[Chimera-users] Modelling missing residues in a protein

[Marco Sette]

Dear Edmund,

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).

Best

Marco


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
>     <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 <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
>     >
>
>
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-- 
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
Tel.: +39-0672594424
Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette

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