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

Xiao Lei xiaoleiusc at gmail.com
Fri Apr 29 17:22:05 PDT 2016

Hi Thu,

Thank you very much for the suggestion! The PDB file editor works great in
this case. One thing I learned is that: beside setting half occupancy, I
also need to set altloc (alternative locations), so that the subsequent
refine program (either Refmac or Phenix) would not think two peptides are
too close and have repulsion to each other.

On Thu, Apr 28, 2016 at 7:45 PM, Ngoc Anh Thu Ho <nho604 at aucklanduni.ac.nz>

> Hi XIao,
> Since you want to do this in Coot, this suggestion might be redundant, but
> If you don’t mind switching back and forth between programs (which I
> usually do), the 'PDB Tools' and 'PDB file editor' (Model tools section) in
> Phenix GUI is very handy in modifying occupancy of a residue range. I
> myself prefer file editor for the task as residue selection is easier.
> Thu
> On 29/04/2016, at 10:48 AM, Xiao Lei <xiaoleiusc at gmail.com> wrote:
> 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
> set_occupancy_**
> 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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