[Chimera-users] modeling insertion or deletion mutants

[Elaine Meng]

Hi Ruchika
I changed the Subject line to describe your current question.  This helps other people decide whether they want to read the answer. 

There is no simple tool in Chimera for modeling insertions or deletions, but I can think of two possibilities. Neither is necessarily a good approach for your project, so you may need to investigate other programs instead.  I only mention them since you're asking what is available in Chimera.

(A) If you have a template structure and target-template sequence alignment, you could use Chimera to run Modeller to build the target protein using a web service.  Help page for this feature:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
Tutorial example:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>

(B) Another possibility is to manually delete or add residues, delete and form new bonds as needed (see Build Structure tool), and minimize the result.  However, minimization only has a very limited ability to "fix" a structure and it is most definitely not a prediction of how the structure would really change, or whether it could even form a stable fold.  Here are the help pages for these tools:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.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 Sep 23, 2020, at 2:32 PM, Ruchika <Ruchika at ucsf.edu> wrote:
> 
> Hi Elaine
> Thanks for the confirmation !! I tried looking into these details, however, I still wanted to confirm with you. Thanks again !!
> I have another question. I do understand that I can mutate a residue to the different one using the rotamer tool. I am just wondering if I would like to make an insertion or deletion mutation in the protein, are there any available tools in the chimera. Please let me know. 
> Thanks !!
> Regards
> Ruchika