From: Jason Vertrees <jv@cs...> - 2009-06-08 12:08:34
> Message: 1
> Date: Wed, 03 Jun 2009 13:52:25 -0700
> From: Jim Remington <remington@...>
> Subject: [PyMOL] Distinct labels on white background (ray tracing)?
> To: pymol-users@...
> Message-ID: <4A26E289.3040901@...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> I would like to have distinct labels for hydrogen bond lengths on a
> ball-and-stick image
> with white background (as required for publication in a particular
> journal). No matter
> what I do, the labels come out washed out and usually light grey. This
> experimenting with label color, size and font (is there a bold font?).
> For the record, I've tried the clues in the wiki and forum, for example
> I've turned off
> ray-trace-fog, depth cueing, ray-shadowing and very high resolution images.
> I still get light grey labels on white background. Does anyone have
> further suggestions?
> Thanks much, Jim
I can also reproduce this. I think it's either a bug or one of the 600
settings has a default that is throwing this off. If you need this ASAP
and don't mind the extra steps, here's a workaround. You make two
photos and composite them. Here's how (with comments):
# prepare the scene; and hide your labels
set ray_opaque_background, 1;
# set up your scene & ray trace it
png layer1.png, ray=1, height=yourSize, width=yourWidth, dpi=yourDPI
# now hide everything but the labels and ray trace the scene
# in mode3--which does make black labels:
set ray_opaque_background 0;
set ray_trace_mode, 3;
# do NOT move the scene in any way; ray trace it
png layer2.png, ray=1, height=yourSize, width=yourWidth, dpi=yourDPI
# go into the GIMP or Photoshop and composite the images
# (put layer2 on top of layer1) or if you have ImageMagick
system composite layer2.png layer1.png finalImage.png
# [optional] Send me $50. :-)
To get an idea of compositing, check out the 2nd example image/script from:
Lastly, Warren I'm sure has a one-line answer, but this should get you
Jason Vertrees, PhD
Dartmouth College : jv@...
Boston University : jasonv@...
PyMOLWiki : http://www.pymolwiki.org/
From: David Garboczi <dgarboczi@ni...> - 2009-10-09 15:45:45
I get too much white space around the molecule when ray tracing and
then writing a png file. How can I make the png file more like a
ray 1800, 1800