[Chimera-users] Linking two chains in a PDB file

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 9 11:31:25 PDT 2013

Hi Gerald,
If you are familiar with text-editing PDB files, you could save what you have as a PDB file (see File menu), make two copies of the file, and edit to delete atoms so that one copy contains just the protein with fused linker and the other copy contains just the other protein.  Then you can open those two files resulting in two separate models, then use the Join Models tab in Build Structure (in menu under Tools... Structure Editing) to perform the final connection.

I mentioned text-editing first because I don't know whether your proteins have different chain IDs.  However, if your current protein+linker has one chain ID and the other protein to be joined has another chain ID, you can simply use the command "split" to make each chain a separate model, thus avoiding the text-editing and reopening steps.  Then proceed with Join Models as above.

Even if you don't have protein+linker with one chain ID and the other protein with another chain ID, you may be able to assign chain IDs so that they are, using Change Chain IDs (in menu under Tools... Structure Editing).
I would try that if you are averse to text-editing PDB files.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 8, 2013, at 3:07 PM, Maxwell Cherf wrote:

> Hi Sir/Madam
> I have a PDB file of three proteins bound together (in one model). I would like to fuse the N terminus of one protein to the C terminus of another protein by adding a peptide linker between the termini. Is it possible to do this using Chimera?
> So far, I have built a linker and joined it to one of the termini, but doing that combined the linker and all proteins in the file into one model. Now, I can't connect the free end of the linker to the other terminus because they are part of the same model. Any help would be much appreciated!
> Best,
> Gerald Cherf, PhD candidate
> Cochran Lab
> Bioengineering Department
> Stanford University

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