[ccp4bb] Assistant Professor in cryoEM, University of Alberta

[M. Joanne Lemieux]

Dear colleagues,


We are hiring! See the link and details below regarding a faculty position
in our department. The applicant will take advantage of the exciting new
centre for cryo-electron microscopy at the University of Alberta - a new
Krios G4 is arriving in 2023. We have a vibrant and collaborative research
environment in our Department. Please see the link and details below:


To apply see: https://www.careers.ualberta.ca/Competition/A115548377/


Position summary

The Department of Biochemistry, Faculty of Medicine & Dentistry at the
University of Alberta, invites applications for an Assistant Professor
(tenure-track) in the area of structural biology and single particle
cryogenic electron microscopy.

The successful candidate is expected to establish an innovative research
program that will take advantage of the exciting new centre for
cryo-electron microscopy at the University of Alberta. The centre is being
established around a Titan Krios G4 and a Talos L120C. The applicant’s
research program will also be evaluated based on strategic linkages to
several areas of research strengths at the University including: cancer
biology; microbiology; virology; immunology; membrane protein structure and
function; enzymology; neurobiology; women and children’s health; drug
design. The position will have 75% committed time for research, 20% for
teaching and 5% for administration. The applicant will be expected to
contribute to the teaching of undergraduate and graduate students in one or
more areas of Biochemistry related to their expertise and research
strengths. Applicants are required to have a Ph.D. or equivalent degree in
biochemistry or a closely-related discipline, as well as post-doctoral
experience in the area of structural biology with significant experience in
cryo-EM.


Department summary

The Department of Biochemistry at the University of Alberta has strengths
in structural biology and biophysics, enzymology, membrane proteins, mass
spectrometry, systems biology, and cancer biology. The Department has
extensive state-of-the-art core facilities including X-ray crystallography,
NMR spectroscopy, mass spectrometry, biophysical instrumentation, as well
as cellular imaging facilities and other facilities for cellular and animal
model studies within the Faculty of Medicine & Dentistry. Of special
interest for this position is a new centre for cryoEM featuring Titan Krios
G4 and Talos L120C microscopes.

Joanne

**
M. Joanne Lemieux, Ph.D.
Professor
Director, Membrane Protein Disease Research Group
Department of Biochemistry
Member of LKSIOV, WCHRI, NMHI, CRINA, GlycoNet
College of Health Sciences
Faculty of Medicine & Dentistry
University of Alberta
Medical Sciences Bldg.
Office 4-53
Lab4-51
University of Alberta
Edmonton AB, T6G 2H7

office phone: 780-492-3586
lab phone:780-492-3465
fax: 780-492-0886

Lab web pages:
*https://lemieuxlab.biochem.ualberta.ca/
*
http://www2.biochem.ualberta.ca/LemieuxLab

Membrane Protein Disease Research Group:
http://www.mpdrg.com

*Upcoming meetings*
May 2023 (Calgary) : Biophysical Society of Canada
https://biophysicalsociety.ca/bsc-annual-meetings/upcoming-events/
Aug 2026 (Calgary): IUCr https://www.amercrystalassn.org/iucr-2026-calgary

The University of Alberta is located in ᐊᒥᐢᑿᒌᐚᐢᑲᐦᐃᑲᐣ (Amiskwacîwâskahikan) on
Treaty 6 territory, the territory of the Papaschase, and the homeland
of the Métis
Nation.

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[ccp4bb] Improved EM validation with Q-score

[Deborah Harrus]

Dear all,

As announced previously, wwPDB validation of 3DEM structures for which 
there is both a model and an EM volume will now include the Q-score 
metric (Pintilie, G., et al., 2020, Nat. Methods). This follows 
recommendations from the wwPDB/EMDB workshop on cryo-EM data management, 
deposition and validation in 2020 (white paper in preparation), as well 
as EM Validation Challenge events (Lawson C., et al., 2020, Struct. 
Dyn.; Lawson, et al., 2021, Nat. Methods). This will be the first 
quantitative parameter of residue and chain resolvability for EM maps in 
wwPDB validation reports and will provide an additional map-model 
assessment criterion.


The Q-score calculates the resolvability of atoms by measuring 
similarity of the map values around each atom relative to a 
Gaussian-like function for a well resolved atom. Q-score of 1 indicates 
that the similarity is perfect whilst closer to 0 indicates the 
similarity is low. If the atom is not well placed in the map then a 
negative Q-score value may be reported. Therefore, Q-score values in the 
reports will be in a range of -1 to +1.


The wwPDB EM validation reports will provide Q-scores for single 
particle, helical reconstruction, electron crystallography and 
subtomogram averaging entries for which both an EM map and coordinate 
model have been deposited.


Validation reports (PDF files) will contain images of the average 
per-residue Q-scores color-mapped onto ribbon models with views from 
three orthogonal directions. Similar images will also be introduced to 
visualize the per-residue atom-inclusion scores. Comparison of these two 
sets of images will assist in visual assessment of the model-to-map fit 
and quality.


To see example images of models where residues are colored according to 
their Q-score, please visit the news page on the wwPDB website: 
http://www.wwpdb.org/news/news?year=2022#63288a46831916e52206a1f0



The validation reports will also contain a table of average per-chain 
values of both metrics (Q-score and atom inclusion) as well as their 
overall average values for the entire model.


The per-residue and the per-chain average atom-inclusion and Q-score 
values will also be provided in the mmCIF and XML formatted validation 
files. The mmCIF categories _pdbx_vrpt_summary_entity_fit_to_map and 
_pdbx_vrpt_model_instance_map_fitting will be introduced to include both 
the Q-scores and atom-inclusion values. The existing items, 
_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion 
(https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Items/_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion.html) 
and _pdbx_vrpt_model_instance_geometry.residue_inclusion 
(https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Items/_pdbx_vrpt_model_instance_geometry.residue_inclusion.html) 
for atom inclusion will no longer be used.


The PDB Core Archive holds validation reports that assess each 3DEM 
model in the PDB along with the associated experimental 3D volume in 
EMDB. Validation reports of 3DEM structures (map and model) can be 
downloaded at the following wwPDB mirrors:


- wwPDB: https://ftp.wwpdb.org/pub/pdb/validation_reports/
- RCSB PDB: https://ftp.rcsb.org/pub/pdb/validation_reports/
- PDBe: https://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/
- PDBj: https://ftp.pdbj.org/pub/pdb/validation_reports/

The EMDB Core Archive holds validation reports that assess each EMDB 
map/tomogram entry. Validation reports for all EMDB volumes can be 
downloaded at the following wwPDB mirrors:


- EMDB: https://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/
- wwPDB: https://ftp.wwpdb.org/pub/emdb/validation_reports/
- RCSB PDB: https://ftp.rcsb.org/pub/emdb/validation_reports/
- PDBj: https://ftp.pdbj.org/pub/emdb/validation_reports/

Additional information about validation reports is available:

- for EM map+model: 
http://www.wwpdb.org/validation/2017/EMValidationReportHelp


- EM map-only: 
http://www.wwpdb.org/validation/2017/EMMapValidationReportHelp


- EM tomograms: 
http://www.wwpdb.org/validation/2017/EMTomogramValidationReportHelp


If you have any questions or queries about wwPDB validation, please 
contact us at validat...@mail.wwpdb.org.


Kindest regards,

Deborah Harrus.

--
---
Deborah Harrus, Ph.D.
Lead Annotator
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] Crystallography position at Exscientia

[Simone Culurgioni]

Dear all,

We are looking for experienced Crystallographers to join the Discovery
Biology department at Exscientia.
The Experimental Discovery Biology team in Exscientia is responsible for
enabling small-molecule therapeutic projects and integrates with the
Artificial Intelligence (AI) driven drug discovery platform.

The ideal candidates should have a strong experience in structural biology
with a focus on crystallography.

Please apply through the link:
https://apply.workable.com/exscientia/j/2BF259FB21/
or
https://www.exscientia.ai/careers


Best wishes,

Simone

-- 
Dr Simone Culurgioni
Director of Crystallography
Exscientia Ltd.
The Schrödinger Building
Heatley Road
The Oxford Science Park
Oxford
OX4 4GE

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Re: [ccp4bb] issues running PANDDA with anisotropic data

[Nichols, Charlie]

Dear All,

Having some difficulty running PANDDA with a large batch of structures with 
significantly anisotropic data:

  1.  We have to use Autoproc / Staraniso processing for all datasets.
  2.  The default Dimple (Refmac) pipeline gives weird maps with large areas of 
-ve density for no apparent reason which then really mess up the 
difference-difference map calculations critical for PANDDA success.
  3.  Test refinements showed that Buster refinement of the Staraniso output 
gave better maps which we hope will improve the interpretability of the PANDDA 
maps.
  4.  Pipedream run on 1000 datasets but PANDDA fails as it requires complete 
datasets with any missing reflections filled in from Fcalc
  5.  Unfortunately PANDDA does not have the correct structure factor names in 
the check list – It looks for these pairs: FWT and PHWT, 2FOFCWT_fill and 
PH2FOFCWT_fill and 2FOFCWT and PH2FOFCWT
  6.  Pipedeam/Buster outputs iso and aniso filled data so it has 
2FOFCWT-iso-fill/PH2FOFCWT_iso-fill and 2FOFCWT-aniso-fill/PH2FOFCWT_aniso-fill 
which PANDDA does not see so crashes out.

My scripting is not great so I wondered if anyone could hep me with a short 
script to recursively look for ‘refine.mtz’ within subdirectories from the 
top-level ‘model-building’ directory and then run CAD to change the column 
names from 2FOFCWT-iso-fill and PH2FOFCWT_iso-fill to 2FOFCWT_fill and 
PH2FOFCWT_fill so PANDDA can ‘see’ the correct data columns

NB: output .mtz name must still be ‘refine.mtz’ as PANDDA only checks the 
top-level directory for each refinement and ‘pipedream.mtz’ symlinks pointing 
to ‘pipedream/pipedreamDir/refine/refine.mtz’ are already in place.

Full path:

model_building/target_x/pipedream/pipedreamDir/refine/refine.mtz



Thanks for your help,

Take care, Charlie.







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Re: [ccp4bb] Jenkins?

[Charles Ballard - STFC UKRI]

Can solve the mystery of Jenkins, it is our build system.

Charles

On 25/09/2022, 19:36, "CCP4 bulletin board"  wrote:
Hello David,

maybe a binary in $CBIN with the same name as a system command?
(try, e.g. 'apropos truncate'
truncate (1) - shrink or extend the size of a file to the
specified size
)

there used to be a switch to place $CBIN at the end of the $PATH -
maybe this helps?

Cheers,
Tim


On Sun, 25 Sep 2022 14:37:38 +
"David J. Schuller" mailto:schul...@cornell.edu>> wrote:

> CCP4 8.0.004
> Scientific Linux 7, kernel 3.10.0-1160.76.1.el7.x86_64
> mate-desktop-1.16.2-1.el7.x86_64
>
> This morning I updated my Nvidia graphics driver, then rebooted. When
> I logged in again, my desktop (Mate) was all messed up, no
> applications menus, etc. I perused the log files and found many lines
> similar to these in /var/log/messages:
>
> Sep 25 09:45:32 titan mate-session[1718]: WARNING: Could not connect
> to Systemd: Failed to connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directorySep 25 09:45:34 titan journal: Error
> connecting to system bus: Failed to connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directory Sep 25 10:12:35 titan pulseaudio[22894]:
> [alsa-sink-ALC887-VD Analog] core-util.c: Failed to connect to system
> bus: Failed to connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directory Sep 25 10:12:40 titan pulseaudio[23162]:
> [pulseaudio] core-util.c: Failed to connect to system bus: Failed to
> connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directory Sep 25 10:12:40 titan pulseaudio[23162]:
> [pulseaudio] core-util.c: Failed to connect to system bus: Failed to
> connect to socket
> /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
> No such file or directory
>
> I do not have, and have never had, a user "jenkins" on my system.
> Note that the CCP4 workspace is implicated.
>
> I took the CCP4 startup stuff out of my .cshrc login script and
> restarted, and everything appeared to be normal. # source
> /usr/local/xtal/ccp4/bin/ccp4.setup-csh  >& /dev/null
>
> Why is jenkins mucking about with  my desktop settings, and how do I
> keep him from doing so?
>
>
> ===
>  All Things Serve the Beam
>  ===
>  David J. Schuller
>  modern man in a post-modern world
>  MacCHESS, Cornell University
>  
> schul...@cornell.edu
>
> 
>
> 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
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--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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