Re: [ccp4bb] Lower b-factors with increasing T

[Tom Peat]

I think the basic question being asked is why are the B-factors going the 
'wrong' way?
That is, as the temperature increases, one might expect higher B-factors (at 
least that is what we are taught) whereas what Matt is seeing is the opposite- 
decreasing B-factors as one goes up in temperature (which I also think is a 
little strange and I don't have an explanation).
cheers, tom

From: CCP4 bulletin board  on behalf of Phoebe A. Rice 

Sent: Thursday, September 8, 2022 10:48 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Lower b-factors with increasing T


I guess the big question is what is the question that you’re trying to address 
from those numbers?   I’d be nervous about making conclusions about trends in B 
factors from just 1 data set per temperature.  As you probably know, the B 
factors will reflect static differences in atomic position across asymmetric 
units as well as thermal motion, and it can be difficult to control variables 
such as exactly how fast a crystal freezes or how much trauma it experiences in 
its journey from sitting happily in a drop to the frozen state.



From: CCP4 bulletin board  on behalf of Matt McLeod 

Date: Wednesday, September 7, 2022 at 1:57 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Lower b-factors with increasing T

Hi everyone,

I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K 
(2.2A) and I am curious as to the details in determining B-factors.

I have treated these datasets more-or-less identically for comparison's sake.  
I used DIALS to index, integrate, and scale the data.  I scaled the data to a 
~0.6 CC1/2 cutoff.

After fully refining the datasets, there is an odd trend with respect to 
temperature (from what has been previously published) and I assume that this is 
because of "behind-the-scenes" computation rather than a biophysical 
observation.  The B-factors slightly decrease from 252-293K, and then 
significantly drop at 313K.  The maps look pretty well identical across the 
datasets.

253K - 53.8 A^2
273K - 48.4 A^2
293K - 45.5 A^2
313K - 18.6 A^2

I compared the wilson intensity plots from DIALS scaling for 273K and 313K and 
they are very comparable.

I am looking for suggestions as to where to look at how these b-factors are 
selected or how to validate that these B-factor are or are not accurate.  Also, 
any relevant literature would be welcomed.  From what I have read, there is a 
general trend that as T increase, the atoms have more thermal energy which 
raises the b-factors and this trend is universal when comparing datasets from 
different temperatures.

Thank you and happy to supply more information if that is helpful,
Matt



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Re: [ccp4bb] Lower b-factors with increasing T

[Phoebe A. Rice]

I guess the big question is what is the question that you’re trying to address 
from those numbers?   I’d be nervous about making conclusions about trends in B 
factors from just 1 data set per temperature.  As you probably know, the B 
factors will reflect static differences in atomic position across asymmetric 
units as well as thermal motion, and it can be difficult to control variables 
such as exactly how fast a crystal freezes or how much trauma it experiences in 
its journey from sitting happily in a drop to the frozen state.

From: CCP4 bulletin board  on behalf of Matt McLeod 

Date: Wednesday, September 7, 2022 at 1:57 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Lower b-factors with increasing T
Hi everyone,

I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K 
(2.2A) and I am curious as to the details in determining B-factors.

I have treated these datasets more-or-less identically for comparison's sake.  
I used DIALS to index, integrate, and scale the data.  I scaled the data to a 
~0.6 CC1/2 cutoff.

After fully refining the datasets, there is an odd trend with respect to 
temperature (from what has been previously published) and I assume that this is 
because of "behind-the-scenes" computation rather than a biophysical 
observation.  The B-factors slightly decrease from 252-293K, and then 
significantly drop at 313K.  The maps look pretty well identical across the 
datasets.

253K - 53.8 A^2
273K - 48.4 A^2
293K - 45.5 A^2
313K - 18.6 A^2

I compared the wilson intensity plots from DIALS scaling for 273K and 313K and 
they are very comparable.

I am looking for suggestions as to where to look at how these b-factors are 
selected or how to validate that these B-factor are or are not accurate.  Also, 
any relevant literature would be welcomed.  From what I have read, there is a 
general trend that as T increase, the atoms have more thermal energy which 
raises the b-factors and this trend is universal when comparing datasets from 
different temperatures.

Thank you and happy to supply more information if that is helpful,
Matt



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Re: [ccp4bb] Lower b-factors with increasing T

[Ethan A Merritt]

On Wed, Sep 7, 2022 at 11:57 AM Matt McLeod  wrote:

> Hi everyone,
>
> I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A),
> 313K (2.2A) and I am curious as to the details in determining B-factors.
>



In the larger physical universe those temperatures are not very far apart.
I would not expect much change in the physical properties of the crystal
or its content.There is a reason that "cryo" crystallography generally
means "liquid nitrogen temperature", i.e. 77K but more like 100K at the
position of a crystal in a boil-off nitrogen stream.

The first thing you should check when comparing B factors is whether the
different refinements use the same, or closely comparable, overall
B correction.  Typically this is an anisotropic correction; you would
want to add an isotropic approximation of this overall term to the
individual refined atomic B factors and then compare the sums.
That gives you a back-of-the-envelope comparison.

To do a more thorough job is complicated.

I am of course highly biased towards the power of TLS 
My suggestion would be to first use the refined B factors you have to
construct a segmented TLS model. I would then reset all the Bs to a
constant and refine the data sets in parallel using a "pure TLS" model,
i.e. no individual atomic B factors.
Afterward I would compare the magnitude of the principle components
of each TLS segment as a function of the data collection temperature.
The rationale is that the individual TLS segments are chunks of the
structure, domains, subdomains, loops, etc, that may be relatively
free to vibrate within the crystal lattice.  You would expect the
magnitude of this vibration to increase with temperature.
Not so much the individual atomic vibrations described by atomic
B factors.

Ethan


> I have treated these datasets more-or-less identically for comparison's
> sake.  I used DIALS to index, integrate, and scale the data.  I scaled the
> data to a ~0.6 CC1/2 cutoff.
>
> After fully refining the datasets, there is an odd trend with respect to
> temperature (from what has been previously published) and I assume that
> this is because of "behind-the-scenes" computation rather than a
> biophysical observation.  The B-factors slightly decrease from 252-293K,
> and then significantly drop at 313K.  The maps look pretty well identical
> across the datasets.
>
> 253K - 53.8 A^2
> 273K - 48.4 A^2
> 293K - 45.5 A^2
> 313K - 18.6 A^2
>
> I compared the wilson intensity plots from DIALS scaling for 273K and 313K
> and they are very comparable.
>
> I am looking for suggestions as to where to look at how these b-factors
> are selected or how to validate that these B-factor are or are not
> accurate.  Also, any relevant literature would be welcomed.  From what I
> have read, there is a general trend that as T increase, the atoms have more
> thermal energy which raises the b-factors and this trend is universal when
> comparing datasets from different temperatures.
>
> Thank you and happy to supply more information if that is helpful,
> Matt
>
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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[ccp4bb] Postdoctoral researcher at the Techical University of Denmark

[Jens Preben Morth]

Postdoctoral researcher at the Technical University of Denmark
This position is offered in connection to the project Center for enzymatic 
deconstruction of thermoset plastics for a sustainable society (En’Zync). The 
center, which will start this coming fall and operate for at least six years, 
is made possible through the support of the Novo Nordisk Foundation. The center 
will offer excellent opportunities for further development of your carrier 
within biotechnology in general and enzyme technology in particular, and it 
houses leading expertise in the range of disciplines that are required for the 
discovery and -engineering industrial biocatalysts. Main center activities are 
within molecular biology, enzymology, structural biology, organic synthesis and 
computational biochemistry.
Responsibilities and qualifications
For the current position, we are seeking a postdoc, who can take a leading role 
in the organization and implementation of En`zync’s work at DTU. This includes 
direct participation in different research activities such enzyme screening, 
enzyme structural- and functional characterization and heterologous expression 
in fungal strains. In addition, we expect the post doc to participate in the 
supervision of younger students and the coordination of En`zync activities both 
internally at DTU and more broadly with researchers in the center located at 
Aarhus University, the Danish Technological Institute (DTI) and University of 
Porto.
To read more and apply for the position, please go to
https://www.dtu.dk/english/about/job-and-career/vacant-positions/job?id=cfb6eda2-09ca-4ca8-be5e-5790fa35d415




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Re: [ccp4bb] Lower b-factors with increasing T

[Matt McLeod]

In addition, I computed the wilson B.s

253 - 41
273 - 35.4
293 - 36.5
313 - 0.19

Looks like there is definitely an issue with the data scaling.  Still looking 
for suggestions as to what to tweak.

Matt



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[ccp4bb] Installing previous Coot version in a Conda environment

[Joshua Rose]

Hi Everyone,

I'm experiencing some issues with Coot 0.9 which I have running under Mac OS 
when I try to use some older CCP4 packages. It seems to work fine on other 
computers running Coot 0.89.

I think a good way to handle this issue is to download an older version of Coot 
to run in a separate Conda environment. But before I run off and try to do this 
I thought it might be nice to get some input on what the best way is to set it 
up.

Any thoughts? I still want to have access to current versions of Coot as well.



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[ccp4bb] Lower b-factors with increasing T

[Matt McLeod]

Hi everyone,

I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K 
(2.2A) and I am curious as to the details in determining B-factors.

I have treated these datasets more-or-less identically for comparison's sake.  
I used DIALS to index, integrate, and scale the data.  I scaled the data to a 
~0.6 CC1/2 cutoff.  

After fully refining the datasets, there is an odd trend with respect to 
temperature (from what has been previously published) and I assume that this is 
because of "behind-the-scenes" computation rather than a biophysical 
observation.  The B-factors slightly decrease from 252-293K, and then 
significantly drop at 313K.  The maps look pretty well identical across the 
datasets.

253K - 53.8 A^2
273K - 48.4 A^2
293K - 45.5 A^2
313K - 18.6 A^2

I compared the wilson intensity plots from DIALS scaling for 273K and 313K and 
they are very comparable.

I am looking for suggestions as to where to look at how these b-factors are 
selected or how to validate that these B-factor are or are not accurate.  Also, 
any relevant literature would be welcomed.  From what I have read, there is a 
general trend that as T increase, the atoms have more thermal energy which 
raises the b-factors and this trend is universal when comparing datasets from 
different temperatures.

Thank you and happy to supply more information if that is helpful,
Matt



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[ccp4bb] Two postdoctoral positions are available in the laboratories of Drs. Juan Du and Wei Lü at Van Andel Institute

[Juan Du]

The Du Lab and the Lü Lab are interested in understanding the molecular 
mechanisms of how the body perceives sensory information (e.g. taste, smell, 
vision, and temperature), transmits signals to the brain, and generates 
responses. We focus on ion channels involved in the basic senses. We employ a 
range of structural and biophysical approaches, including single-particle 
cryo-EM, patch-clamp electrophysiology, and other biochemical methods. The 
cryo-EM facility at Van Andel Institute hosts a Titan Krios equipped with a K3 
camera, and a Talos Arctica equipped with a K2 camera.  
For more information, please visit our lab website: dululabs.com 

Qualifications
Experience in structural biology, membrane protein biochemistry, or ion channel 
electrophysiology is preferred, but not required. 

How to Apply
•   Online Application: 
•   CV 
•   Cover Letter 
Send the CV, Cover Letter and a list of 2-3 referees to Juan Du 
(juan...@vai.org) or Wei Lü, wei...@vai.org 

Van Andel Institute (VAI) provides postdoctoral training opportunities to 
scientists beginning their research careers. The fellowships are to help 
promising scientists advance their knowledge and research experience and at the 
same time support the research endeavors of VAI under the mentorship of a VAI 
Faculty member. 

While this project is currently funded, an integral part of postdoctoral 
training is the process of preparing a research proposal and writing a 
fellowship application. All VAI Postdoctoral Fellows are encouraged to apply 
for external funding as soon as it is practical and reasonable after hire. 
Receiving a fellowship award provides recognition for both the fellow and VAI!

Postdoctoral Fellows at VAI are full-time employees and receive an annual 
competitive salary. Salary is based on Doctorate/MD receipt date according to a 
set stipend schedule. Benefits include:
•   Medical, dental and vision coverage 
•   Employer-sponsored life and AD insurance 
•   Additional voluntary life and AD insurance for employees and 
dependents 
•   Short-term and long-term disability insurance 
•   Flexible-spending accounts for health and child/elder care 
•   401 K retirement savings plans with employee/employer contributions 
•   Paid vacation, holidays, personal days 
•   Relocation Assistance

If you have questions about the application process or working at VAI you are 
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megan.do...@vai.org. 
 
VAI is committed to achieving excellence through increasing diversity. We 
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Van Andel Institute is an Equal Employment Opportunity (EEO) and Vietnam Era 
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As Van Andel Institute is a drug and alcohol-free employer, all prospective new 
employees undergo a urinalysis/drug test as part of our pre-employment process. 
 This is a 7-panel drug screen and it includes testing for Marijuana, Cocaine, 
Amphetamines, Opiates, PCP, Barbiturates, and Benzodiazepines.

About Grand Rapids, MI
Van Andel Institute is located in downtown Grand Rapids, MI which is the second 
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With a medical and life sciences industry boom, strong entrepreneurial 
activity, dedication to green building and living, and innovative employers, 
Grand Rapids' diverse economy continues to grow, offering endless career 
opportunities.
es.  



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[ccp4bb] Two challenging Postdoc positions in cryo-EM/muscle structural biology –UMass Chan Medical School (Padron-Craig lab)

[Raul Padron]

Dear all,

We are looking for two highly motivated, dynamic and driven postdocs to join 
our cryo-EM muscle structural biology team at the Division of Cell Biology and 
Imaging, UMass Chan Medical School in Worcester, MA. 

The Padron/Craig lab (https://www.umassmed.edu/padron-craig/) has focused on 
the structure of myosin molecules and muscle thick filaments since discovering 
the myosin interacting-heads motif (IHM) in filaments by cryo-EM in 2005 
(Woodhead et al 2005, Nature 436, 1195-1199 - 
https://www.nature.com/articles/nature03920), leading to the recently published 
4.3 Å resolution structure of the myosin II molecule in the inhibited state 
(Yang et al. 2020, Nature 588, 521-525 - 
https://www.nature.com/articles/s41586-020-3007-0

Ideal candidates to join this adventure, solving the near-atomic cryo-EM 
structure of the IHM in situ, with implications for muscle relaxation and 
activation, muscle disease, and drug treatment, will possess a broad curiosity 
and a passion for discovery. Having expertise in cryo-EM/ET or X-ray 
crystallography will be a plus but is not required, as these positions 
(NIH-funded for 4-5 years) are an excellent opportunity as well to learn 
cryo-EM or expand your existing cryo-EM capabilities. 

Our cryo-EM Core 
(https://www.umassmed.edu/research/cores/cryo-em-core-facility/) is superbly 
equipped and staffed to carry out this work (Titan Krios, Talos-Arctica, 
Glacios, with K3 cameras and energy filters, Aquilos FIB-SEM, etc.) and to 
provide excellent hands-on training.

Please send your cover letter and resume to raul.pad...@umassmed.edu and  
roger.cr...@umassmed.edu

All the best,

Raul Padron & Roger Craig



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[ccp4bb] workshop Advances in Protein Design: From Therapeutic Proteins to Synthetic Biology

[Julia Shifman]

Dear colleagues, 
 
I would like to bring to your attention a workshop that I am organising 
together with Dror Noy: Advances in  Protein Design: From Therapeutic Proteins 
to Synthetic Biology  that will take place in the upper Galilee, Israel on 
October 23-27, 2022. We have a line up of rgreat speakers coming to the 
workshop and would like to invite you to participate in the meeting. The 
abstract deadline is  September 10th. Some abstracts will be selected for oral 
presentations. 
You can read more about this workshop here: https://www.isfproteindesign.com/ 

I invite you participate in this workshop and also to spread the word to your 
students and colleagues.
 

Julia Shifman
Prof. of Biophysics and Biochemistry
Chair, Department of Biological Chemistry
Hebrew University of Jerusalem
Phone:   972-2-658-4078

WEB:  www.bio.huji.ac.il/shifman





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[ccp4bb] Postdoctoral researcher at Lund Medical Faculty/CureVac/Institut Laue-Langevin

[Trevor Forsyth]

Postdoctoral researcher at Lund Medical Faculty/CureVac/Institut Laue-Langevin

We seek a highly motivated  postdoctoral researcher to be based in the 
Molecular Biophysics Group within the Biomedical Centre (BMC) in the Medical 
Faculty of Lund University, led by Professor Trevor Forsyth. The project will 
be carried out in close collaboration with CureVac (https://www.curevac.com/en/ 
) in Germany, and with the LSS and Life Sciences Groups at the Institut Laue 
Langevin (ILL - https://www.ill.eu/ ) in France. CureVac is a leading global 
clinical-stage biopharmaceutical company dedicated to the development of new 
classes of drugs based on the use of messenger RNA (mRNA) technologies. The ILL 
is the most intense neutron source in the world and holds a leading position 
for neutron science in life sciences, soft condensed matter, and hard condensed 
matter.The researcher will be based in the Lund Medical Faculty, with good 
access to state-of-the-art facilities both within the Medical, Science, and 
Engineering faculties, and in close proximity to the nearby MAX-IV synchrotron 
and ESS neutron beam facilities, as well as access to the ILL and ESRF sources 
in Grenoble, France.

The work will focus on the structural characterization of mRNA lipid 
nanoparticles (LNPs) using techniques such as small-angle X-ray and neutron 
scattering (SAXS/SANS), selective deuteration, and electron microscopy. We seek 
advanced structural characterization of mRNA LNPs relating  to pharmaceutical 
stability  and in vivo efficacy. These structural details are critical for the 
development of better vaccines in the future.

The desired starting date is December 2022 or by agreement.

To apply for the position, please go to 
https://lu.varbi.com/en/what:job/jobID:540560/

Informal enquiries:
Trevor Forsyth (trevor.fors...@med.lu.se)
Gemma Navarro (gemma.nava...@curevac.com)
Sylvain Prevost (prev...@ill.eu)


--
___
Trevor Forsyth
Director
LINXS Institute of Advanced Neutron and X-ray Science
Delta 5, 5th and 6th floors, IDEON Building,
Scheelevagen 19, 223 70 Lund
Sweden trevor.fors...@linxs.lu.se 
Tel:+46(0)730816074

Professor of Biophysics
Faculty of Medicine
Lund University
SE-221 84 Lund
Sweden trevor.fors...@med.lu.se 
Tel:+46(0)730816074
[cid:image002.jpg@01D8C2CD.C5AA5BB0]
https://www.linxs.se/
https://orcid.org/-0003-0380-3477
___





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[ccp4bb] New CrystalDirect Plate-to-beam experimental modalities at ESRF MASSIF 1 open for user access through the EMBL HTX lab.

[Jose A. Marquez]

Dear All,

Under the umbrella of the EMBL-ESRF Joint Structural Biology Group a 
collaborative project to upgrade MASSIF-1 and exploit synergies with the 
EMBL High Throughput Crystallization facility (HTX Lab) in Grenoble has 
been established. An integral part was the installation of one of the 
CrystalDirect automatic crystal harvesting robots into the beam line 
environment, enabling new experimental modalities. Thanks to the hard 
work of the EMBL Instrumentation, Synchrotron Crystallography and HTX 
Lab Teams, and the ESRF Structural Biology group, the installation is 
now completed.


We are now opening access to newly developed CrystalDirect plate-to-beam 
experimental modalities at MASSIF-1 via the EMBL HTX Lab. We are 
inviting applications for either collaborative or user access. 
Opportunities for funded access are available through iNEXT Discovery. 
If you are interested in any of the new experiments listed below please 
contact us at h...@embl.fr or mass...@esrf.fr


•    Automated Protein-to-structure pipelines with CrystalDirect 
plate-to-beam cryogenic data collection. Either for full diffraction 
data collection or rapid diffraction-based screening and prioritization 
of initial crystallization hits.


•    Automated high throughput room temperature data collection to help 
identify conformational variability with potential insights into protein 
dynamics.


•    Automated crystal dehydration experiments to modulate crystal 
parameters.


Pure samples can be shipped to the EMBL HTX Lab were crystallization 
experiments will be carried out. Online experimental design and 
real-time access to results is facilitated via the Crystallographic 
Information Management System (CRIMS) web interface. Typical 
experimental workflows include crystallization screening and 
optimization, crystal harvesting and CrystalDirect-plate-to-beam data 
collection at MASSIF-1.


contact   h...@embl.fr or mass...@esrf.fr

Best wishes

_

Jose A. Marquez Ph.D.
Team Leader, Head of the Crystallization Facility
EMBL Grenoble Outstation
Postal address: European Molecular Biology Laboratory
71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Delivery address: European Molecular Biology Laboratory
71, Avenue des Martyrs
38000 Grenoble, France
Phone +33 (0)476 20 74 25
Fax. +33 (0)476 20 71 99

https://www.embl.org/groups/marquez/
https://www.embl.org/services-facilities/grenoble/high-throughput-crystallisation/
https://htxlab.embl.fr/
_



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