Hello Thomas ,
you're right, now everything runs smoothly.
Thanks for your help!
Best regards,
Ricardo.
---
Biological Chemistry and Physics
Faculty of Pharmaceutical Sciences at Ribeirão Preto
University of São Paulo - Brazil
----- Mensagem original -----
> 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: Quarta-feira, 15 de Janeiro de 2014 17:32:00
> Assunto: Re: [PyMOL] Ray tracing with no GUI yields segmentation
> fault
> 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
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