Andreas, Gilleain, & others,
Agreed -- there is strong demand for annotations within scenes & session files.  Currently this is only possible when you define (or redefine a scene) using the command line:
scene 001, store, This is the view of the binding site.
And note that you can pass in a multi-line string using Python:
cmd.scene("001","store","This is the view of the binding site.\nPlease note the ligand in yellow.")
We have much work to do to make annotations more general and more accessible...
DeLano Scientific LLC
Subscriber Support Services
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From: [] On Behalf Of Andreas Forster
Sent: Monday, February 12, 2007 3:32 AM
To: gilleain torrance
Subject: Re: [PyMOL] image metadata plugin

I was actually thinking about a related approach.  Could one include a feature in PyMOL allowing the user to save notes with a session?  I've really come to like saving sessions but going back to them later I often wonder what the objects are exactly, what the views were meant to represent, which views are saved, which color scheme I used.  Briefly, details that help recreate scenes or images.

I've sent emails not too long ago arguing that one should simply write scripts, and all will be obvious.  I stand corrected (thanks, Warren) because it won't.  If you're pdb file is gone, your script will only take you on a long search through the dark corners of all available hard disks but not to brilliant figures.

Gilleain, I'm not sure you would want to save a session with every png because that would inflate the size of your image significantly.  But it'd sure be cool to have a snapshot saved in the session file to have a thumbnail to look at.


On 2/12/07, gilleain torrance <> wrote:
Hello everybody,

I just had an idea for a plugin, but I know I won't have time to make
it, sooooo...I thought I would mention it in the hope someone else
can. :)

Basically, I often make snapshot images (pngs) of scenes. The problem
with doing this is that I have learned to be careful to make the
filename tell me what it is. For example : nacatgrip_1fmn_201_203.png.
Otherwise, I look at the picture 6 months later and wonder what it

This would be a lot easier if there was a snapshot plugin that could
store an image and metadata about the image - the path to the
structure file, structure names, comments, etc.

In fact, a truly clever thing would be to store the session along with
the image, and you could browse sessions by looking at thumbnail

Anyway, just a thought.

gilleain torrance