[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 15:48:07 PDT 2016

It seems python in Coot only supports: 1. zero_occupancy_residue_range
(which set occupancy to 0); and 2. fill_occupancy_residue_range (which set
residue occupancy to 1) in 0.8.3 EL version. I could not find the command

On Thu, Apr 28, 2016 at 12:37 PM, Xiao Lei <xiaoleiusc at gmail.com> wrote:

> Paul,
> Thanks for the suggestions. After I type command in the python script and
> get error msg:
> set_occupancy_residue_range(1,"G",108,120,0.5)
> 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>
> wrote:
>> 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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