[Chimera-users] scripting pseudobond display style

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 3 12:36:44 PDT 2012

Hi Vamsee,
You can use the "setattr" command (general command to set attribute values).  It works on lots of things, including pseudobonds and pseudobond groups.  

The command requires knowing the name of the attribute, its possible values, and whether it is an attribute of an individual pseudobond ("p" in the command) or the whole pseudobond group ("g).

You can figure out all this stuff by looking in the GUI:  Pseudobond attributes panel or the Selection Inspector, and using its balloon help (pop-up text when you put the mouse cursor over some option):

A few example commands:

setattr g lineWidth 3
setattr g lineType 1
setattr p color hot pink 
setattr p label " "

Those would change all pseudobonds, but you can limit the scope by specifying atoms at the end (meaning all pseudobonds with both endpoint atoms specified).

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

On Aug 3, 2012, at 12:15 PM, vamsee wrote:

> Hello,
> I am trying to script distance measurements (distance monitor) between the Calpha of a residue and a few Hydrogens. I have pretty much everything working except that I am not able to figure out how to change the attributes (color, line style etc..) of the distances (pseudo-bonds). I know it can be changed using the GUI but I would rather script it. Any suggestions? 
> Thank you
> Vamsee

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