pymol-users-boun...@lists.sourceforge.net wrote on 10/25/2006 08:11:27 PM:
> Hello everybody, > > I wish to represent the backbone of my protein in cartoon with a > transparency of 0.6. Around it I show the surface with a transparency of > 0.4. (the aim is to highlight some specific residues by showing their > side chains in stick without transparency). > I can see the wanted result in OpenGL view. But when I raytrace the > picture a kind of "Copperfield" effect happens: the cartoon backbone > disappears (NB: it happens for any kind of combination of transparency > value for cartoon and surface). > Is anybody have an idea of what is happening ? > > Thanks, > > Emeric Hi Emeric - Pymol has a few different ways of handling multiple nested transparent surfaces. The default is to just show the one closest to the viewer (uni-layer transparency). This gives prettier pictures with a single surface, since you don't see the backside of the protein or any pockets in the surface. However, for your purposes, you want multi-layer transparency. To select this, choose "Setting->Transparency->Multi-layer". I just confirmed that this works. I find the results a bit busy, unless you're looking at just a small part of the protein. You may need to hide background details with the clipping planes. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
