[Chimera-users] join models

[Stewart Morley]

Thank you!

On Wed, Dec 5, 2018 at 1:40 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Stewart,
> You have to select specific atoms in the backbone, not the ribbon segments
> (which would select all of the atoms in the residues).  Hide the ribbons to
> see the backbone atoms, e.g. commands
>
> ~ribbon
> disp @n,ca,c,o
>
> Then (assuming you are using the “C-N peptide bond” option in Join Models)
> select just the N-terminal N of one peptide and the C-terminal C of the
> other.  Just two atoms will be selected.
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
> >
>
> Note that this may change the spatial relationship of the two peptides.
>
> In the past when I’ve done a similar overlap/splicing operation, the
> matching puts the peptides exactly where I want them, so instead of using
> Join Models I just  delete the extra overlapping atoms, combine the two
> models into one (see “copy/combine” function in model panel, or “combine”
> command), and then add the missing bond with “bond” command or the Build
> Structure tool “Adjust Bonds” section.
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Dec 5, 2018, at 11:01 AM, Stewart Morley <stewmorley at gmail.com>
> wrote:
> >
> > I cannot for the life of me get join models to work.
> >
> >       • I have two structures.
> >       • The structures overlap.
> >       • I align them using matchmaker.
> >       • I delete the overlapped residue from one chain.
> >       • I select the appropriate C and N terminal residues
> >       • I try to use join models under Build structure
> >       • The apply box remains gray, no matter what residue or atom I
> select.
> > What are common problems that cause join models to not work?
> >
> > Stewart
> > Morley
>
>
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