Re: [PyMOL] Anaglyph stereo output from command line
Hi Thomas, Fantastic! I can confirm that this works on my end. Thanks everyone. Cody On 4/25/18, 5:07 PM, "Thomas Holder" wrote: Hi Cody, I found a simple workaround to get stereo working in batch mode. Just set the "stereo" setting to 1 after switching to anaglyph, like this: stereo anaglyph set stereo Cheers, Thomas > On Apr 24, 2018, at 8:29 AM, Thomas Holder wrote: > > Thanks Jared and Cody! There is not much I can add, yes this looks like a bug and we should fix it. > > Cheers, > Thomas > >> On Apr 23, 2018, at 11:51 PM, Jared Sampson wrote: >> >> Hi Cody - >> >> I can confirm that I see similar behavior on 2.1.0 (stereo rendered properly from the GUI but not in batch mode) but the issue is not limited to just anaglyph stereo. Rather, (admittedly not having tested all stereo_mode options) it seems stereo in general doesn't get rendered as expected in batch mode. I imagine Thomas will chime in as well, but I would file a bug report with pymol-dev-gr...@schrodinger.com and/or via https://sourceforge.net/p/pymol/bugs/. >> >> Cheers, >> Jared >> >> On April 23, 2018 at 6:59:03 PM, Cody Jackson (cjack...@scripps.edu) wrote: >> >>> Hi Everyone, >>> >>> I'm trying to make anaglyph 3D figures and movies in command line mode and I'm having some trouble - using incentive version 2.1.1 right now. >>> >>> It seems like anaglyph stereo is only ray traced when the GUI is open. Here's a quick example adapted from the wiki, it saves the desired red-cyan png when I run it with @script.pml in the GUI, but I only get the 2D output when I run pymol -c script.pml. Is there a trick to getting stereo images in the command line/batch mode? Is it not possible? >>> >>> -- >>> fetch 1ESR, async=0 >>> as cartoon >>> set cartoon_smooth_loops >>> spectrum >>> bg white >>> stereo anaglyph >>> ray 640,480 >>> png demo.png >>> -- >>> >>> Thank you for any input. >>> >>> Best, >>> Cody Jackson -- 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
Re: [PyMOL] Anaglyph stereo output from command line
Hi Cody, I found a simple workaround to get stereo working in batch mode. Just set the "stereo" setting to 1 after switching to anaglyph, like this: stereo anaglyph set stereo Cheers, Thomas > On Apr 24, 2018, at 8:29 AM, Thomas Holder > wrote: > > Thanks Jared and Cody! There is not much I can add, yes this looks like a bug > and we should fix it. > > Cheers, > Thomas > >> On Apr 23, 2018, at 11:51 PM, Jared Sampson >> wrote: >> >> Hi Cody - >> >> I can confirm that I see similar behavior on 2.1.0 (stereo rendered properly >> from the GUI but not in batch mode) but the issue is not limited to just >> anaglyph stereo. Rather, (admittedly not having tested all stereo_mode >> options) it seems stereo in general doesn't get rendered as expected in >> batch mode. I imagine Thomas will chime in as well, but I would file a bug >> report with pymol-dev-gr...@schrodinger.com and/or via >> https://sourceforge.net/p/pymol/bugs/. >> >> Cheers, >> Jared >> >> On April 23, 2018 at 6:59:03 PM, Cody Jackson (cjack...@scripps.edu) wrote: >> >>> Hi Everyone, >>> >>> I'm trying to make anaglyph 3D figures and movies in command line mode and >>> I'm having some trouble - using incentive version 2.1.1 right now. >>> >>> It seems like anaglyph stereo is only ray traced when the GUI is open. >>> Here's a quick example adapted from the wiki, it saves the desired red-cyan >>> png when I run it with @script.pml in the GUI, but I only get the 2D output >>> when I run pymol -c script.pml. Is there a trick to getting stereo images >>> in the command line/batch mode? Is it not possible? >>> >>> -- >>> fetch 1ESR, async=0 >>> as cartoon >>> set cartoon_smooth_loops >>> spectrum >>> bg white >>> stereo anaglyph >>> ray 640,480 >>> png demo.png >>> -- >>> >>> Thank you for any input. >>> >>> Best, >>> Cody Jackson -- 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
Re: [PyMOL] Multiple PyMOL Instances in Python Script
> On Apr 24, 2018, at 7:17 PM, Yang Su wrote: > > OK, thanks. If you don't mind, I can add it to the wiki: > https://pymolwiki.org/index.php/Launching_From_a_Script Sure, that would be great. Thanks a lot! Cheers, Thomas -- 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
