Hi
Sorry for not following up on this, I got side-tracked by a bunch of other
stuff.
The problem still persists, unfortunately.
I'm working on some visualization of volumetric data. My exact script is copied
below.
While this runs, and I see all the commands being printed on screen, the
resulting png-files contain nothing but a white background, when running in
command mode (pymol -c script.pml). This is tested with both v 1.4.1 and 1.5.03.
I've tested Jason's method from below, which works except I have to use:
ray=1
png ~/foo.png, height=768, width=1024
instead of:
png ~/foo.png, height=768, width=1024, ray=1
I'm thankful for any suggestions.
My final objective is to see if I can use povray (not available on my local
machine) to render the volume visualization, but I'm working my way up towards
that goal.
Many thanks
/Per
# Load stuff
load density,dx, density
cmd.volume("density","density",1.0)
# Set the maximuym range to be displayed to 5 "sigma"
set volume_data_range, 5
# White background
bg_color white
# Make a color ramp
from pmg_tk.skins.normal.ColorRampModel import ColorRamp
r = ColorRamp(nColors=256)
r.addColor(0,(0,0,0,0),0) # white color for zero-density regions
r.addColor(1,(0.39,0.67,1,0.01),0) #light blue
r.addColor(55,(0,0,1,0.1),0) # darker blue
r.addColor(105,(0.48,0.99,0,0.5),0) # green
r.addColor(155,(1,0.0,0.0,1),0) # red
r.addColor(255,(1,0,0,0.25),0) # red for max density regions
ramp_colors = r.getRamp()
cmd.volume_color("density_volume",ramp_colors)
# Ray trace necessary when running in command mode, make png-pictures
set ray_volume,1
turn x, -90
ray
png volume_x.png,height=768,width=1024
turn y,-90
ray
png volume_y.png,height=768,width=1024
turn x, 90
ray
png volume_z.png,height=768,width=1024
27 nov 2012 kl. 14:58 skrev EPF (Esben Peter Friis):
> 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
>
>
> Best Regards
> Esben Peter Friis
> Science Manager
>
> Novozymes A/S
> Krogshoejvej 36
>
> 2880 Bagsvaerd Denmark
> Phone: +45 44461334
> Mobile: +45 30771334
> E-mail: [email protected]
>
> -----------------------------------
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>
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>
> -----Original Message-----
> From: Jason Vertrees [mailto:[email protected]]
> Sent: 26. november 2012 17:48
> To: Per Larsson
> Cc: [email protected]
> 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 <[email protected]> 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) [email protected]
> (o) +1 (603) 374-7120
>
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