[Chimera-users] disulfides: naive question

[Eric Pettersen]

On Mar 20, 2012, at 11:16 AM, George Tzotzos wrote:

> Apologies for the earlier message. I need to clarify.
>
> Loading the topology and trajectory files onto Chimera and selecting  
> functional group/disulfides shows the bonds throughout the trajectory.
>
> The problem I have is that I don't see the bonds in pdb files that  
> I've generated from the topology files.

Hi George,
	Disulfide bonds are indicated in PDB files by the presence of CONECT  
records containing the serial numbers of the bonded sulfur atoms.  I'm  
imagining your PDB files are lacking these CONECT records.  If Chimera  
had written these PDB files the CONECT records would be there, so you  
must be using some other tool to generate the PDB files.
	Probably your simplest workaround (aside from using Chimera to  
generate the PDB files in the first place) is when you have such a PDB  
file open, use the command "sel :CYS at SG" to select all the cysteine  
sulfurs and the use the "Adjust Bonds" tab of the Build Structure tool  
to "Add reasonable bonds between selected atoms".  You could then save  
a new PDB files so that you wouldn't have to do those steps over later.

--Eric

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


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