Hi Eric, I tried your solution. The problem is that having selected the respective :CYS@SG atoms and clicking on "Add reasonable bonds between selected atoms" does not result in bond formation. At least the bond is not visible and in saving the structure I do not get connect records. Am I missing something? Regards George On Mar 20, 2012, at 9:16 PM, Eric Pettersen wrote:
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@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