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
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
> 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
> I hope this makes sense. Just email if you want more details.
> On Friday, April 4, 2003, at 05:56 AM, <camille@...>
>> 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,
>> p.s. I'm running npymol on OS X.
> Scott Classen, Ph.D.
> 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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