Re: [ccp4bb] Depositing data reduced with HKL2000 - ~half as many reflections in log file statistics

2020-11-21 Thread Edward A. Berry 

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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Re: [ccp4bb] Depositing data reduced with HKL2000 - ~half as many reflections in log file statistics

2020-11-21 Thread Igor Petrik 
Thanks Jon,

> 23k used versus 31k Friedel pairs available

Actually this was a mistake on my part; I uploaded the wrong coordinates
and final mtz that don't correspond to this sca file. The correct
coordinates and mtz file that correspond to this sca file do contain 31k
reflections as well.

> just interested if there was a particular reason for that e.g. selenomet.

We work with metalloproteins and have found it best practice to retain the
anomalous signal.

> Can you just provide an explanation or does the web form not let you
proceed?

I haven't tried to just proceed. It was a big red error message, so I
assumed it had to be fixed, but maybe I can just explain it. I will fix the
deposition with the right coordinates and final mtz file, and try to
deposit.

- Igor Petrik, PhD

On Sat, Nov 21, 2020 at 12:27 PM Jon Cooper 
wrote:

> Hello,
>
> so the structure was presumably refined with F(+) and F(-) treated as
> separate observations. That's not a problem, but just interested if there
> was a particular reason for that e.g. selenomet., etc. It seems it hasn't
> used all the F(+)/(-) data for some reason (23k used versus 31k Friedel
> pairs available). Did you have to cut the resolution back somewhat in
> refinement? If so I can't see an obvious problem. Can you just provide an
> explanation or does the web form not let you proceed?
>
> Best wishes, Jon Cooper
>
>
>
>  Original Message 
> On 21 Nov 2020, 19:42, Igor Petrik < petr...@illinois.edu> 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.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>



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Re: [ccp4bb] Depositing data reduced with HKL2000 - ~half as many reflections in log file statistics

2020-11-21 Thread Jon Cooper 
Hello,

so the structure was presumably refined with F(+) and F(-) treated as separate 
observations. That's not a problem, but just interested if there was a 
particular reason for that e.g. selenomet., etc. It seems it hasn't used all 
the F(+)/(-) data for some reason (23k used versus 31k Friedel pairs 
available). Did you have to cut the resolution back somewhat in refinement? If 
so I can't see an obvious problem. Can you just provide an explanation or does 
the web form not let you proceed?

Best wishes, Jon Cooper

 Original Message 
On 21 Nov 2020, 19:42, 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.
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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[ccp4bb] Depositing data reduced with HKL2000 - ~half as many reflections in log file statistics

2020-11-21 Thread Igor Petrik 
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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