[Chimera-users] Colored Rays

Mark Cunningham Mark_Cunningham at berea.edu
Sun Jun 11 20:27:41 PDT 2006

        Elaine, thanks for your response to my question on the coordinate system problem. My problem, as you suggested,  was not related to coordinate systems, rather there was a problem with GOLD  writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine.
        But now I have another question. Occassionally, while visualizing and manipulating a protein structure 
(1XAP) with Chimera, I get  colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear.
Mark A. Cunningham, Ph.D.
Assistant Professor of Chemistry
CPO 2191
Berea College
Berea, KY 40404
(859)985-3029 Office
(859)985-3303 Fax

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