Zach, Unfortunately, there is currently no good solution to problem (a). PyMOL doesn't yet support automatic repositioning of CA coordinates to reflect the cartoon representation.
Regarding (b), the PyMOL light source is directional, not positional. The direction is controlled using the light setting which has a default value of [ -0.40000, -0.40000, -1.00000 ], which means that the light appears to come downward over the right shoulder of the observer. It's a direction vector. For example: [0,-1,0] is straight down [0,0,-1] is straight forward [1,0,0] is from the left etc. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC 400 Oyster Pt. Blvd., Ste 213 South San Francisco, CA 94080 (650)-346-1154 Fax:(650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Zach > Sent: Tuesday, October 05, 2004 9:53 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Questions about ray-tracing > > Hello to all, > > I am trying to ray trace a picture using pymol and I have a > couple of questions: > > a) I am using a cylindrical helix representation. Some of > these helices have side chains sticking out of them > represented as sticks. The connection between the alpha > carbon (within the helix) and the beta atom (the first on the > side chain) is not connected and the residue seems to float. > I know I can change the radius of the cylinders through the > cartoon_helix_radius setting but this would imply making my > helices fatter and I do not want to do this. As a matter of > fact, what I would like to do is to decrease the radii of the > helices so that I can unclutter the picture but this would > make the problem of floating residues even worse. > What can I do? > > b) I would like to know how I can know the position of my > light source with respect to the object I am trying to > render. I know I can change the position through the light > setting but I am not sure where it is located or what effect > I will get by changing the coordinates of the light source. > Trial and error is proving to be a difficult choice as I am > not sure what I am doing. > > Any help is really appreciated! > > Zach > > > > ------------------------------------------------------- > This SF.net email is sponsored by: IT Product Guide on > ITManagersJournal Use IT products in your business? Tell us > what you think of them. Give us Your Opinions, Get Free > ThinkGeek Gift Certificates! Click to find out more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
