Hi Thomas! Glad you like the silhouette edges. You can change VDW radii with the command "vdwdefine," for example: vdwdef 1.15 Fe vdwdef +0.1 @ca where the first example sets the radius to 1.15 A, the second increases the existing radius by 0.1 A. You could use "sel" for selected atoms, instead of element or name as in my examples. You could also change VDW radii with the command "setattr," or using the Selection Inspector (GUI). What you saw in the Quick Ref was how to specify atoms of a particular radius, for example, in a command to color atoms with radius < 1.5 A yellow: color yellow @/radius<1.5 You can change the appearance of pseudobonds (such as used to show metal coordination) with the command "settatr" ... the tricky part is that requires knowing the attribute name and values, and knowing whether it is an attribute of individual pseudobonds or pseudobond groups. I'll just show examples and then explain a bit more... setattr p color green ions z<4 setattr g lineType 1 ions z<4 setattr g lineWidth 2 ions z<4 The "ions z<4" part specifies only the pseudobonds between atoms within a 4-A zone of any ion, including the ion. I can tell which are individual pseudobond attributes ("p") or pseudobond group attributes ("p") by looking at the pseudobond attributes panel (Tools... General Controls... PseudoBond Panel, click "attributes..."). Color is usually just named "color" but I had to check with a programmer about "lineType" and its allowed values (integers 1-5 in the same order as the styles are shown in the attributes dialog), and guessed "lineWidth" myself. We are thinking of adding balloon help to the attributes dialog that will show the actual names of the attributes and their allowed values, to make this easier to figure out. Unfortunately there isn't a command for controlling effects such as silhouette edges, although we would like to have that in the future. Man pages for vdwdefine and setattr: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> I hope this helps, 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 Mar 19, 2009, at 11:52 AM, Dipl.-Ing. Thomas Mitterfellner wrote:
Hello again!
I could not find out how to change radii of selected atom via the command line. I had hoped this would work via '@/radius=', which I read in the quick reference, but I turns out that I obviously misunderstood the usage of the hints given there. Is it also possible to change the color and linestyle of coordinative bonds in the command line? Related to this: can the status and color of the molecule silhouette be changed from the command line?
Thank you very much!
P.S.: Chimera really produces great pictures and I especially like the silhouette effect, which I, up to now, always had to (partially) draw myself with some image editor.