Re: [PyMOL] Pymol in command mode - no output

Hi Per 


If you're still having problems, you can try to install and run pymol under the X virtual frame buffer (xvfb).


Cheers,

Esben


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-----Original Message-----
From: Jason Vertrees [mailto:jas...@sc...] 
Sent: 26. november 2012 17:48
To: Per Larsson
Cc: pym...@li...
Subject: Re: [PyMOL] Pymol in command mode - no output

Hi Per,

You'll probably want to use something like this:

# load the file

load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb,
myMolecule

# ray trace and save the image; you need to do this since you're running # PyMOL headlessly

png ~/foo.png, height=768, width=1024, ray=1


As far as missing output that's most likely because you're running remotely and the stdout/stderr are being piped elsewhere. This is common on clusters.

Cheers,

-- Jason

On Mon, Nov 26, 2012 at 10:28 AM, Per Larsson <per...@sb...> wrote:
> Hi Pymol-users,
>
> I'm running a pml-script file to render some images on a remote server, using pymol 1.4, but I do not get any output at all. And no error message, so it is hard to troubleshoot, unfortunately.
>
> To reduce the complexity of my script, I have reduced it to basically just loading a pdb-file and saving as a png-image (two lines in the pml-script), but even that does not work. Any suggestions?
>
> I envoke the whole thing using
> $pymol -c script.pml
>
>
> Thanks
> /Per
>
>
>
>
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--
Jason Vertrees, PhD
Director of Core Modeling Product Management Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

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