[Chimera-users] disulfides: naive question

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 21 10:43:24 PDT 2012

Hi George,
	So how far apart are these SG atoms?  They should be around 2.0 to  
2.1 angstroms.  Chimera should accept S-S distances of up to 2.44  
angstroms as "reasonable" bond lengths.
	Try this:

open 1zzz
(change to all-atom preset)
sel disulfide (should show several disulfide bonds)
~bond sel (disulfide bonds removed)
start Build Structure
add "reasonable" bonds between selected atoms (make sure to click Apply)
do the disulfides come back?

If the disulfides come back in 1zzz and they don't in your structure,  
and the distances in your structure aren't more than 2.44 angstroms  
then send me the structure and I'll investigate further.  If your  
distances are longer then you will have to select pairs you want  
bonded and then use the command "bond sel" to bond them.


On Mar 21, 2012, at 6:01 AM, George Tzotzos wrote:

> Hi Eric,
> I tried your solution. The problem is that having selected the  
> respective :CYS at 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 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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