[Chimera-users] crosslinks

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 9 10:53:33 PST 2013

Hi Trisha,
Chimera can show "pseudobonds," which are essentially lines or sticks (other than real bonds) connecting any pair of atoms.  One way to add a bunch of pseudobonds is to make a list of the pairs of atoms to be connected and read it in with Pseudobond Reader (in menu under Tools... Depiction).  The format of the list is described here:

That uses the same syntax for specifying atoms as the Chimera command line.

If you are not familiar with the atom specification syntax and would rather create the connections interactively, another way is to just add distance measurements between the pairs of atoms.  Then you can hide the distance labels, change line/stick style or color, etc. just like any other pseudobonds. How to change pseudobond display is described near the bottom of the Pseudobond Reader page (link agove).

One way to add a distance measurement: Ctrl-click to select one atom, Shift-Ctrl-doubleclick a second atom and then choose "Show Distance" from the resulting context menu.  One way to change display properties of a pseudobond is to Ctrl-click to select it, then click the green magnifying glass near the bottom right corner of the Chimera window to open the Selection Inspector, then change values in the "Pseudobond" and "Pseudobond group" sections of that dialog.

Attached is an image showing several crosslinks on rhodopsin; in that case, I used Pseudobond Reader to connect CA atoms rather than the actual sidechains for visual simplicity, and used different colors to signify inhibition or lack of inhibition. 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

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On Jan 8, 2013, at 5:20 PM, Trisha Davis wrote:

> We would like to show the cross links we recently observed between proteins within a complex.  Is there an easy way to specify where to put these 15 cross links? In the past, when we had just a few, we drew them in and positioned them by hand.
> Trisha Davis

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