This message was sent ~2 weeks ago but with pictures attached, so I'm guessing
it ended up in the internet ether :).
I'm trying out Pymol (windows, 1.2r8) and Acrobat extended 9 to embed
structures in PDF files for students. Following the procedure from JBC
(http://www.jbc.org/cgi/content/full/284/32/21101), I can get the capture
process to work, but the shading on the protein is sometimes there, sometimes
it's not. In the less problematic image you can see that some of the loops
look a little flat, while in the more problematic image there is no shading
at all. Not sure why this is happening, I've tried changing various settings
(colour space, lighting, the way I select residues for colouring) but nothing
seems to get it to work consistently.
I have screen captures that better demonstate what I'm seeing.
Steffen Graether, Ph.D.
University of Guelph
office: SCIE 3455
phone: 519-824-4120 ext. 56457