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

Maxwell Cherf maxcherf at gmail.com
Mon Sep 2 12:46:11 PDT 2013

Thanks so much Elaine! I finally got this to work. It took me a while to
figure out how to text edit pdb files.

If anyone on the forum is interested, here is what I did:

1. Opened the original pdb file in text edit containing the receptor and
two ligands (3 chains total).
2. Inserted a linker sequence between the two ligands with x,y,z
coordinates set to zero and occupation set to -1.
3. Used a python script to renumber all the atoms in the correct order give
both ligands and the linker the same chain ID. At this point, I had ligand
1 - linker - ligand two, all in the same chain with atoms in sequential
order. I also deleted all the secondary structure information (HELIX and
SHEET lines at the beginning of the pdb file) and manually added these back
in later. Pymol will add secondary structure back in automatically, but it
seems Chimera has trouble with this sometimes.
4. Saved the file in .pdb format, and opened in Chimera.
5. Opened a fasta file with the amino acid sequence of my
ligand1-linker-ligand2 construct.
6. Highlighted the linker sequence in the sequence file and opened Modeller
(loops/refinement), selected "chimera selection region", "models to
generate" = 5, "apply".

This was all done with the receptor in place. Of the 5 generated models, 3
contained linkers that did not clash with the receptor and had acceptable
ramachandran plots.

Thanks again for all your help!


Gerald Maxwell Cherf
PhD candidate
Stanford University, Bioengineering Dept.

On Mon, Aug 12, 2013 at 11:44 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Gerald,
> You don't need to do any linker-building, you can use Modeller to fill it
> in for you, keeping the ends (ligands) in their input positions.  There are
> probably a few alternative routes, but what I would do is:
> (1) Save PDB containing the peptide ends (the two ligands) in the
> positions that you want.  What you want at the end is just these two
> ligands with the same chain ID, and no other atoms.  That can be achieved
> either by text-editing the PDB after writing it out, or by changing chain
> IDs if necessary (Tools… Structure Editing… Change Chain IDs) of the
> ligands before writing it out.  The PDB save dialog gives you the option of
> saving only selected atoms, so you could select the ligands only and use
> that option.
>  ** Here's probably the biggest caveat of the approach, which I realized
> after I sent the last message:  via the Chimera-Modeller interface it is
> not possible to model one chain while taking other additional chains into
> account.  In other words, it won't help to include the protein in the file
> because it will be ignored.  Modeller itself is capable of doing that but
> the Chimera-Modeller interface only accesses a subset of Modeller's many
> capabilities… you'd have to run Modeller yourself independent of Chimera,
> which is much more difficult.  However, all may not be lost: the ensemble
> of possible solutions (linker conformations) may include some that happen
> to avoid intersecting with the protein.
> (2) Create plain text sequence file (FASTA, named something.fa) which
> contains the sequence of entire peptide: the ligand ends and the missing
> linker portion.  I would just create it in a text editor.  FASTA format is
> very simple, basically one line starting with > followed by a comment or
> description (or nothing, whatever you want) followed by one or more lines
> containing the amino acid sequence.
> (3) In Chimera, open the new PDB file containing the two ligands, and open
> the FASTA sequence file.  Then from the sequence window menu, choose
> Structure… Modeller (loops/refinement).  In the resulting dialog, you will
> want to model "non-terminal missing structure" or "all missing structure"
> (equivalent in this case).  You will probably aso want to change "Allow
> this many residues adjacent to missing regions to move" to 0 and increase
> the number of models to generate … I'd try something much higher like 20 or
> 50 in hopes of getting something that doesn't intersect with the protein.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building
> >
> 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 9, 2013, at 7:19 PM, Maxwell Cherf <maxcherf at gmail.com> wrote:
> > Hi Elaine,
> >
> > Using modeller sounds like the exact solution I'm looking for. Both the
> ligands and the linker I will connect them with are peptides.
> >
> > I tried using modeller, but I haven't gotten it to work yet. Here's what
> I've done:
> >
> > 1. built peptide linker using the "build structure" function
> > 2. attached the linker to one ligand1 using the "join" function
> > 3. combined the ligand1-linker with the second ligand into one model
> using the "combine" function
> > 4. added an unrealistic ~40 angstrom bond between the linker and second
> ligand (now we have ligand1 - linker - 40A bond - ligand 2, all in one
> model).
> > 5. I then tried using the "model/refine loop" function to find
> acceptable orientations for the linker (including the 40A bond) I
> incorporated, but I was unable to do this because the two ligands were
> still separate chains, and the "model/refine loop" function requires them
> to be in the same chain. If I use the "join" command instead of the
> "combine" command to attach the ligand1-linker to ligand2, I get one chain
> and then the model/refine loop function works perfectly to remodel the
> linker. However, using the join function changes the orientation of the
> ligands relative to the receptor, and I need the ligands to remain docked
> properly to the receptor.
> >
> > Is there a way to join both ligands into the same chain without changing
> their orientation? Or, do you know of an alternate approach for adding a
> linker between the two ligands without changing their orientation using
> modeller?
> >
> > Thanks again,
> > Gerald
> >
> >
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