[Chimera-users] join models

[Elaine Meng]

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