Are you sure about the aspect ratio? If not just do ray and check the 
resolution of the png. Then multiply the horisontal and vertical resolution 
by a number and use the commands you mentioned. Or maybe it picks up only 
one 2000, I have never actually tried that. Taller figures are usually 
easier to look at than wide.

Now you open gimp or photoshop and put the images side by side and set the 
width to 12 cm (keep all the pixels though) or 2x the spacing you want. 
Around 6cm spacing is fine for me. And add labels, since they are most 
likely required by the reviewers anyway. Put a label to the left figure and 
duplicate it and move horisontally onto the right figure until it is at the 
appropriate depth.

Good luck,

~Lari~

Quoting Robert Court <co...@mrc-lmb.cam.ac.uk>:

# Hi all.
# 
# Help desperately needed. I need to make some stereo figures of electron
# denisty for first thing tomorrow morning. I have the images made and
# have
# ray-traced the stereo views using the commands:
# 
# set antialias,1
# ray 2000,2000,angle=-3
# png image_left.png
# ray 2000,2000,angle=3
# png image_right.png
# 
# What do I do now?!
# 
# I know that they have to be put into the same file a specific distance
# apart but should that distance etc. be input into Pymol before
# ray-tracing? Also, what distance is best? The journal help page is
# particuarly unhelpful.
# 
# Thanks in advance!
# Rob
# 
# 
# 
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Institute of Biotechnology
Macromolecular X-ray crystallography
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