This morning I upgraded from pymol 0.97 to pymol 0.98 and I've
discovered some fairly substantial differences in behavior between the
two versions.
I first noticed that some objects were being drawn much darker than
before. Specifically, protein surfaces and anything drawn using sticks
(instead of lines) are very difficult to see. This is illustrated in
this screen capture:
http://www.mindspring.com/~greglandrum/pymol/normal-0.98.jpg
notice how bright the h-bond lines are compared to everything else; if I
draw the molecule with lines instead of sticks, they come out this bright.
As a check, I then raytraced that scene and got something much more
reasonable:
http://www.mindspring.com/~greglandrum/pymol/traced-0.98.jpg
(this scene took *way* too long to raytrace, I'll comment on that below).
Here's a similar scene as it appears in version 0.97:
http://www.mindspring.com/~greglandrum/pymol/normal-0.97.jpg
So I tried exporting a session file from 0.97 and loading it into 0.98.
The resulting rendering is, once again, way too dark:
http://www.mindspring.com/~greglandrum/pymol/normal-0.98-import.jpg
(notice that's it's also not exactly the same view, despite the fact I
loaded a session file. This is also a problem)
The raytracing results from 0.97 and 0.98 using the 0.97 session file
are similar (aside from the view/perspective differences):
http://www.mindspring.com/~greglandrum/pymol/traced-0.97.jpg
and:
http://www.mindspring.com/~greglandrum/pymol/traced-0.98-import.jpg
Any clues as to what's going on here?
A note about raytracing time:
The initial raytrace with 0.98 took 227 seconds on this machine, the
other raytraces took 2.3 seconds (using 0.97) and 9.9 seconds (using
0.98 with the 0.97 session file). Why is 0.98 so much slower than 0.97?
The scenes were generated programatically using the same sequences of
commands (with the exception of details of the view, which I got close
by hand), so any differences in the surfaces themselves must be due to
changed default settings in the surface generation routines?
These results were obtained on a Windows 2K box, using Python 2.3.4
Thanks for any help,
-greg
