[Chimera-users] Modelling missing residues in a protein

[Elaine Meng]

Hello Edmund,
No.  However, there are probably dozens (hundreds?) of web services that will model proteins and write out PDB files that you can then open in any molecular graphics program.

Within Chimera, besides the Modeller interface, you can "manually" build peptides of specified sequence and phi/psi angles and join them together (see Build Structure tool), or add amino acid residues one by one at the terminus ("addaa" command) or virtually mutate residues ("swapaa" command or Rotamers tool).

Build Structure
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
Rotamers
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
addaa
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html>
swapaa
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 13, 2020, at 4:22 PM, Edmund Marinelli <edmundmarinelli at gmail.com> wrote:
> 
> Hello:
> I see that Chimera uses Modeller for modeling missing residues .  Does Chimera have access to any other web based services that would perform similar function?  
> Thanks,
> Edmund R Marinelli, PhD 
>