Re: [PyMOL] PyMOL-users Digest, Vol 27, Issue 3

2008-08-18 Thread DeLano Scientific
OJ, I think Photoshop (or Gimp?) is probably the tool for this -- PyMOL's ray_trace_mode cannot distinguish between the underlying representations, but you could probably accomplish this through recoloring select portion of a single rendering or through composition of multiple renderings. Cheers,

[PyMOL] cylindrical representation

2008-08-18 Thread Chun Tang
Dear all, I don't know if this has been discussed before. I noticed that the structure is completely wrong when I have cylindrical representation of helices turned on. This happens when I have multiple structures loaded up - rendering of single pdb file seems all right. I am using version 1.1 on

Re: [PyMOL] PyMOL-users Digest, Vol 27, Issue 3

2008-08-18 Thread O. J. Ganesh
Hey again everyone, I've working with a model in pymol which needs to end up as a greyscale image (for a journal). The model is fairly complicated, and contains several molecules - some represented as spheres, some as sticks, etc. I was working with: set ray_trace_mode, 2; To produce a