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

Maxwell Cherf maxcherf at gmail.com
Fri Aug 9 13:44:54 PDT 2013

Hi Elaine,

Thank you for your reply! I was able to attach both ligands using the split
command followed by the join command.

I have another problem now though -  my goal is to build a peptide linker
that attaches the termini of two ligands that are bound to a receptor (the
PDB contains three protein structures) ; I also want both ligands to remain
properly docked to the receptor while I incorporate the linker. Using the
slit/join commands allowed me to link both ligands, but ended up changing
their orientation relative to the receptor. Is there a way to build a
peptide linker that attaches the termini of the two ligands without
changing their orientation using Chimera?

Thanks again,

Gerald Cherf, PhD candidate
Cochran Lab
Bioengineering Department
Stanford University

On Fri, Aug 9, 2013 at 11:31 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
> 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).
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html
> >
> I would try that if you are averse to text-editing PDB files.
> I hope this helps,
> Elaine
> -----
> 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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