[Chimera-users] Changing properties by command line

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 19 12:44:39 PDT 2009

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:

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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.

More information about the Chimera-users mailing list