pymol-users

[PyMOL] Trouble making pictures in a script

[Michael L. <mgl...@gm...>]

Hi,

I have a Python script that sets a system up and then calls cmd.png()
to render an image. I use it to process several files at a time, and
there's no need to look at it while it's working, so I use

pymol -qcr myscript.py

to launch it. It works fine when I ray trace things, but if I just set
the system up and call cmd.png(), I get this error:

 ScenePNG-WARNING: invalid context or no image.

Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things.
Any ideas? Some of the systems are big enough that cmd.ray() fails, so
I'd like to be able to find a workaround.

Thanks,

-michael

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner

Re: [PyMOL] Trouble making pictures in a script

[DeLano S. <de...@de...>]

Michael,

The "-c" option forces PyMOL to run in command-line-only mode which means it
doesn't have access to the OpenGL hardware (used by cmd.draw and interactive
graphics).  In command-line-only mode, ray tracing (cmd.ray) is the only
option.

Cheers,
Warren
 
> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Michael Lerner
> Sent: Thursday, October 25, 2007 8:31 AM
> To: pymol mailinglist
> Subject: [PyMOL] Trouble making pictures in a script
> 
> Hi,
> 
> I have a Python script that sets a system up and then calls 
> cmd.png() to render an image. I use it to process several 
> files at a time, and there's no need to look at it while it's 
> working, so I use
> 
> pymol -qcr myscript.py
> 
> to launch it. It works fine when I ray trace things, but if I 
> just set the system up and call cmd.png(), I get this error:
> 
>  ScenePNG-WARNING: invalid context or no image.
> 
> Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things.
> Any ideas? Some of the systems are big enough that cmd.ray() 
> fails, so I'd like to be able to find a workaround.
> 
> Thanks,
> 
> -michael
> 
> --
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and 
> a browser.
> Download your FREE copy of Splunk now >> 
> http://get.splunk.com/ _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Trouble making pictures in a script

[EPF (E. P. Friis) <EP...@no...>]

Hi Michael

If the system is very big and causes the ray tracing to crash, try to
lower the hash_max setting. I think the default is 100. If the setting
is lower, it will be slower, but use less memory. (and vice versa :-)

All the best

Esben



> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of DeLano Scientific
> Sent: 25. oktober 2007 18:11
> To: 'Michael Lerner'; 'pymol mailinglist'
> Subject: Re: [PyMOL] Trouble making pictures in a script
>=20
> Michael,
>=20
> The "-c" option forces PyMOL to run in command-line-only mode=20
> which means it doesn't have access to the OpenGL hardware=20
> (used by cmd.draw and interactive graphics).  In=20
> command-line-only mode, ray tracing (cmd.ray) is the only option.
>=20
> Cheers,
> Warren
> =20
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of=20
> > Michael Lerner
> > Sent: Thursday, October 25, 2007 8:31 AM
> > To: pymol mailinglist
> > Subject: [PyMOL] Trouble making pictures in a script
> >=20
> > Hi,
> >=20
> > I have a Python script that sets a system up and then calls
> > cmd.png() to render an image. I use it to process several=20
> files at a=20
> > time, and there's no need to look at it while it's working, so I use
> >=20
> > pymol -qcr myscript.py
> >=20
> > to launch it. It works fine when I ray trace things, but if=20
> I just set=20
> > the system up and call cmd.png(), I get this error:
> >=20
> >  ScenePNG-WARNING: invalid context or no image.
> >=20
> > Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things.
> > Any ideas? Some of the systems are big enough that=20
> cmd.ray() fails, so=20
> > I'd like to be able to find a workaround.
> >=20
> > Thanks,
> >=20
> > -michael
> >=20
> > --
> > Biophysics Graduate Student
> > Carlson Lab, University of Michigan
> > http://www.umich.edu/~mlerner
> >=20
> > --------------------------------------------------------------
> > -----------
> > This SF.net email is sponsored by: Splunk Inc.
> > Still grepping through log files to find problems?  Stop.
> > Now Search log events and configuration files using AJAX and a=20
> > browser.
> > Download your FREE copy of Splunk now >> http://get.splunk.com/=20
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and=20
> a browser.
> Download your FREE copy of Splunk now >>=20
> http://get.splunk.com/ _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20