[Chimera-users] How to change the default color for pseudobonds?

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 6 09:24:30 PST 2013

Hi Oliver,
Currently there isn't a way to set default color for distance monitors, which I agree would be useful.  FindHBond does remember the last applied settings and the metal-complexation pseudobond default color can be set in the New Molecules category of preferences, but as far as I know the distance monitor color can only be changed after the fact.

Besides using the Pseudobond Attributes panel or selecting the pseudobond and using the Selection Inspector, you can also change color, line style, linewidth with the setattr command.  

An additional inconvenience, however, is that to specify the pseudobonds in the command line, you have to specify some set of atoms that includes both their endpoints (extra atoms are OK, though).  If you don't specify any atoms in the command, it will just change ALL the pseudobonds, which might not be what you wanted, e.g.:

setattr p color green

You could limit it by specifying atoms, e.g.

setattr p color green :1-50

would get all pseudobonds with both endpoint atoms within residues 1-50.

If changing them all is OK, you could put the first command above in a custom preset or as an alias, for example

alias ^greenpb setattr p color green

... which would create an Aliases menu with "greenpb" and also allow you to use "greenpb" in the command line.  The alias is automatically remembered in your preferences file.

Sorry about the suboptimality,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 5, 2013, at 4:45 PM, Oliver Clarke wrote:

> Greetings,
> Is there any way to change the default color for pseudo bonds (e.g. distance monitors)?
> I generally work on a white background, and the default of yellow is very difficult to see. Pretty much everything else in the Chimera GUI seems to be customizable, which I love, but I can’t see how to alter the default in this particular instance.
> Many thanks,
> Oliver.

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