[Chimera-users] Preference/default for H-bond representation

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 12 12:28:09 PST 2017

Hi Markus,
Although there is something like that for distance monitors (Save button in the Distances tool), unfortunately there isn’t for H-bond pseudobonds, nor is there an option in the findhbond command or dialog to make them dashed in the first place.

That leaves changing them after the fact, e.g. the following command would make all pseudobonds dashed:

setattr g lineType 2

You can also specify subsets but only by endpoint atoms, not by the pseudobond group name.

GUI ways to make them dashed:

(A) Pseudobond Panel (under Tools… General Controls), choose “hydrogen bonds” and click “attributes…” on the right, and in the attributes dialog change “line style”
- OR -
(B) select any H-bond pseudobond, click green magnifying glass icon to open Selection Inspector, Inspect: pseudobond group, change “line style”

How I know to use”setattr” command “g” (pseudobond group” and the attribute name “lineType” and its possible values are by seeing in either of the above dialogs that it is a pseudobond group attribute, and then mousing over “line type” in the dialog to show balloon help with the attribute name and possible values.

There must be some place in the code to change it to always dashed, but somebody else would have to advise on that...

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

> On Jan 10, 2017, at 2:08 PM, Markus Heller <mheller at cdrd.ca> wrote:
> Hello,
> Is there a way to set the preference for H-bonds to be represented as dashed lines, not as solid lines?  I don't seem to be able to find anything in the Preferences or the documentation.
> Thanks and Cheers
> Markus

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