[ccp4bb] Postdoctoral Positions

[Patel, Trushar]

Dear colleagues,

We have two positions available for postdoctoral researchers. Details can be 
found here - 
https://www.nature.com/naturecareers/job/postdoctoral-researcher-university-of-lethbridge-752362

If you require any additional information, please let me know.

Thank you and stay safe.

Trushar
--
Trushar R Patel, PhD
Associate Professor and Canada Research Chair (Tier II),
Laboratory of Medicinal Biophysics,
Dept. of Chemistry and Biochemistry, University of Lethbridge, Canada

Co-Founder and CEO, Quadrumix Biotechnology

https://trpatel.com

Our University’s Blackfoot name is Iniskim, meaning Sacred Buffalo Stone. The 
University of Lethbridge is located in Blackfoot Confederacy territory. We 
honour the Blackfoot people and their traditional ways of knowing in caring for 
this land, as well as all Aboriginal peoples who have helped shape and continue 
to strengthen our University community.





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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
===



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[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
===



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Re: [ccp4bb] Validation of structure prediction

[Tristan Croll]

Hard but not impossible - even when you *are* fitting to low-res density. See 
https://twitter.com/crolltristan/status/1381258326223290373?s=21 for example - 
no Ramachandran outliers, 1.3% sidechain outliers, clashscore of 2... yet 
multiple regions out of register by anywhere up to 15 residues! I never 
publicly named the structure (although I did share my rebuilt model with the 
authors), but the videos and images in that thread should be enough to 
illustrate the scale of the problem.

And that was *with* a map to fit! Take away the map, and run some MD energy 
minimisation (perhaps with added Ramachandran and rotamer restraints), and I 
think it would be easy to get your model to fool most “simple” validation 
metrics (please don’t actually do this). The upshot is that I still think 
validation of predicted models in the absence of at least moderate-resolution 
experimental data is still a major challenge requiring very careful thought.

— Tristan

On 13 Jan 2022, at 18:41, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

Agree with Pavel.

Something I think worth adding is a reminder that the MolProbity score only 
looks at bad clashes, ramachandran and rotamer outliers.

MPscore=0.426∗ln(1+clashscore)+0.33∗ln(1+max(0,rota_out−1))+0.25∗ln(1+max(0,rama_iffy−2))+0.5

 It pays no attention whatsoever to twisted peptide bonds, C-beta deviations, 
and, for that matter, bond lengths and bond angles. If you tweak your weights 
right you can get excellent MP scores, but horrible "geometry" in the 
traditional bonds-and-angles sense. The logic behind this kind of validation is 
that normally nonbonds and torsions are much softer than bond and angle 
restraints and therefore fertile ground for detecting problems.  Thus far, I am 
not aware of any "Grand Unified Score" that combines all geometric 
considerations, but perhaps it is time for one?

Tristan's trivial solution aside, it is actually very hard to make all the 
"geometry" ideal for a real-world fold, and especially difficult to do without 
also screwing up the agreement with density (R factor).  I would argue that if 
you don't have an R factor then you should get one, but I am interested in 
opinions about alternatives.

I.E. What if we could train an AI to predict Rfree by looking at the 
coordinates?

-James Holton
MAD Scientist

On 12/21/2021 9:25 AM, Pavel Afonine wrote:
Hi Reza,
If you think about it this way... Validation is making sure that the model 
makes sense, data make sense and model-to-data fit make sense, then the answer 
to your question is obvious: in your case you do not have experimental data (at 
least in a way we used to think of it) and so then of these three validation 
items you only have one, which, for example, means you don’t have to report 
things like R-factors or completeness in high-resolution shell.
Really, the geometry of an alpha helix does not depend on how you determined 
it: using X-rays or cryo-EM or something else! So, most (if not all) model 
validation tools still apply.
Pavel

On Mon, Dec 20, 2021 at 8:10 AM Reza Khayat 
mailto:rkha...@ccny.cuny.edu>> wrote:

Hi,

Can anyone suggest how to validate a predicted structure? Something similar to 
wwPDB validation without the need for refinement statistics. I realize this is 
a strange question given that the geometry of the model is anticipated to be 
fine if the structure was predicted by a server that minimizes the geometry to 
improve its statistics. Nonetheless, the journal has asked me for such a 
report. Thanks.

Best wishes,

Reza


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031



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Re: [ccp4bb] Validation of structure prediction

[James Holton]

Agree with Pavel.

Something I think worth adding is a reminder that the MolProbity score 
only looks at bad clashes, ramachandran and rotamer outliers.


MPscore=0.426∗ln(1+clashscore)+0.33∗ln(1+max(0,rota_out−1))+0.25∗ln(1+max(0,rama_iffy−2))+0.5

 It pays no attention whatsoever to twisted peptide bonds, C-beta 
deviations, and, for that matter, bond lengths and bond angles. If you 
tweak your weights right you can get excellent MP scores, but horrible 
"geometry" in the traditional bonds-and-angles sense. The logic behind 
this kind of validation is that normally nonbonds and torsions are much 
softer than bond and angle restraints and therefore fertile ground for 
detecting problems.  Thus far, I am not aware of any "Grand Unified 
Score" that combines all geometric considerations, but perhaps it is 
time for one?


Tristan's trivial solution aside, it is actually very hard to make all 
the "geometry" ideal for a real-world fold, and especially difficult to 
do without also screwing up the agreement with density (R factor).  I 
would argue that if you don't have an R factor then you should get one, 
but I am interested in opinions about alternatives.


I.E. What if we could train an AI to predict Rfree by looking at the 
coordinates?


-James Holton
MAD Scientist

On 12/21/2021 9:25 AM, Pavel Afonine wrote:

Hi Reza,

If you think about it this way... Validation is making sure that the 
model makes sense, data make sense and model-to-data fit make sense, 
then the answer to your question is obvious: in your case you do not 
have experimental data (at least in a way we used to think of it) and 
so then of these three validation items you only have one, which, for 
example, means you don’t have to report things like R-factors or 
completeness in high-resolution shell.


Really, the geometry of an alpha helix does not depend on how you 
determined it: using X-rays or cryo-EM or something else! So, most (if 
not all) model validation tools still apply.


Pavel


On Mon, Dec 20, 2021 at 8:10 AM Reza Khayat  wrote:

Hi,


Can anyone suggest how to validate a predicted structure?
Something similar to wwPDB validation without the need for
refinement statistics. I realize this is a strange question given
that the geometry of the model is anticipated to be fine if the
structure was predicted by a server that minimizes the geometry to
improve its statistics. Nonetheless, the journal has asked me for
such a report. Thanks.


Best wishes,

Reza


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031



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[ccp4bb] Structural Biology Position at Syngenta, Jealott's Hill

[Jenny Moore]

The team is looking for a motivated and independent structural biologist with Masters or PhD level qualifications, ideally having worked with a range of protein targets being soluble and/or membrane-bound. On a 2-year contract, this position is a great opportunity for scientists interested in an industrial career to gain practical industry experience, working on structural biology platform activities which would mostly be structure solution but also with the potential for construct design, protein _expression_, purification and biophysics depending on the project. Prior experience in structure solution by crystallography is essential, whilst the rest of the pipeline described above as well as other structure solution methods such as cryo-EM would be considered an advantage.
Main Responsibilities:

Provide guidance for construct design, _expression_ and purification, resulting in proteins suitable for crystallography
Characterize proteins intended for crystallization and carry out crystallization trials, crystal optimization and structure solution for proteins and protein-ligand complexes
Effectively communicate results through presentations, e-mails and reports, and actively participate in structure-based design efforts

Key Requirements:

PhD or MSc degree in structural biology or a related field
1-3 years experience in practical structure solution, ideally across a number of protein families

For any informal enquiries, please don't hesitate to get in touch with me (jenny.mo...@syngenta.com) and if you wish to apply, please find the link here - https://www.srgtalent.com/jobs/j2163326-structural-biologist





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[ccp4bb] Lectureship Position at University of Essex

[Prischi, Filippo]

Dear all,

We have a Lectureship (Teaching & Research permanent contract) position 
available in the School of Life Sciences at University of Essex. We encourage 
applicants with a skillset and research interest in structural biology, 
biochemistry, molecular biology and computational biology.
For more info and details on how to apply, please follow this link 
https://vacancies.essex.ac.uk/tlive_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=993552PJqA=9918109NEm=USA
Kind Regards,
Filippo

~~
Dr Filippo Prischi
Senior Lecturer in Biochemistry
School of Life Sciences
University of Essex

T.  +44 (0)1206 873370
E.  fpris...@essex.ac.uk
► http://www.essex.ac.uk/bs/staff/profile.aspx?ID=4512



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