Dear JD, stick radius = (individual bond radius)*(model stickScale) ball radius = (individual VDW radius)*(model ballScale) Unlike VDW radii, the bond radii don't really have any chemical meaning in Chimera, and all are 0.2 Angstroms by default. To adjust stick thickness for whole model(s) just change the model attribute stickScale (default is 1.0). This can be done with the command setattr, for example: setattr m stickScale 1.8 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> The stick scale could also be changed in the molecule model attributes panel or in the Selection Inspector. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/moleculeattrib.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html> I'd also recommend changing ballScale rather than VDW radii if the main purpose is to adjust the appearance of ball-and-stick. If you change the VDW radii, it will change the molecular surface, contact/ clash calculations, perhaps other things. You can change ballScale (default 0.25) with all the same approaches as stickScale. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 8, 2009, at 1:34 AM, Jean Didier Pie Marechal wrote:
Dear all, I know how to change the size of the balls using the vdwdefine, but I don't see the command/option to change the diameter of the cylinder in bs representation. Can I do this? best JD