Hi Ricardo, you didn't mention that you launch pymol from a script (with "finish_launching"), which is not very well supported. The recommended mode for GUI-less scripts is to run pymol like that:
pymol -cqr yourscript.py Cheers, Thomas On 15 Jan 2014, at 13:48, Ricardo O. S. Soares <rsoa...@fcfrp.usp.br> wrote: > Hello Thomas, > thanks for your reply. > > You are right, I unintentionally switched the antialias and angle parameters, > sorry about that. > But that does not change mush the outcome, any cmd.ray gives me the > segmentation fault. > I'm getting no output from cmd.png unless I use the ray command first (which > works fine only with loaded GUI), and that seems to be a rather common issue > in GUI-less mode (http://pymolwiki.org/index.php/Png). > You said you weren't getting a seg. fault with the latest SVN code, did you > ran it GUI-less? > The representations I'm using are surfaces, however I get the same error with > any of them, and in different machines. > > Here's a example of script that gives me the error: > > import __main__ > #__main__.pymol_argv = [ 'pymol', '-qc'] # Quiet and no GUI > __main__.pymol_argv = [ 'pymol', '-q' ] > import pymol, time > > pymol.finish_launching() > pymol.cmd.load("temp.pdb") > pymol.cmd.ray() -----> this > line gives segmentation fault > pymol.cmd.png("image.png", 640, 640, 300,1) -----> this wont work without > loaded GUI > > pymol.cmd.quit() > > Cheers, > > Ricardo. > > --- > Biological Chemistry and Physics > Faculty of Pharmaceutical Sciences at Ribeirão Preto > University of São Paulo - Brazil > De: "Thomas Holder" <thomas.hol...@schrodinger.com> > Para: "Ricardo O. S. Soares" <rsoa...@fcfrp.usp.br> > Cc: "pymol-users" <pymol-users@lists.sourceforge.net> > Enviadas: Terça-feira, 14 de Janeiro de 2014 18:18:37 > Assunto: Re: [PyMOL] Ray tracing with no GUI yields segmentation fault > > Hi Ricardo, > > you probably want to do this, without calling the ray command: > > cmd.png("image.png", 640, 640, dpi=300, ray=1) > > Also, your ray command sets antialias=300 and angle=-1, which I guess was not > your intention. I'm not getting a segmentation fault with the latest SVN code > using your command, though. Do you have any volume representation? Volume is > not fully supported with ray tracing. > > Cheers, > Thomas > > On 14 Jan 2014, at 13:36, Ricardo O. S. Soares <rsoa...@fcfrp.usp.br> wrote: > > > Hello everyone, > > > > I wrote a python script where pymol performs some color changes, ray > > tracing and image export. > > The script works perfectly if I enable the GUI, however if I load pymol > > without the GUI (-c flag) I receive a segmentation fault error. > > I found out that this issue is resolved by commenting the line > > "pymol.cmd.ray(640,640,300,-1)". > > I'd like to solve this, so the script can run in a loop without opening the > > GUI every time. > > It may help to clarify that I'm running a LinuxMint14 machine (AMD64), with > > GCC compiler version 4.7.2. > > > > I appreciate any help. > > > > Ricardo. > > --- > > Biological Chemistry and Physics > > Faculty of Pharmaceutical Sciences at Ribeirão Preto > > University of São Paulo - Brazil > > -- > Thomas Holder > PyMOL Developer -- Thomas Holder PyMOL Developer ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ 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
