Hi Tom, As you have analyzed very correctly, volume is only available with on-screen rendering. I've added a section to the PyMOLWiki which describes the options and limitations:
https://pymolwiki.org/index.php/Volume#Ray_Tracing Hope that helps. Cheers, Thomas On 23 Feb 2017, at 13:19, Thomas Grant <tomer...@gmail.com> wrote: > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ 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
