This came up on phnix BB recently:
On 10/20/2020 01:30 PM, John Berrisford wrote:
Dear Armando and Pavel
During the deposition process we compare two values
_reflns.number_obs
And
_refine.ls_number_reflns_obs
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.
On 10/20/2020 02:16 PM, Boaz Shaanan wrote:
Hi Pavel,
When I marked explicitly 'no ano' in the gui (whenever I didn't want to use
anomalous), this doubling on the output file was gone. As I recall it also
depends on the labels one chooses to use from the data file. This was on older
builds though.
Cheers,
Boaz
On 11/21/2020 02:42 PM, Igor Petrik wrote:
This may be a basic question, but a few google searches did not turn up
anything helpful.
I am trying to deposit a structure, from data reduced with HKL2000 and solved
and refined with Phenix. The data were scaled with the Anomalous option
selected.
For depositing, I upload the coordinates, the *_refine_data.mtz file from Phenix, and the *.log file
from HKL2000 scaling. When I do this, the PDB deposition website complains on the Data Collection
Statistics page that the "Number of unique reflections measured" (16343) "Has value
< Total number of reflections refined against (see Refinement page) [23562]"
When I open the original sca file in Phenix, I see:
Number of Miller indices: 31365
Bijvoet pairs: 15030
What is the correct way to reconcile these numbers for the deposition?
Thanks,
- Igor Petrik, PhD
P.S. I collected and processed the data 5+ years ago, and no longer have access
to HKL2000.
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