[phenixbb] Number of unique reflections

John Berrisford jmb at ebi.ac.uk
Tue Oct 20 10:30:16 PDT 2020

Dear Armando and Pavel

During the deposition process we compare two values


We expect the number of observed reflections to be higher (or the same) as
the number of reflections used in refinement. 
We would expect that these two mmCIF items handle Friedel pairs consistently
- if the number of reflections observed is reported with Friedel pairs
separately then the number of reflections in refinement should also report
Friedel pairs separately.

My assumption here is that there is a mismatch in reporting these values. 

Hope this helps


-----Original Message-----
From: phenixbb-bounces at phenix-online.org
<phenixbb-bounces at phenix-online.org> On Behalf Of Pavel Afonine
Sent: 20 October 2020 18:16
To: Armando Albert <xalbert at iqfr.csic.es>; phenixbb at phenix-online.org
Subject: Re: [phenixbb] Number of unique reflections

Hi Armando,

> We have realise that the output  mtz and mmcif files duplicate the 
> number of miller indices (the number of unique reflections) with 
> respect to those in the mtz input file. We guessed that this 
> correspond to the friedel pairs,

data handling machinery in Phenix (cctbx) counts F+ and F- as separately,
that is (1, 1, 2) and (-1, -1, -2) are two entries, not one.

> but it is annoying for pdb submission, as the server warns that the
observations measured are less that those used in the refinement.
> What shall we do fro correct this issue?

Perhaps talk to PDB stuff and suggest to make the process less annoying...

I'm not sure what we can do at our end. I guess if we count them as one then
I'm sure some one will come around asking 'why you are counting two
reflections as one?'.


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