Hi Oliver
 and am I right that the deposition of Hendrickson-Lattman
coefficients is still allowed? If that is correct then I don't
understand what happened to mine in the case of 1e3h? That was
deposited with you at EBI so perhaps you can check back to the
pre-2013 version of the SF file for 1e3h and see if the HL
coefficients in that can be reformalized and appear for users of my
data.
 Thanks in advance.
  Best regards
  Martyn

Martyn Symmons
Cambridge

On Mon, Jan 25, 2016 at 4:03 PM, Oliver Smart <[log in to unmask]> wrote:
> Eze,
>
> I have recently taken responsibility for maintaining and extending the X-ray
> version of the wwPDB validation pipeline.
>
> On Thu, 21 Jan 2016 19:53:35 +0000, Eze Chivi wrote:
>
>> Hello, for deposition, "Reflection Data Used for Final Structure Refinement"
>> is submitted, this file corresponds to the input mtz used for refinement
>> (only F and SIGF).
>
> In the free set used should also be deposited. Please note that deposition of map
> coefficients is possible, but not routinely done.  Deposition of coefficients
> for the maps examined by the crystallographer after the final refinement is
> valuable.  The deposition of map coefficients has been discussed in
> the recently held wwPDB/CCDC/D3R Ligand Validation Workshop and
> wwPDB X-ray Validation Task Force that provides expert advice on
> "best" practice and is likely to be included in recommendations.
>
> Currently the validation pipeline/server does not make any use of such
> map information but it is possible that this might change in the future.
> Calculation of standardized ED maps and metrics using the same protocol/progra,
> for every entry will still be useful.
>
>> Therefore, the deposition server calculates the map to evaluate "Fit of model
>> and data". I've noted that validation runs differ in the number of RSRZ>2
>> when input or output mtz files (for refinement) are used, then I deduce that
>> refinement program and validation server differ in the treatment of some
>> parameters (bulk solvent, overall scaling?).
>
> Depending on the refinement program and options the output mtz file can
> contain a sub-set of the input structure factors. This might lie behind
> the differences you see?
>
>> Additionally, "How the map in the EDS server is calculated if map coefficient
>> are not submitted during deposition? I would appreciate further information
>> or clarification, thank you.
>
> As Robbie said please see http://eds.bmc.uu.se/eds/eds_help.html and the
> "Uppsala Electron-Density Server" paper: http://doi.org/csm35r .  The validation
> pipeline uses procedures that are based on EDS. We are currently working on improved
> documentation for the wwPDB validation report and server, including FAQs (like this one).
>
> Best regards,
>
> Oliver
>
> --
> Dr Oliver S. Smart, PDBe, EMBL-EBI, Hinxton, UK
> https://www.ebi.ac.uk/about/people/oliver-smart