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

Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu