[Chimera-users] Introduce a-helices into protein structure ab initio

[Chara Spanou]

 Hi Elaine,
Thank you so much for explaining all this!
I will try it immediately.

Thanks a lot for your time and help,Chara
    On Thursday, January 6, 2022, 08:00:38 PM GMT+1, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Hi Chara,
In the Build Structure tool (menu: Tools... Structure Editing... Build Structure) 
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

....you can:

- use the Start Structure section to build a peptide de novo.  You can choose the sequence and all of the individual backbone angles, so it can be whatever conformation you want (alpha-helix, etc.)

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

- use the Join Models section to put different peptides together pairwise.  So you could get some peptides from de novo building as explained above, and/or you could open known PDB structures and delete the parts you don't want, to use sections of those known structures.

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>  

E.g. if you build 1 de novo peptide as model #0, then open a PDB structure as model #1 and delete the sections you don't want, then you can use the Join Models section of the Build Structure tool to join #0 and #1 to make a new single-chain model.  Then if you had another peptide in a different model, you could use Join Models again to make yet another model that has all three pieces bonded together.

You may also be interested in the other sections of Build Structure for modifying your structure.

One more possibility:
If you already have most of the protein and you just want to build more residues on one end or the other, you can do it using the "addaa" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.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 Jan 6, 2022, at 6:12 AM, Chara Spanou via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello chimera-users,
> 
> I would like to introduce a-helices into my protein structure ab initio.
> 
> Is it possible to do this with chimera?
> 
> Another option that I have is to take a-helical pieces of sequence from a different model
> 
> and introduce these into the desired model.
> 
> Would that be more feasible?
> 
> There is a chance I also need to introduce loops and turns ab initio to best localize the
> 
> introduced a-helices within my protein structure.
> 
> Can you please indicate how can a chimera user build all this ab initio?
> 
> 
> Thank you in advance for your time and help,
> 
> Chara Spanou
> PhD student
> University of Cologne

  
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