[Chimera-users] Show me the disulfides!

Eric Pettersen pett at cgl.ucsf.edu
Fri Mar 3 13:29:13 PST 2006

Todd Talley writes:
> Hay,
>             I am sure that this is a dumb problem BUT I am unable  
> to “turn on” the disulfide bonds in my structures.  They are a  
> crucial part of the structures that I am publishing and I really  
> would like to use Chimera to render the images for our publication  
> but I am not a code guy and none of the combos I have tried  
> worked.  If anyone is out there with the answer please let me know!
> Thanks!

Deposited PDB structures specify disulfide linkages using CONECT  
records, which Chimera honors.  So one way to go is to add such  
CONECT records to your structures.  CONECT records are documented  
here:  http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_69.html

You can also add the linkages directly in Chimera.  If you select a  
pair of sulfurs that should have the linkage, then the command "bond  
sel" (Favorites->Command Line) will add the linkage.  Sessions and  
PDB files that you save thereafter will have the linkage information  
(i.e. a saved PDB file will have the appropriate CONECT record).

If you have a lot of disulfide bonds or a lot of structures, I could  
send you a short Python script to add the linkages automatically.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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