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
----- 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: 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
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