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

[Maxwell Cherf]

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

______
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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