[Chimera-users] Modelling missing residues in a protein

[Edmund Marinelli]

Hello Elaine:

So far I find no service that does what Modeller does, believe it or not.
As an example Swiss-Model failed to fill in the missing residues, to my
surprise.  A couple of web services that I ran across rely on Modeller and
one has to buy a license for Modeller or at least convince the Modeler lab
that you are not commercial and qualify as academic, which is harder to do
than one might think.  There does exist the French server Pepfold3 and
related versions but those don't handle the entire protein; instead one
might get a 30-mer modeled 'on its own'.  Then comes the question of : how
would one mate that piece , which might have a different coordinate frame
of reference , to the protein which lacks those residues in the PDB.  This
is a question, which on its own, is important.  If you have any insight to
that issue I would appreciate it.

If you know of any service that actually models the protein and rebuilds
the missing residues (note that the missing residues are listed in the PDB
file , but of course no coordinates); I would be appreciative to know what
they are.

Best regards,

Edmund R Marinelli (Ed)

On Tue, Oct 13, 2020 at 4:52 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> >
>
>
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