Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Dom Bellini]

Hi Clemens,

I was aware of these possibilities with autoprocess and buster combination but 
this is a very neat and useful explanation, many thanks. 

The case I’m dealing most often these days with our users is when the raw data 
are from staraniso (ie mmcif available) and the refined mtz is from 
phenix.refine (mtz). 

I usually use the mtz from staraniso rather than the mmcif file to combine it 
with the mtz from phenix.refine using CAD, and then I submit the result to PDB. 
But I would like to know if there is a better or more correct way to go around 
this. 

Many thanks,

D





> On 17 Jan 2022, at 09:07, Clemens Vonrhein  wrote:
> 
> Dear Dom,
> 
>> On Fri, Jan 14, 2022 at 10:56:32PM +, Dom Bellini wrote:
>> Thanks for your inputs. I wonder why the PDB doesn’t allow to submit
>> two separate mtz files,
> 
> Ideally, these would actually be mmCIF files since MTZ files (1) can not hold
> all meta data a PDBx/mmCIF compatible file could potentially carry and (2) it
> will require a conversion after upload. Of course, if your 
> processing/refinement
> software doesn't produce mmCIF files you are limited to that format and the
> online tool Marcin mentioned is probably the best way to go.
> 
>> one from data processing and one from refinement with map
>> coefficients.
> 
> If your processing and refinement package produces mmCIF files directly, it
> would be best to take them as-is into deposition.
> 
> As an example, the combination autoPROC [1] and BUSTER [2] allows for this 
> [3]:
> taking the mmCIF file from data processing (including scaled merged and 
> unmerged
> data with enriched meta data and full data quality metrics) plus the mmCIF 
> file
> from refinement (including map coefficients in various forms) and combining 
> them
> via the aB_deposition_combine command (which takes care of alternative 
> indexing,
> test-set flags etc, since it might not be just a case of concatenating ASCII
> mmCIF files together). This should work in creating a full reflection mmCIF 
> with
> all relevant types of reflection data.
> 
> There are probably similar systems in place to achieve something very similar 
> in
> other packages.
> 
> Cheers
> 
> Clemens
> 
> [1] https://www.globalphasing.com/autoproc
> [2] https://www.globalphasing.com/buster
> [3] https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Clemens Vonrhein]

Dear Dom,

On Fri, Jan 14, 2022 at 10:56:32PM +, Dom Bellini wrote:
> Thanks for your inputs. I wonder why the PDB doesn’t allow to submit
> two separate mtz files,

Ideally, these would actually be mmCIF files since MTZ files (1) can not hold
all meta data a PDBx/mmCIF compatible file could potentially carry and (2) it
will require a conversion after upload. Of course, if your processing/refinement
software doesn't produce mmCIF files you are limited to that format and the
online tool Marcin mentioned is probably the best way to go.

> one from data processing and one from refinement with map
> coefficients.

If your processing and refinement package produces mmCIF files directly, it
would be best to take them as-is into deposition.

As an example, the combination autoPROC [1] and BUSTER [2] allows for this [3]:
taking the mmCIF file from data processing (including scaled merged and unmerged
data with enriched meta data and full data quality metrics) plus the mmCIF file
from refinement (including map coefficients in various forms) and combining them
via the aB_deposition_combine command (which takes care of alternative indexing,
test-set flags etc, since it might not be just a case of concatenating ASCII
mmCIF files together). This should work in creating a full reflection mmCIF with
all relevant types of reflection data.

There are probably similar systems in place to achieve something very similar in
other packages.

Cheers

Clemens

[1] https://www.globalphasing.com/autoproc
[2] https://www.globalphasing.com/buster
[3] https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Dom Bellini]

Hi Marcin,

Thanks for your inputs. I wonder why the PDB doesn’t allow to submit two 
separate mtz files, one from data processing and one from refinement with map 
coefficients. It would be very straightforward for depositions. I guess there 
must be a valid reason for not allowing that.  

BW,

D






> On 14 Jan 2022, at 18:52, Marcin Wojdyr  wrote:
> 
> Then I'm afraid you'd need to first use CAD to combine both mtz files
> (merged intensities and map coefficients) into one merged mtz file.
> Or perhaps there is a better way - I don't know. Perhaps ccp4i2 and
> Ccp4 Cloud can combine MTZ files.
> 
> I'll think about supporting multiple merged MTZs in mxdepo.html in the future.
> 
> Best,
> Marcin
> 
>> On Fri, 14 Jan 2022 at 17:42, Dom Bellini - MRC LMB
>>  wrote:
>> 
>> Hi Marcin,
>> 
>> This is very helpful, thanks a lot. Ezra and Jasmine from wwPDB have
>> also replied just to me that they will send me a work around asap; if it
>> will differ from your method I will post it.
>> 
>> Can I please also ask you would be the best way to proceed if I would
>> like to combine, as well as the merged data used for refinement and the
>> unmerged mtz file, also the mtz output from the refinement software
>> containing the map coefficients?
>> 
>> Many thanks,
>> 
>> D
>> 
>>> On 14/01/2022 16:32, Marcin Wojdyr wrote:
>>> Dear Dom,
>>> 
>>> you can upload only a single data file to OneDep.
>>> Currently, if you want to deposit unmerged data with extensions
>>> introduced in 2021 (importantly, these extensions include image
>>> numbers and rotation angles) and if the software that you use doesn't
>>> output such ready-to-use files, you need to first input two files:
>>> - merged data that was used for refinement (MTZ or mmCIF)
>>> - scaled unmerged data (MTZ or XDS_ASCII)
>>> to this converter:
>>> https://project-gemmi.github.io/wasm/mxdepo.html
>>> and then you can upload the resulting cif file to the wwPDB deposition 
>>> system.
>>> 
>>> Best wishes
>>> Marcin
>>> 
>>> On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB
>>>  wrote:
 Dear Jasmine,
 
 But can we now upload two mtz/mmcif files now for the structure factors? 
 as in, the one from the processing software containing the raw data, as 
 well as the one with the weighted amplitudes and the phases from 
 Refinement software? Or do we still have to use CAD to create a single mtz 
 file and then convert it to mmcif for depostion? Or is there another 
 better way to do it?
 
 Many thanks for your help,
 
 Dom
 
 
 
 
 On 13/01/2022 19:19, Jasmine Young wrote:
 
 Dear all,
 
 Extensions to the PDBx/mmCIF dictionary for reflection data with 
 anisotropic diffraction limits, for unmerged reflection data, and for 
 quality metrics of anomalous diffraction data are now supported in OneDep.
 
 In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was 
 convened to develop a richer description of experimental data and 
 associated data quality metrics. Members of this Data Collection and 
 Processing Subgroup are all actively engaged in development and support of 
 diffraction data processing software. The Subgroup met virtually for 
 several months discussing, reviewing, and finalizing a new set dictionary 
 content extension that were incorporated into the PDBx/mmCIF dictionary on 
 February 16, 2021. A reference implementation of the new content 
 extensions has been developed by Global Phasing Ltd.
 
 These extensions facilitate the deposition and archiving of a broader 
 range of diffraction data, as well as new quality metrics pertaining to 
 these data. These extensions cover three main areas:
 
 scaled and merged reflection data that have been processed to take account 
 of diffraction anisotropy, by providing descriptors for that anisotropy, 
 in terms of (1) a parameter-free definition of a cut-off surface by means 
 of a per-reflection “signal” and a threshold value for that signal, and 
 (2) the ellipsoid providing the best fit to the resulting cut-off surface;
 scaled and unmerged reflection data, by providing extra item definitions 
 aimed at ensuring that such data can be meaningfully re-analysed, and 
 their quality assessed independently from the associated model, after 
 retrieval from the archive;
 anomalous diffraction data, by adding descriptors for numerous relevant, 
 but previously missing, statistics.
 
 The new mmCIF data extensions describing anisotropic diffraction now 
 enable archiving of the results of Global Phasing’s STARANISO program. 
 Developers of other software can make use of them or extend the present 
 definitions to suit their applications. Example files created by autoPROC, 
 BUSTER (version 20210224) and Gemmi that are compliant with the new 
 dictionary extensions are provided in a 

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Marcin Wojdyr]

Then I'm afraid you'd need to first use CAD to combine both mtz files
(merged intensities and map coefficients) into one merged mtz file.
Or perhaps there is a better way - I don't know. Perhaps ccp4i2 and
Ccp4 Cloud can combine MTZ files.

I'll think about supporting multiple merged MTZs in mxdepo.html in the future.

Best,
Marcin

On Fri, 14 Jan 2022 at 17:42, Dom Bellini - MRC LMB
 wrote:
>
> Hi Marcin,
>
> This is very helpful, thanks a lot. Ezra and Jasmine from wwPDB have
> also replied just to me that they will send me a work around asap; if it
> will differ from your method I will post it.
>
> Can I please also ask you would be the best way to proceed if I would
> like to combine, as well as the merged data used for refinement and the
> unmerged mtz file, also the mtz output from the refinement software
> containing the map coefficients?
>
> Many thanks,
>
> D
>
> On 14/01/2022 16:32, Marcin Wojdyr wrote:
> > Dear Dom,
> >
> > you can upload only a single data file to OneDep.
> > Currently, if you want to deposit unmerged data with extensions
> > introduced in 2021 (importantly, these extensions include image
> > numbers and rotation angles) and if the software that you use doesn't
> > output such ready-to-use files, you need to first input two files:
> > - merged data that was used for refinement (MTZ or mmCIF)
> > - scaled unmerged data (MTZ or XDS_ASCII)
> > to this converter:
> > https://project-gemmi.github.io/wasm/mxdepo.html
> > and then you can upload the resulting cif file to the wwPDB deposition 
> > system.
> >
> > Best wishes
> > Marcin
> >
> > On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB
> >  wrote:
> >> Dear Jasmine,
> >>
> >> But can we now upload two mtz/mmcif files now for the structure factors? 
> >> as in, the one from the processing software containing the raw data, as 
> >> well as the one with the weighted amplitudes and the phases from 
> >> Refinement software? Or do we still have to use CAD to create a single mtz 
> >> file and then convert it to mmcif for depostion? Or is there another 
> >> better way to do it?
> >>
> >> Many thanks for your help,
> >>
> >> Dom
> >>
> >>
> >>
> >>
> >> On 13/01/2022 19:19, Jasmine Young wrote:
> >>
> >> Dear all,
> >>
> >> Extensions to the PDBx/mmCIF dictionary for reflection data with 
> >> anisotropic diffraction limits, for unmerged reflection data, and for 
> >> quality metrics of anomalous diffraction data are now supported in OneDep.
> >>
> >> In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was 
> >> convened to develop a richer description of experimental data and 
> >> associated data quality metrics. Members of this Data Collection and 
> >> Processing Subgroup are all actively engaged in development and support of 
> >> diffraction data processing software. The Subgroup met virtually for 
> >> several months discussing, reviewing, and finalizing a new set dictionary 
> >> content extension that were incorporated into the PDBx/mmCIF dictionary on 
> >> February 16, 2021. A reference implementation of the new content 
> >> extensions has been developed by Global Phasing Ltd.
> >>
> >> These extensions facilitate the deposition and archiving of a broader 
> >> range of diffraction data, as well as new quality metrics pertaining to 
> >> these data. These extensions cover three main areas:
> >>
> >> scaled and merged reflection data that have been processed to take account 
> >> of diffraction anisotropy, by providing descriptors for that anisotropy, 
> >> in terms of (1) a parameter-free definition of a cut-off surface by means 
> >> of a per-reflection “signal” and a threshold value for that signal, and 
> >> (2) the ellipsoid providing the best fit to the resulting cut-off surface;
> >> scaled and unmerged reflection data, by providing extra item definitions 
> >> aimed at ensuring that such data can be meaningfully re-analysed, and 
> >> their quality assessed independently from the associated model, after 
> >> retrieval from the archive;
> >> anomalous diffraction data, by adding descriptors for numerous relevant, 
> >> but previously missing, statistics.
> >>
> >> The new mmCIF data extensions describing anisotropic diffraction now 
> >> enable archiving of the results of Global Phasing’s STARANISO program. 
> >> Developers of other software can make use of them or extend the present 
> >> definitions to suit their applications. Example files created by autoPROC, 
> >> BUSTER (version 20210224) and Gemmi that are compliant with the new 
> >> dictionary extensions are provided in a GitHub repository.
> >>
> >> These example files, and similarly compliant files produced by other data 
> >> processing and/or refinement programs, are suitable for direct uploading 
> >> to the wwPDB OneDep system. Automatic recognition of that compliance, 
> >> implemented by means of explicit dictionary versioning using the new 
> >> pdbx_audit_conform record, will avoid unnecessary pre-processing at the 
> >> time of 

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Dom Bellini - MRC LMB]

Hi Marcin,

This is very helpful, thanks a lot. Ezra and Jasmine from wwPDB have 
also replied just to me that they will send me a work around asap; if it 
will differ from your method I will post it.


Can I please also ask you would be the best way to proceed if I would 
like to combine, as well as the merged data used for refinement and the 
unmerged mtz file, also the mtz output from the refinement software 
containing the map coefficients?


Many thanks,

D

On 14/01/2022 16:32, Marcin Wojdyr wrote:

Dear Dom,

you can upload only a single data file to OneDep.
Currently, if you want to deposit unmerged data with extensions
introduced in 2021 (importantly, these extensions include image
numbers and rotation angles) and if the software that you use doesn't
output such ready-to-use files, you need to first input two files:
- merged data that was used for refinement (MTZ or mmCIF)
- scaled unmerged data (MTZ or XDS_ASCII)
to this converter:
https://project-gemmi.github.io/wasm/mxdepo.html
and then you can upload the resulting cif file to the wwPDB deposition system.

Best wishes
Marcin

On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB
 wrote:

Dear Jasmine,

But can we now upload two mtz/mmcif files now for the structure factors? as in, 
the one from the processing software containing the raw data, as well as the 
one with the weighted amplitudes and the phases from Refinement software? Or do 
we still have to use CAD to create a single mtz file and then convert it to 
mmcif for depostion? Or is there another better way to do it?

Many thanks for your help,

Dom




On 13/01/2022 19:19, Jasmine Young wrote:

Dear all,

Extensions to the PDBx/mmCIF dictionary for reflection data with anisotropic 
diffraction limits, for unmerged reflection data, and for quality metrics of 
anomalous diffraction data are now supported in OneDep.

In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was convened 
to develop a richer description of experimental data and associated data 
quality metrics. Members of this Data Collection and Processing Subgroup are 
all actively engaged in development and support of diffraction data processing 
software. The Subgroup met virtually for several months discussing, reviewing, 
and finalizing a new set dictionary content extension that were incorporated 
into the PDBx/mmCIF dictionary on February 16, 2021. A reference implementation 
of the new content extensions has been developed by Global Phasing Ltd.

These extensions facilitate the deposition and archiving of a broader range of 
diffraction data, as well as new quality metrics pertaining to these data. 
These extensions cover three main areas:

scaled and merged reflection data that have been processed to take account of 
diffraction anisotropy, by providing descriptors for that anisotropy, in terms 
of (1) a parameter-free definition of a cut-off surface by means of a 
per-reflection “signal” and a threshold value for that signal, and (2) the 
ellipsoid providing the best fit to the resulting cut-off surface;
scaled and unmerged reflection data, by providing extra item definitions aimed 
at ensuring that such data can be meaningfully re-analysed, and their quality 
assessed independently from the associated model, after retrieval from the 
archive;
anomalous diffraction data, by adding descriptors for numerous relevant, but 
previously missing, statistics.

The new mmCIF data extensions describing anisotropic diffraction now enable 
archiving of the results of Global Phasing’s STARANISO program. Developers of 
other software can make use of them or extend the present definitions to suit 
their applications. Example files created by autoPROC, BUSTER (version 
20210224) and Gemmi that are compliant with the new dictionary extensions are 
provided in a GitHub repository.

These example files, and similarly compliant files produced by other data 
processing and/or refinement programs, are suitable for direct uploading to the 
wwPDB OneDep system. Automatic recognition of that compliance, implemented by 
means of explicit dictionary versioning using the new pdbx_audit_conform 
record, will avoid unnecessary pre-processing at the time of deposition. This 
improved OneDep support will ensure a lossless round trip between data 
processing/refinement in the lab and deposition at the PDB.

wwPDB strongly encourages structural biologists to always use the latest 
versions of structure determination software packages to produce data files for 
PDB deposition. wwPDB also encourages crystallographers wishing to deposit new 
structures together with their associated diffraction data to use the software 
which guarantees consistency between data and final model. This consistency is 
difficult to achieve when separate diffraction data files and model coordinate 
files are pieced together a posteriori by ad hoc means.

wwPDB also encourages depositors to make their raw diffraction images available 
from one of the public 

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Marcin Wojdyr]

Dear Dom,

you can upload only a single data file to OneDep.
Currently, if you want to deposit unmerged data with extensions
introduced in 2021 (importantly, these extensions include image
numbers and rotation angles) and if the software that you use doesn't
output such ready-to-use files, you need to first input two files:
- merged data that was used for refinement (MTZ or mmCIF)
- scaled unmerged data (MTZ or XDS_ASCII)
to this converter:
https://project-gemmi.github.io/wasm/mxdepo.html
and then you can upload the resulting cif file to the wwPDB deposition system.

Best wishes
Marcin

On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB
 wrote:
>
> Dear Jasmine,
>
> But can we now upload two mtz/mmcif files now for the structure factors? as 
> in, the one from the processing software containing the raw data, as well as 
> the one with the weighted amplitudes and the phases from Refinement software? 
> Or do we still have to use CAD to create a single mtz file and then convert 
> it to mmcif for depostion? Or is there another better way to do it?
>
> Many thanks for your help,
>
> Dom
>
>
>
>
> On 13/01/2022 19:19, Jasmine Young wrote:
>
> Dear all,
>
> Extensions to the PDBx/mmCIF dictionary for reflection data with anisotropic 
> diffraction limits, for unmerged reflection data, and for quality metrics of 
> anomalous diffraction data are now supported in OneDep.
>
> In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was 
> convened to develop a richer description of experimental data and associated 
> data quality metrics. Members of this Data Collection and Processing Subgroup 
> are all actively engaged in development and support of diffraction data 
> processing software. The Subgroup met virtually for several months 
> discussing, reviewing, and finalizing a new set dictionary content extension 
> that were incorporated into the PDBx/mmCIF dictionary on February 16, 2021. A 
> reference implementation of the new content extensions has been developed by 
> Global Phasing Ltd.
>
> These extensions facilitate the deposition and archiving of a broader range 
> of diffraction data, as well as new quality metrics pertaining to these data. 
> These extensions cover three main areas:
>
> scaled and merged reflection data that have been processed to take account of 
> diffraction anisotropy, by providing descriptors for that anisotropy, in 
> terms of (1) a parameter-free definition of a cut-off surface by means of a 
> per-reflection “signal” and a threshold value for that signal, and (2) the 
> ellipsoid providing the best fit to the resulting cut-off surface;
> scaled and unmerged reflection data, by providing extra item definitions 
> aimed at ensuring that such data can be meaningfully re-analysed, and their 
> quality assessed independently from the associated model, after retrieval 
> from the archive;
> anomalous diffraction data, by adding descriptors for numerous relevant, but 
> previously missing, statistics.
>
> The new mmCIF data extensions describing anisotropic diffraction now enable 
> archiving of the results of Global Phasing’s STARANISO program. Developers of 
> other software can make use of them or extend the present definitions to suit 
> their applications. Example files created by autoPROC, BUSTER (version 
> 20210224) and Gemmi that are compliant with the new dictionary extensions are 
> provided in a GitHub repository.
>
> These example files, and similarly compliant files produced by other data 
> processing and/or refinement programs, are suitable for direct uploading to 
> the wwPDB OneDep system. Automatic recognition of that compliance, 
> implemented by means of explicit dictionary versioning using the new 
> pdbx_audit_conform record, will avoid unnecessary pre-processing at the time 
> of deposition. This improved OneDep support will ensure a lossless round trip 
> between data processing/refinement in the lab and deposition at the PDB.
>
> wwPDB strongly encourages structural biologists to always use the latest 
> versions of structure determination software packages to produce data files 
> for PDB deposition. wwPDB also encourages crystallographers wishing to 
> deposit new structures together with their associated diffraction data to use 
> the software which guarantees consistency between data and final model. This 
> consistency is difficult to achieve when separate diffraction data files and 
> model coordinate files are pieced together a posteriori by ad hoc means.
>
> wwPDB also encourages depositors to make their raw diffraction images 
> available from one of the public repositories to allow direct access to the 
> original diffraction image data.
>
>
> --
> Regards,
>
> Jasmine
>
> ===
> Jasmine Young, Ph.D.
> Biocuration Team Lead
> RCSB Protein Data Bank
> Research Professor
> Institute for Quantitative Biomedicine
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Rd
> 

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Dom Bellini - MRC LMB]

Dear Jasmine,

But can we now upload two mtz/mmcif files now for the structure factors? 
as in, the one from the processing software containing the raw data, as 
well as the one with the weighted amplitudes and the phases from 
Refinement software? Or do we still have to use CAD to create a single 
mtz file and then convert it to mmcif for depostion? Or is there another 
better way to do it?


Many thanks for your help,

Dom




On 13/01/2022 19:19, Jasmine Young wrote:


Dear all,

Extensions to the PDBx/mmCIF dictionary for reflection data with 
anisotropic diffraction limits, for unmerged reflection data, and for 
quality metrics of anomalous diffraction data are now supported in OneDep.


In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group 
 was convened to develop a richer 
description of experimental data and associated data quality metrics. 
Members of this Data Collection and Processing Subgroup are all 
actively engaged in development and support of diffraction data 
processing software. The Subgroup met virtually for several months 
discussing, reviewing, and finalizing a new set dictionary content 
extension that were incorporated into the PDBx/mmCIF dictionary 
 on 
February 16, 2021. A reference implementation of the new content 
extensions has been developed by Global Phasing Ltd. 



These extensions facilitate the deposition and archiving of a broader 
range of diffraction data, as well as new quality metrics pertaining 
to these data. These extensions cover three main areas:


 1. scaled and merged reflection data that have been processed to take
account of diffraction anisotropy, by providing descriptors for
that anisotropy, in terms of (1) a parameter-free definition of a
cut-off surface by means of a per-reflection “signal” and a
threshold value for that signal, and (2) the ellipsoid providing
the best fit to the resulting cut-off surface;
 2. scaled and unmerged reflection data, by providing extra item
definitions aimed at ensuring that such data can be meaningfully
re-analysed, and their quality assessed independently from the
associated model, after retrieval from the archive;
 3. anomalous diffraction data, by adding descriptors for numerous
relevant, but previously missing, statistics.

The new mmCIF data extensions describing anisotropic diffraction now 
enable archiving of the results of Global Phasing’s STARANISO program. 
Developers of other software can make use of them or extend the 
present definitions to suit their applications. Example files created 
by autoPROC, BUSTER (version 20210224 
) 
and Gemmi that are compliant with the new dictionary extensions are 
provided in a GitHub repository 
.


These example files, and similarly compliant files produced by other 
data processing and/or refinement programs, are suitable for direct 
uploading to the wwPDB OneDep system. Automatic recognition of that 
compliance, implemented by means of explicit dictionary versioning 
using the new pdbx_audit_conform record, will avoid unnecessary 
pre-processing at the time of deposition. This improved OneDep support 
will ensure a lossless round trip between data processing/refinement 
in the lab and deposition at the PDB.


wwPDB strongly encourages structural biologists to always use the 
latest versions of structure determination software packages to 
produce data files for PDB deposition. wwPDB also encourages 
crystallographers wishing to deposit new structures together with 
their associated diffraction data to use the software which guarantees 
consistency between data and final model. This consistency is 
difficult to achieve when separate diffraction data files and model 
coordinate files are pieced together /a posterior/i by /ad hoc/ means.


wwPDB also encourages depositors to make their raw diffraction images 
available from one of the public repositories 
 to allow direct access to 
the original diffraction image data.



--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 

[ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

[Jasmine Young]

Dear all,

Extensions to the PDBx/mmCIF dictionary for reflection data with 
anisotropic diffraction limits, for unmerged reflection data, and for 
quality metrics of anomalous diffraction data are now supported in OneDep.


In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group 
 was convened to develop a richer 
description of experimental data and associated data quality metrics. 
Members of this Data Collection and Processing Subgroup are all actively 
engaged in development and support of diffraction data processing 
software. The Subgroup met virtually for several months discussing, 
reviewing, and finalizing a new set dictionary content extension that 
were incorporated into the PDBx/mmCIF dictionary 
 on 
February 16, 2021. A reference implementation of the new content 
extensions has been developed by Global Phasing Ltd. 



These extensions facilitate the deposition and archiving of a broader 
range of diffraction data, as well as new quality metrics pertaining to 
these data. These extensions cover three main areas:


1. scaled and merged reflection data that have been processed to take
   account of diffraction anisotropy, by providing descriptors for that
   anisotropy, in terms of (1) a parameter-free definition of a cut-off
   surface by means of a per-reflection “signal” and a threshold value
   for that signal, and (2) the ellipsoid providing the best fit to the
   resulting cut-off surface;
2. scaled and unmerged reflection data, by providing extra item
   definitions aimed at ensuring that such data can be meaningfully
   re-analysed, and their quality assessed independently from the
   associated model, after retrieval from the archive;
3. anomalous diffraction data, by adding descriptors for numerous
   relevant, but previously missing, statistics.

The new mmCIF data extensions describing anisotropic diffraction now 
enable archiving of the results of Global Phasing’s STARANISO program. 
Developers of other software can make use of them or extend the present 
definitions to suit their applications. Example files created by 
autoPROC, BUSTER (version 20210224 
) 
and Gemmi that are compliant with the new dictionary extensions are 
provided in a GitHub repository 
.


These example files, and similarly compliant files produced by other 
data processing and/or refinement programs, are suitable for direct 
uploading to the wwPDB OneDep system. Automatic recognition of that 
compliance, implemented by means of explicit dictionary versioning using 
the new pdbx_audit_conform record, will avoid unnecessary pre-processing 
at the time of deposition. This improved OneDep support will ensure a 
lossless round trip between data processing/refinement in the lab and 
deposition at the PDB.


wwPDB strongly encourages structural biologists to always use the latest 
versions of structure determination software packages to produce data 
files for PDB deposition. wwPDB also encourages crystallographers 
wishing to deposit new structures together with their associated 
diffraction data to use the software which guarantees consistency 
between data and final model. This consistency is difficult to achieve 
when separate diffraction data files and model coordinate files are 
pieced together /a posterior/i by /ad hoc/ means.


wwPDB also encourages depositors to make their raw diffraction images 
available from one of the public repositories 
 to allow direct access to 
the original diffraction image data.



--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Improved support for extended PDBx/mmCIF structure factor files in OneDep

[Jasmine Young]

Extensions to the PDBx/mmCIF dictionary for reflection data with 
anisotropic diffraction limits, for unmerged reflection data, and for 
quality metrics of anomalous diffraction data are now supported in OneDep.


In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group 
 was convened to develop a richer 
description of experimental data and associated data quality metrics. 
Members of this Data Collection and Processing Subgroup are all actively 
engaged in development and support of diffraction data processing 
software. The Subgroup met virtually for several months discussing, 
reviewing, and finalizing a new set dictionary content extension that 
were incorporated into the PDBx/mmCIF dictionary 
 on 
February 16, 2021. A reference implementation of the new content 
extensions has been developed by Global Phasing Ltd. 



These extensions facilitate the deposition and archiving of a broader 
range of diffraction data, as well as new quality metrics pertaining to 
these data. These extensions cover three main areas:


1. scaled and merged reflection data that have been processed to take
   account of diffraction anisotropy, by providing descriptors for that
   anisotropy, in terms of (1) a parameter-free definition of a cut-off
   surface by means of a per-reflection “signal” and a threshold value
   for that signal, and (2) the ellipsoid providing the best fit to the
   resulting cut-off surface;
2. scaled and unmerged reflection data, by providing extra item
   definitions aimed at ensuring that such data can be meaningfully
   re-analysed, and their quality assessed independently from the
   associated model, after retrieval from the archive;
3. anomalous diffraction data, by adding descriptors for numerous
   relevant, but previously missing, statistics.

The new mmCIF data extensions describing anisotropic diffraction now 
enable archiving of the results of Global Phasing’s STARANISO program. 
Developers of other software can make use of them or extend the present 
definitions to suit their applications. Example files created by 
autoPROC, BUSTER (version 20210224 
) 
and Gemmi that are compliant with the new dictionary extensions are 
provided in a GitHub repository 
.


These example files, and similarly compliant files produced by other 
data processing and/or refinement programs, are suitable for direct 
uploading to the wwPDB OneDep system. Automatic recognition of that 
compliance, implemented by means of explicit dictionary versioning using 
the new pdbx_audit_conform record, will avoid unnecessary pre-processing 
at the time of deposition. This improved OneDep support will ensure a 
lossless round trip between data processing/refinement in the lab and 
deposition at the PDB.


wwPDB strongly encourages structural biologists to always use the latest 
versions of structure determination software packages to produce data 
files for PDB deposition. wwPDB also encourages crystallographers 
wishing to deposit new structures together with their associated 
diffraction data to use the software which guarantees consistency 
between data and final model. This consistency is difficult to achieve 
when separate diffraction data files and model coordinate files are 
pieced together /a posterior/i by /ad hoc/ means.


wwPDB also encourages depositors to make their raw diffraction images 
available from one of the public repositories 
 to allow direct access to 
the original diffraction image data.





--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/