Dear Armando and Pavel During the deposition process we compare two values _reflns.number_obs http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number_ obs.html And _refine.ls_number_reflns_obs http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_numb er_reflns_obs.html 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 John -----Original Message----- From: [email protected] On Behalf Of Pavel Afonine Sent: 20 October 2020 18:16 To: Armando Albert ; [email protected] 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?'. Pavel _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]