[cctbxbb] F_obs values

[Pavel Afonine]

Hi AC Research,

getitng the file off PDB

phenix.fetch_pdb 3hz7 --mtz

and looking into its content

phenix.mtz.dump 3hz7.mtz

I see there are more than one data array in it.

So I think your "a = arrays[0]" is the root of trouble.

Also, doing this "f_obs = a.f_sq_as_f().map_to_asu()" unconditionally is 
not a good idea.

So loop over miller arrays, look at labels and pick the one that has the 
label you want.

Then, depending whether it is F or I, and depending on what you want (I 
or F) you can convert F to I or I to F, as desired.

Pavel

On 6/7/20 14:34, Academic Research wrote:
> Hello Everyone,
>
> I am trying to follow the script on the CCTBX website to get the F_obs 
> values for my 3hz7.mtz file.
>
> my code is as follows:
>
> from iotbx.reflection_file_reader import any_reflection_file
> hkl_file = any_reflection_file('3hz7.mtz')
> arrays = hkl_file.as_miller_arrays(merge_equivalents=False)
> a = arrays[0]
> f_obs = a.f_sq_as_f().map_to_asu()
>
> I get this following error:
> Traceback (most recent call last):
>   File "crystal.py", line 143, in <module>
>     if __name__ == '__main__': main()
>   File "crystal.py", line 140, in main
>     Cls.features('3hz7.mtz')
>   File "crystal.py", line 63, in features
>     f_obs = a.f_sq_as_f().map_to_asu()
>   File 
> "/home/acresearch/Desktop/CCTBX/mc3/envs/tenv/lib/python3.8/site-packages/cctbx/miller/__init__.py", 
> line 2374, in f_sq_as_f
>     result = array(self, converter(self.data()).f)
> Boost.Python.ArgumentError: Python argument types in
> array_f_sq_as_f_xtal_3_7.__init__(array_f_sq_as_f_xtal_3_7, int)
> did not match C++ signature:
>     __init__(_object*, scitbx::af::const_ref<double, 
> scitbx::af::trivial_accessor>)
>     __init__(_object*, scitbx::af::const_ref<double, 
> scitbx::af::trivial_accessor>, scitbx::af::const_ref<double, 
> scitbx::af::trivial_accessor>)
>     __init__(_object*, scitbx::af::const_ref<double, 
> scitbx::af::trivial_accessor>, scitbx::af::const_ref<double, 
> scitbx::af::trivial_accessor>, double)
>
>
> When I run:
> print(i_obs.info())
> I get:
> 3hz7.mtz:FREE
>
> print(a.observation_type())
> gives:
> None
>
> I repeated this script to many structure from the PDB (all solved by 
> x-rays) yet I get the exact same output for all of them.
>
> How can I get the F_obs values? Can someone please assist me?
>
> Regards,
>
> AC Research
>
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> cctbxbb at phenix-online.org
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