[Chimera-users] managing bond order

[Elaine Meng]

Hi Victor,
Missing segments in structures are indicated with dotted lines  
(pseudobonds) that can be hidden with the command:

~longbond

(show the command line by choosing Favorites... Command Line from the  
menu)
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html

That should take care of it.  Another possible cause is when PDB  
files have ATOM lines that should be HETATM, but it sounds like  
missing segments are the reason here.
Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Feb 21, 2008, at 4:46 PM, Victor Kenyon wrote:

> hi all,
> typically when i import a paired back active site of a protein,  
> chimera
> wants to connect atoms that should not be connected. is there a way to
> select bonds that violate a certain bond length so i can remove  
> them? or a
> possible work around?
> thanks for your help.
> victor
>
> Victor A. Kenyon
> kenyon at chemistry.ucsc.edu
> 831.252.7667.
>
>