[PyMOL] how to outline as in ray_trace_mode=2

Hey once again everyone, This is along the lines as my previous questions... When I do: set ray_trace_mode, 2; It produces a 'black and white image', however this really is of the outlines of the objects in the model. Is there a way I can manually make certain objects into this outline r

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

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

[PyMOL] dot representation transparency setting

Hey everyone, Is there a transparency setting for the dots representation? Something like stick_transparency? Thanks.

Re: [PyMOL] sheared spheres for dots in dot representation

12/2008 11:27 AM To: 'Tsjerk Wassenaar'; O. J. Ganesh Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] sheared spheres for dots in dot representation I think he means: "sheared" as in garden :) Creating a separate object is one route. Another would be: flag ignore

[PyMOL] sheared spheres for dots in dot representation

Hello again. I'm having a bit of trouble with the dot representation again. When I use the dot representation on an object, the sphere on which the dots reside ends up sheared; that is, I do not get a nice round sphere to hold up the dots. I've adjusted vdw of the object I'd like to have i

[PyMOL] dots representation

Hello, everyone. I'm having a hard time understanding the different properties of the dots representation in pymol. I just updated the wiki with what I've been able to piece together, but I still have many questions: 1) Why is the difference between dot_radius and dot_width (other than dot_

[PyMOL] showing peptide planes

Hey everyone, I checked the pymol wiki for this one, but didn't find it. Is there an easy way to create/show the OCNH peptide plane throughout a protein (or maybe in certain sections of a protein)? I'd like to make planes that look like the ones from Ramachandran Plot Explorer: http://bosc

[PyMOL] (no subject)

Hey again PyMOL gurus, >* O. J. Ganesh [2006-05-18 16:09] wrote: >> >> Hey PyMOL gurus: >> >> I have a 'perfect' helix. Is there some way to 'loosen' all of the >> angles in the helix so instead of 3.6 residues per turn, I could >

[PyMOL] loosen secondary structure

Hey PyMOL gurus: I have a 'perfect' helix. Is there some way to 'loosen' all of the angles in the helix so instead of 3.6 residues per turn, I could have, say, 8 residues per turn. My goal is to make the helix more 'coil-like'. Is this possible? Thanks!