[ccp4bb] Postdoctoral Position - Ohio State University

[krish]

Dear All,



Applications are invited for a joint postdoctoral scientist position in the
laboratories of Dr. Sarah Heissler and Dr. Krishna Chinthalapudi at the
Ohio State University. The research project focuses on understanding the
role of myosin motors and other cytoskeletal proteins in health and
disease. We combine state-of-the-art structural biology approaches
including X-ray crystallography and cryo-EM with biochemical, biophysical
and cell biological methods to investigate how protein structure is related
to its function. Our laboratories are equipped with state-of-the-art
instrumentation for the proposed studies and have generous access to a
Titan Krios G3i Cryo-TEM equipped with a bioquantum imaging filter and a K3
direct electron detector, imaging phase plates, STEM/TEM tomography, and an
image spherical aberration corrector. In addition, our labs have access to
a Glacios with a falcon III detector and Ceta-D camera for MicroED analysis
at the world-class Center for Electron Microscopy and Analysis (CEMAS) at
the Ohio State University.



Selected examples of our work include:



Heissler SM, Arora AS, Billington N, Sellers JR, Chinthalapudi K. Cryo-EM
structure of the autoinhibited state of myosin-2. Sci Adv. 2021 Dec
24;7(52):eabk3273. doi: 10.1126/sciadv.abk3273.



Chinthalapudi K, Heissler SM, Preller M, Sellers JR, Manstein DJ.
Mechanistic insights into the active site and allosteric communication
pathways in human nonmuscle myosin-2C. Elife. 2017 Dec 19;6:e32742. doi:
10.7554/eLife.32742.



Candidates must have (or will be shortly awarded) a Ph.D. degree and strong
practical experience in biochemistry and structural biology. Experiences
with molecular biology techniques, protein expression and purification,
cell biology and/or high-resolution imaging are desirable.



For more information, please contact us and/or visit our lab websites.



https://medicine.osu.edu/find-faculty/non-clinical/physiology-and-cell-biology/sarah-heissler



https://medicine.osu.edu/find-faculty/non-clinical/physiology-and-cell-biology/krishna-chinthalapudi



To be considered for this position, please email your curriculum vitae, a
short cover letter with research experience and interests and contact
information for three references to Sarah Heissler (sarah.heiss...@osumc.edu)
and Krishna Chinthalapudi (krishna.chinthalap...@osumc.edu).



Thank you,

Sarah & Krishna



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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] Updating Ubuntu 18 LTS to 20?

[Jim Fairman]

Hi Domen,

I have been running 20.04 for quite some time now without any issues.  In
my experience, performing in-place upgrades from a previous version (eg:
14.04 to 16.04, 16.04 to 18.04) caused some issues and I usually ended up
having to wipe the system and perform fresh installs, but your mileage may
vary.  My standard operating procedure is to backup your home directory and
any important files and perform a fresh install.

The rolling release distributions like Arch and Manjaro avoid the issues of
having to perform upgrades across major versions, but always running the
"latest" packages may sometimes cause issues.  However, I haven't found
this in my usage of them over the past 4 or 5 years.

Cheers, Jim
--
Jim Fairman
C: 1-240-479-6575


On Fri, Jan 14, 2022 at 1:00 PM Domen Zafred  wrote:

> Hi all,
>
> has anyone updated the Ubuntu 18.04 LTS Bionic Beaver to the never 20.04?
> That means with programs we usually have installed (java, phython, xds,
> ccp4 & coot, phenix, R, data warrior, pymol, nomacine, etc)? Any troubles,
> recommendations?
> 22 LTS is coming out this year, I'm not sure if jumping from 18 to 22
> would be a good idea, but 18 is getting old.
>
> Thanks for any hints
>
> Domen
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Updating Ubuntu 18 LTS to 20?

[Domen Zafred]

Hi all,

has anyone updated the Ubuntu 18.04 LTS Bionic Beaver to the never 20.04?
That means with programs we usually have installed (java, phython, xds,
ccp4 & coot, phenix, R, data warrior, pymol, nomacine, etc)? Any troubles,
recommendations?
22 LTS is coming out this year, I'm not sure if jumping from 18 to 22 would
be a good idea, but 18 is getting old.

Thanks for any hints

Domen



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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
> 

[ccp4bb] Postdoctoral research positions in structural biology

[Jon R Sayers]

HEADS UP (there will be an official announcement soon)

We are looking for two postdoctoral researchers to join
an exciting structure-based drug design project funded by the Bill
Gates foundation to develop inhibitors of a Plasmodium nuclease involved in
DNA replication.

One post requires a PDRA with proven experience in protein
structure determination by NMR.
The other requires a PDRA with experience in X-ray crystallography and
protein biochemistry.

This Sheffield University based project is supported by extensive Medicinal
Chemistry, ADME/PK and parasite testing resources from collaborators
arranged by the foundation.

The posts are for up to 18 months depending on how soon official
advertisements etc can be processed. The posts are both time sensitive. You
will join a group of three other PDRAs working on this project and an MCIF
fellow working on a related program in Trypanosomes. The NMR work will be
carried out in Prof. Jon Waltho's lab and crystallography is supervised by
Dr Pat Baker (both Sheffield).

The posts are both based in Sheffield, UK.


-- 
Professor Jon R Sayers, FRSB
Department of Infection, Immunity & Cardiovascular Disease
University of Sheffield Medical School
Beech Hill Rd
Sheffield
S10 2RX
United Kingdom

Tel: +44 (0)114 215 9552
Fax: +44 (0)114 271 1863
Email: j.r.say...@sheffield.ac.uk

https://www.sheffield.ac.uk/iicd/profiles/sayers




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Re: [ccp4bb] EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

[Marco MARCIA]

Dear all
a kind reminder about this course application deadline, which is 
approaching now in 2 weeks.

Regards
Marco



On 19/12/2021 16:11, Marco MARCIA wrote:

Dear all,
please take note of the EMBO course announced below and do not miss 
its application deadline (Jan 31st)!

Kind regards,
Marco Marcia


**
EMBO Practical Course on Characterization of macromolecular complexes 
by integrative structural biology

May 28 - Jun 04, 2022
EPN campus
Grenoble, France
https://meetings.embo.org/event/21-macromolecular-complexes

This course has been held biennially since 2002, and covers various 
topics that include methods for expressing and purifying complexes, 
characterizing them biophysically, and probing their structures. It is 
addressed to PhD students and postdocs interested in the structural 
biology of large multisubunit complexes.


Deadline for registration: 31 January 2022

We are looking forward to receiving your applications!
Marco

on behalf of the organizing committee: Marco Marcia, Montserrat Soler 
Lopez, Carlo Petosa, Trevor Forsyth, Daniele De Sanctis


*






--
Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)476207634
phone (office): 0033-(0)476207759
fax: 0033-(0)476207199
email: mmar...@embl.fr
web: https://embl.fr/research/unit/marcia/



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Re: [ccp4bb] Validation of structure prediction

[Alexandre Ourjoumtsev]

Hi, James, hi, everybody, 

somehow relevant to your, James, comments : 

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

if somebody missed, there is a couple of papers talking about a single / triple 
measure(s) of model quality : 

Shao et al ., 2017, Structure, 25, 458 

Brzezinski et al ., 2020, The FEBS Journal, 287, 2685 

Best regards, 

Sacha Urzhumtsev 

- Le 13 Jan 22, à 19:40, James Holton  a écrit : 

> 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 
>> |
>> 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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[ccp4bb] Staff Scientist opportunity in "Structural Proteomics" at Human Technopole in Milan, Italy

[Sebastiano Pasqualato]

Dear all,
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PS: sorry for the double posting in different bulletin boards


Sebastiano Pasqualato
Biophysics Platform Manager 







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