[phenixbb] build two helix run in opposite direction and set half occupancy or each in Coot

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Thu Apr 28 06:44:59 PDT 2016

On 28/04/16 05:51, Xiao Lei wrote:
> Hi Phenixbb members,
> Is there a way in the Coot GUI that I can build two helix of the same 
> sequence (or just short 5aa or 6aa peptide chains of the same 
> sequence) that run in the opposite direction (180 degree opposite 
> direction) of each other and set half occupancy of each peptide chain?
> I tried to use Calculate---> Model/fit/refine/----> add alternative 
> conformation, but it seems I only have two options: "split single 
> residue at C-alpha" or "split all of a single residue", which are 
> applying to single residue only, not a short peptide chain.

There isn't a single button to do it, this is what I would do:

Make a molecule of my favourite 6aa helix, centre the blob(?) in which 
you wish to put it at the centre, Move molecule here. Jiggle Fit (as 
needed), mutate residue range, [1], Extensions-> Modelling -> Copy 
Molecule, Other Modelling Tools-> Reverse Fragment, Ca Zone -> 
Main-chain, R/RC [Add Alpha helix restraints], mutate residue range. 
Refine (or Regularize as needed)

(Using modern Coots)
[1] Scripting -> Python -> set_occupancy_residue_range(1, "A", 1,6, 0.5) 
# or some such


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