[Chimera-users] Modelling missing residues in a protein
sette at uniroma2.it
Wed Oct 14 04:21:51 PDT 2020
to my knowledge the SwissPDB Viewer, now Deep View, perform this task.
When you open a pdb file lacking some residues it directly fills the
gaps and gives a message that the build residues are in a different
color (pink or purple, I guess).
Il 14/10/2020 04:19, Edmund Marinelli ha scritto:
> 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
> <mailto: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
> I hope this helps,
> 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 <mailto: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
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette at uniroma2.it
e-mail: m77it at yahoo.it
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users