Hi Jamie,
I've attached an email from a response to a similar question posted
awhile ago. I hope it is helpful.
Ciao,
Scott
On Oct 18, 2004, at 8:07 AM, jwal...@csb.wfu.edu wrote:
Hi,
I am trying to add labels to my figures to get them ready for
publication. I have figures in both stereo and mono, and I'm trying to
figure out how to move/orient labels so that they are easy to view.
Are there ways to move labels in a figure?
cheers
Jamie Wallen
> 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, <cami...@mr...>
> 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.
> 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
> ==============================================
