[Chimera-users] carbon-chlorine bond

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 17 09:47:42 PST 2008

Hi Francesco,
It only means that whatever file(s) you are reading into Chimera do  
not specify the bond explicitly.  I can't tell from the information  
given whether your MD program knows the bond is there; it may know,  
but not write this information into the file that you input to Chimera.

If the file(s) describe trajectory in the format of the MD program  
(AMBER? GROMOS?) and you are using the MD Movie tool in Chimera for  
display, all the bonds should be there.

However, if you are doing something else like writing a PDB file from  
those programs, maybe the PDB file does not specify the bond  
explicitly, and the other viewers might have a more relaxed criterion  
for automatically identifying a bond.

I don't think there is a way to change the automatic criteria, but you  
could just add a CONECT record specifying the bond to the PDB file, or  
just add the bond in Chimera with the command "bond" or the "Add/ 
Delete Bonds" section of Build Structure.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 16, 2008, at 11:00 AM, Francesco Pietra wrote:

> For a monochlorinated small alkaloid docked onto a protein model,
> after molecular dynamics simulations Chimera shows the chlorine atom
> as a dot, without a line to represent the bond. Before dynamics, the
> C-Cl line connecting the two atoms was shown. Other viewers show the
> bond both before and after MD.  For the purpose of presentation, how
> to set a longer C-Cl bond length as a temporary default for Chimera?
> Very likely the parameterization for chlorine in the MD suite is not
> as it should.
> Thanks
> francesco pietra

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