[Chimera-users] Question (solid vs. dashed pseudobonds)

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 25 14:24:16 PDT 2011

Hi Anna,
The set of lines to a metal ion are considered one "group" so you can only change the line style collectively.  However, they can be hidden and shown individually, so one possible workaround is to hide the ones you want to show as solid, then add distance measurements in those places and show those as solid lines without the distance numbers.

To individually hide, Ctrl-click the pseudobond, then click the green magnifying glass on the bottom right corner of the Chimera window to show the Selection Inspector.  In the inspector, make sure it is inspecting "pseudobond" and change the "display" setting to "false."  To change properties of the whole group of pseudobonds you would instead inspect "pseudobond group".

There are several ways to add a distance pseudobond, but one way is to Ctrl-click on one atom to select it, Shift-Ctrl-doubleclick on the second and then from the pop-up menu choose "Show Distance."  To hide the distance number open the Distances tool (under Tools... Structure Analysis in the  menu) and set "Labels" to "None".  This will turn off the number for the whole group of distance measurements.  You could change other display settings of the distance group by clicking "Display options..." on the Distances dialog, or selecting and using the Selection Inspector as described above for the metal coordinate pseudobond.  The "line style" includes dashed and solid options.

Or, if you have a lot of lines to add, instead of adding distance monitors, you can list the atom pairs to be connected in a file and read in the file with PseudoBond Reader (under Tools... Depiction, click Help button on that tool for more details).

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 Oct 25, 2011, at 11:42 AM, Anna Starus wrote:

> Hello,
> I am having difficulty to depict some bonds as solid lines or some as dashed lines for the bonds that are coordinated to the metal. For some reason when I changed one bond to dashed all of the bonds also change to that. How could I ungroup the coordinating bonds to the metal and be able to make some of them dashed and some solid?
> I would greatly appreciate the help.
> Thank you,
> Anna

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