[Chimera-users] Question about the dotted bond

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 13 11:40:32 PST 2007

Hi Hyunmi,
There are a few possible reasons, but it depends on the specific PDB  
file.  Dotted lines are usually "pseudobonds," used to show where  
parts of chains are missing (such as a missing loop in a PDB  
structure due to poor density), metal complexation bonds, and  
distance measurements.

You can hide it if you want by Ctrl-clicking to select it and then  
opening the Selection Inspector (by clicking the button on the lower  
right corner of the Chimera window) - in there, set "displayed" to  
"false".  Or, you can open the PseudoBond Panel (under Tools...  
General Controls), click on the Name of that pseudobond group  
(different names are used for different situations), and then on the  
right side click close (delete) or hide.  Or, you just could change  
how it looks by clicking "attributes..." and adjusting parameters in  
the resulting dialog.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 9, 2007, at 9:06 AM, Hyunmi Sun wrote:

> Dear Whom it may concern
> Hello,
> I am currently using Chimera to access a pdb file. When I fetch the  
> pdb
> file, one of the bonds between two ligands is illustrated as a dotted
> line in the wire representation. Why is this so?
> Thanks for the help!
> Sincerely,
> Hyunmi Sun

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