[phenixbb] build two helix run in opposite direction and set half occupancy or each in Coot
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, , 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)
 Scripting -> Python -> set_occupancy_residue_range(1, "A", 1,6, 0.5)
# or some such
More information about the phenixbb