXStrToMap: Calculated Mean = -0.006, Sigma = 0.251
BRIXStrToMap: Normalizing...
Crystal: Unit Cell 124.162 124.162 47.300
Crystal: Alpha Beta Gamma 90.000 90.000 120.000
Crystal: RealToFrac Matrix
Crystal: 0.0081 0.0046 -0.0000
Crystal: 0.0000 0.0093 -0.0000
Crystal: 0.0000 0.0000 0.0211
Crystal: FracToReal Matrix
Crystal: 124.1625 -62.0812 0.0000
Crystal: 0.0000 107.5279 0.0000
Crystal: 0.0000 0.0000 47.3000
Crystal: Unit Cell Volume 631499.
CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc".
PyMOL>volume 1okyVol, 1oky_2fofc
Executive: object "1okyVol" created.
Volume: created "1okyVol"
PyMOL>set ray_volume, 1
Setting: ray_volume set to on.
PyMOL>png volume.png, ray=0
ScenePNG: wrote 640x480 pixel image to file "volume.png".
--
Thomas D. Grant, Ph.D.
Staff Scientist
BioXFEL Science and Technology Center
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
