[Chimera-users] join models
stewmorley at gmail.com
Wed Dec 5 12:49:02 PST 2018
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
> 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.
> 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.
> I hope this helps,
> 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>
> > 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
> > What are common problems that cause join models to not work?
> > Stewart
> > Morley
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