[Chimera-users] Renaming chains in a PDB file with two chains

[Elaine Meng]

Hi Hari,
You're welcome!

There is no way to change the chain ID in Chimera.  The only way I  
know is to just text-edit the PDB file.  However, the two chains are  
already distinguishable by their model ID numbers #0.1 and #0.2, so  
there is no reason to give them different chain IDs.

FindHBond ignores interactions between models with the same first  
number and different second numbers, so now you are only getting the  
H-bonds within each chain anyway.  In the PDB, multi-model files like  
that are only used to describe multiple conformations of the same  
structure that are on top of each other (such as from NMR), where you  
wouldn't want them to "see" each other.

So there are two issues, (1) how to find H-bonds between them and (2)  
how to separate the results for H-bonds between the structures and  
within each structure.

(1) You cannot find H-bonds between #0.1 and #0.2 with the FindHBond  
graphical interface (GUI) and your current file.  However, the  
"findhbond" command has an option "interSubmodels true" to include  
those interactions:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html

Alternatively, you can edit your file into two separate files; then  
you could use either the GUI or the command.

(2) You can do separate calculations of inter-model and intra-model H- 
bonds, so you do not have to postprocess the combined results.  Both  
the GUI and the command have options to do those calculations  
separately:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ 
findhbond.html

If you did not edit the file, you have to use the command to  
calculate the H-bonds between the structures, as mentioned above.   
For example, these keywords would give only the H-bonds between the  
structures:

hb intersub true intermod false

You could use either GUI or command to calculate H-bonds within each  
structure.
I hope this helps,
Elaine

-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On May 10, 2008, at 10:27 AM, Harinathachari Bahudhanapati wrote:

> Hi Elaine,
>                Thanks for all the answers you give to our questions.
> They are very helpful as I learn more everyday. I have a question.
>
> Is there anyway to rename a chain in a PDB file through the GUI? I  
> have
> a few PATCHDOCK generated PDB files with two different chains named
> under  Chain 'A' as #0.1 and #0.2. When I try to get the list of
> hydrogen bonds between these two chains, the chain name 'A'  appears
> for all of the h-bonding pairs. So, I want to have them named Chain A
> and Chain B for easier analysis than scratching my head figuring out
> which h-bond pair is between the chains or with in the chain. I am
> attaching the pdb file. Please help me.
>
> (I thought of renaming the chains in the PDB file going through the  
> PDB
> header (text file) and manually changing the name. But I am not a
> expert if anything goes wrong.)
>
> Sincerely
> Hari