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. Thanks again George
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
Hi Eric, Indeed this is the case. The protein was derived from homology modelling without connect records. Many thanks for the suggested workaround. 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
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
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. --Eric 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@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
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