[phenixbb] refinement with fake mtz file

Pavel Afonine PAfonine at lbl.gov
Wed Jan 13 10:55:39 PST 2010

Hi Raja,

you should make sure that the fake fobs are real and not complex values.

I presume you used phenix.pdbtools to create fake fobs, then the example 
of a correct command is:

phenix.pdbtools model.pdb --f-model type=real label=f-obs r_free=0.1 

Note, the command above gives you Fcalc computed from atomic model:

Fmodel = scale * exp(-h*U_overall*ht) * (Fcalc + k_sol * exp(-B_sol*s^2) 
* Fmask)

You can also add bulk solvent and anisotropy contributions to have full 

phenix.pdbtools pdb1akg.ent --f-model type=real label=f-obs r_free=0.1 
high_res=1.5 k_sol=0.35 b_sol=50.0 b_cart="1 2 3 4 5 6"

The phenix.refine command below seems to be correct.


On 1/13/10 10:39 AM, Raja Dey wrote:
> Hi,
>     I was trying to refine a model using a fake mtz file created from model. This mtz file contains h, k, l, FMODEL, PHIFMODEL
> I used in the command line as follows:
> phenix.refine model.updated.pdb_modified.pdb elbow.model_updated_pdb_modified_pdb.all.cif model.updated.pdb.mtz input.xray_data.labels=FMODEL strategy=individual_sites main.bulk_solvent_and_scale=false main.number_of_macro_cycles=10
> I got the following error
> iotbx.reflection_file_utils.Sorry_Not_a_suitable_array: Not a suitable array of observed xray data: refinement.input.xray_data.labels=FMODEL
> No array of observed xray data found.
> I think the command I used is not correct. I need to know the correct command to run this refinement.
> Thanks...
> Raja 
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