This is absolutely the coolest tip for adding depth to labels in
raytraced stereopairs, it works great especially when implemented with
Warrens commands for creating the stereo pair
ray angle=-3
png image1.png
ray angle=3
png image2.png
Y
p.s. I am not having session save problems on 0.88 (fink version, OS X)
On Friday, April 4, 2003, at 12:03 PM, Scott Classen wrote:
Hello Camille,
I will tell you how I make absolutely beautiful stereo figures in
PyMOL (with Adobe illustrator too) with nicely depth cued labels. It
takes a little more than clicking a single button, but it works well.
create two PyMOL scripts of your view that are identical with all the
beautiful ray tracing etc. then add:
turn y, -3 to the first script
and
turn y, 3 to the second one
make sure the png files exported from each script have different names
(i.e. Left and Right)
If you are working interactively with PyMOL then just remember to turn
y, 6 and then re-ray trace and export a second PNG.
Now use a program like Illustrator or Canvas to add the stereo/depth
cued labels. This is a little tricky to describe, but I'll give it my
best shot. Place the two images side by side with their centers
separated by 6.0 - 6.5 cm, and aligned horizontally. Now add all your
labels on the LEFT figure. select all of your labels and duplicate
them. Move the duplicated labels to the RIGHT side. For clarity sake
let's assume we have 3 labels on the LEFT side (a,b, and c -- we will
call then aL and aR for the left and right labels, respectively).
Place aL near a recognizable feature of the LEFT figure that you are
trying to label. Now horizontilly align aR with aL. Now using only the
<-- and --> keys move the aR label until the identical portion of the
actual label (let's say the lower right hand tip of the 'a') is
vertically aligned with the identical portion of your model (let's say
where the C alpha-C beta bond leaves the ribbon backbone) on both the
LEFT and RIGHT images. Repeat these steps for each pair of labels.
This is a nice method for adding stereo labels because it does not
require looking at your computer screen in wall-eyed stereo for 2
hours in order to get proper placement of labels.
By assuring that the labels are positioned in the LEFT and RIGHT
images at positions that are identical with respect to the part of the
model that is being labeled you automatically are also placing them so
they are at the proper depth when the figure is finally viewed in
stereo.
I hope this makes sense. Just email if you want more details.
Scott
On Friday, April 4, 2003, at 05:56 AM,
wrote:
Hello fellow Pymol users!
it sounds like I have the same objective as N. Sanishvili (25th Feb
2003) anyone told Nukri how you can ray-trace a stereo figure yet? I
couldn't find a reply to the original question on stereo figs on the
BB. I am also trying to label specific residues in my stereo figure.
Older messages on the BB seem to imply this can't be done in pymol.
Do you know if any progress has been made on this?
Many thanks,
Camille
p.s. I'm running npymol on OS X.
==
Scott Classen, Ph.D.
clas...@uclink4.berkeley.edu
University of California, Berkeley
Department of Molecular & Cell Biology
237 Hildebrand Hall #3206
Berkeley, CA 94720-3206
LAB 510.643.9491
FAX 510.643.9290
==
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