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

Xiao Lei xiaoleiusc at gmail.com
Thu Apr 28 12:37:45 PDT 2016


Thanks for the suggestions. After I type command in the python script and
get error msg:
BL WARNING:: Python error!
(Or you attempted to use an invalid guile command...)
Python error:
name 'set_occupancy_residue_range' is not defined
<type 'exceptions.NameError'>.

What should I do to correct it?

On Thu, Apr 28, 2016 at 6:44 AM, Paul Emsley <pemsley at mrc-lmb.cam.ac.uk>

> 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
> Paul.
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