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

Ngoc Anh Thu Ho nho604 at aucklanduni.ac.nz
Thu Apr 28 19:45:06 PDT 2016

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.


> 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 <mailto: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 <mailto: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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