Re: [ccp4bb] am I doing this right?

[Jacob Keller]

Hi All,

haven't been following CCP4BB for a while, then I come back to this juicy
Holtonian thread!

Sorry for being more practical, but could you use a windowed approach:
integrate values of the same pixel/relp combo (roxel?) over time (however
that works with frame slicing) to estimate the error over many frames, then
shrink the window incrementally, see whether the  successive
plotted shrinking-window values show a trend? Most likely flat for
background? This could be used for the spots as well as background. Would
this lose the precious temporal info?

Jacob

On Fri, Oct 22, 2021 at 3:25 AM Gergely Katona  wrote:

> Hi,
>
>
>
> I have more estimates to the same problem using a multinomial data
> distribution. I should have realized that for prediction, I do not have to
> deal with infinite likelihood of 0 trials when observing only 0s on an
> image. Whenever 0 photons generated by the latent process, the image is
> automatically empty. With this simplification, I still have to hide behind
> mathematical convenience and use Gamma prior for the latent Poisson
> process, but observing 0 counts just increments the beta parameter by 1
> compared to the prior belief. With equal photon capture probabilities, the
> mean counts are about 0.01 and the std is about 0.1 with
> rate≈Gamma(alpha=1, beta=0.1) prior . With a symmetric Dirichlet prior to
> the capture probabilities, the means appear unchanged, but the predicted
> stds starts high at very low concentration parameter and level off at high
> concentration parameter. This becomes more apparent at high photon counts
> (high alpha of Gamma distribution). The answer is different if we look at
> the std across the detector plane or across time of a single pixel.
>
> Details of the calculation below:
>
>
>
>
> https://colab.research.google.com/drive/1NK43_3r1rH5lBTDS2rzIFDFNWqFfekrZ?usp=sharing
>
>
>
> Best wishes,
>
>
>
> Gergely
>
>
>
> Gergely Katona, Professor, Chairman of the Chemistry Program Council
>
> Department of Chemistry and Molecular Biology, University of Gothenburg
>
> Box 462, 40530 Göteborg, Sweden
>
> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
>
> Web: http://katonalab.eu, Email: gergely.kat...@gu.se
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Nave,
> Colin (DLSLtd,RAL,LSCI)
> *Sent:* 21 October, 2021 19:21
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] am I doing this right?
>
>
>
> Congratulations to James for starting this interesting discussion.
>
>
>
> For those who are like me, nowhere near a black belt in statistics, the
> thread has included a number of distributions.  I have had to look up where
> these apply and investigate their properties.
>
> As an example,
>
> “The Poisson distribution is used to model the # of events in the future,
> Exponential distribution is used to predict the wait time until the very
> first event, and Gamma distribution is used to predict the wait time until
> the k-th event.”
>
> A useful calculator for distributions can be found at
>
> https://keisan.casio.com/menu/system/0540
>
> a specific example is at
>
> https://keisan.casio.com/exec/system/1180573179
>
> where cumulative probabilities for a Poisson distribution can be found
> given values for x and lambda.
>
>
>
> The most appropriate prior is another issue which has come up e.g. is a
> flat prior appropriate? I can see that a different prior would be
> appropriate for different areas of the detector (e.g. 1 pixel instead of
> 100 pixels) but the most appropriate prior seems a bit arbitrary to me. One
> of James’ examples was 10^5 background photons distributed among  10^6
> pixels – what is the most appropriate prior for this case? I presume it is
> OK to update the prior after each observation but I understand that it can
> create difficulties if not done properly.
>
>
>
> Being able to select the prior is sometimes seen as a strength of Bayesian
> methods. However, as a strong advocate of Bayesian methods once put it,
> this is a bit like Achilles boasting about his heel!
>
>
>
> I hope for some agreement among the black belts. It would be good to end
> up with some clarity about the most appropriate probability distributions
> and priors. Also, have we got clarity about the question being asked?
>
>
>
> Thanks to all for the interesting points.
>
>
>
> Colin
>
> *From:* CCP4 bulletin board  *On Behalf Of *Randy
> John Read
> *Sent:* 21 October 2021 13:23
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] am I doing this right?
>
>
>
> Hi Kay,
>
>
>
> No, I still think the answer should come out the same if you have good
> reason to believe that all the 100 pixels are equally likely to receive a
> photon (for instance because your knowledge of the geometry of the source
> and the detector says the difference in their positions is insignificant,
> i.e. part of your prior expectation). Unless the exact position of the spot
> where you detect the photon is relevant, detecting 1 photon on a big p

[ccp4bb] PostDoctoral Position in Membrane Protein Structural Biology at USC, Los Angeles

[Cornelius Gati]

PostDoctoral Position in Membrane Protein Structural Biology at USC, Los Angeles

The position is available starting immediately in the Department of Biological 
Sciences at the University of Southern California and is initially limited to 2 
years, with possible extension.

Our research focuses on the structural biology of membrane proteins involved in 
synaptic transmission, using single particle cryoEM and X-ray crystallography, 
complemented by functional assays. We are working in close collaboration with 
the group of Prof. Vadim Cherezov (USC) on the structure determination of GPCRs.

USC has a suite of research facilities and has recently commissioned a 
brand-new cryoEM facility:
• CryoEM suite: Titan Krios with GIF Quantum energy filter and K3 detector, 
Glacios with Falcon 4 detector, Talos Arctica with CCD/side entry holder for NS 
and screening
• Core facility for insect- and mammalian cell expression
• High performance computing for data processing/analysis

Qualified candidates must have a Ph.D. degree with a solid background in 
structural biology and biophysics/biochemistry. Previous work with membrane 
proteins is a plus. A successful candidate is expected to be highly skilled and 
self-motivated and is willing to work in a collaborative environment. The 
Postdoctoral salary depends on qualifications and relevant experiences 
according to USC standards.

Interested candidates should apply directly with Cornelius Gati at 
gati[at]usc.edu. Please attach a cover letter, Curriculum 
Vitae, research statement, publication list and a reference letter. There is no 
deadline for this posting and applications will be evaluated on a rolling basis.

Current group website: https://dornsifecms.usc.edu/labs/gati-lab/


Recent work from our group includes:

H Shaye, A Ishchenko, JH Lam, GW Han, L Xue, P Rondard, JP Pin, V Katritch, C 
Gati*, V. Cherezov*
Structural basis of the activation of a metabotropic GABA receptor. Nature. 
2020.

S Rempel, C Gati*, M Nijland, C Thangaratnarajah, A Karyolaimos, JW de Gier, A 
Guskov*, DJ Slotboom*.
A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds. 
Nature. 2020.



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[ccp4bb] Tenure Track Assistant Professor

[Martin Lawrence]

Dear CCP4 Community,

Montana State University (MSU) invites applications for a tenure-track
faculty position in cryogenic electron microscopy.  The position is
formally a joint appointment between the Department of Chemistry and
Biochemistry, and the Department of Microbiology and Cell Biology.  The
candidate will join an active structural biology group with existing
expertise in X-ray crystallography, NMR and mass spectrometry, and developing
expertise in cryo-EM.  The position will include access to the University’s
newly acquired Talos Arctica microscope equipped with a Gatan K3 camera
capable of high resolution single particle analysis (For example: Mol Cell
2019 74(1):132
).
The campus has interests in Single Particle Analysis, cryo-ET  (Structure
2019 27(11):1634

 ) and helical reconstruction.  Potential applicants with expertise in any
of these areas are encouraged to apply.  Experience in micro-ED and
macromolecular crystallography are a plus.  *Review of applications will
begin December 1st* and continue until the position is filled.

Montana State University maintains a highly collaborative,
interdisciplinary environment with research programs broadly focused in
multiple areas, including  cell and developmental biology,
neurobiology/neuroscience, metalloproteins and metals in biology, innate
and acquired immunity, virology, pathogen microbiology, host/pathogen
interactions, microbial biofilms and environmental microbiology.  There are
numerous opportunities for collaborations in these areas.

We are located in the Northern Rocky Mountain community of Bozeman
Montana.  Bozeman is regularly recognized for its high quality of life,
including its outdoor, cultural and educational amenities:
http://www.montana.edu/about-msu/bozeman/
.

For further details and to apply, visit:
https://jobs.montana.edu/postings/26344

For inquiries and additional questions, please contact:

Martin Lawrence
lawre...@montana.edu

Professor of Chemistry and Biochemistry
Montana State University
Bozeman, MT 59717



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[ccp4bb] Research Associate in Integrated Structural Biology at University of Birmingham

[Klaus Futterer]

Dear colleagues,


Prof Teresa Carlomagno has recently joined the School of Biosciences at the 
University of Birmingham and is in the process of establishing a new research 
group in integrated structural biology. Part of that group is the position of a 
Research Associate position described below.


Full details can be found at: 
https://www.jobs.ac.uk/job/CKC707/research-associate


For informal inquiries, please contact Teresa directly at 
t.carloma...@bham.ac.uk.


Thank you.


Klaus





Research Associate
School of Biosciences
College of Life and Environmental Sciences

Location: University of Birmingham, Edgbaston, Birmingham UK


Full Time FTC for 5 years

Closing date – 30.11.2021



Role/Project Background
The research group to which the post is associated uses integrative structural 
biology to understand functional mechanisms of proteins, nucleic acids and 
their complexes. The Research Associate will express and purify functional 
proteins, produce nucleic acids either by in vitro transcription or chemical 
synthesis, reconstitute large biomolecular particles from recombinant material, 
study the biomolecular complexes with biophysical and biochemical experiments 
and establish functional tests in vitro. The material produced and studied by 
the Research Associate will then be used for structural biology experiments. 
The day-to-daywork includes cloning, bacterial cell culture, protein expression 
and purification, RNA transcription and purification, RNA and protein 
engineering, biophysical studies of biomolecules and of their mutual 
interactions, for example through Isothermal Titration Calorimetry, Multiple 
Angle Light Scattering and Electrophoretic Mobility Assays. In addition, the RA 
will help with laboratory management tasks.


Main duties

  *   •   Collect research data; this may be through a variety of research 
methods, such as scientific experimentation (as described above) and literature 
reviews
  *   •   Analyse research data as directed
  *   •   Present research outputs, including drafting academic 
publications or parts thereof, for example at seminars and as posters
  *   •   Develop or adapt techniques, models and methods
  *   •   Provide guidance as required to support staff and any students 
who may be assisting with research
  *   •   Deal with problems that may affect the achievement of research 
objectives and deadlines
  *   •   Carry out administrative tasks related directly to the delivery 
of the research
  *   •   Promote equality and values diversity acting as a role model and 
fostering an inclusive working culture

Person Specification

•  Degree or equivalent in Biochemistry, Biophysics or Molecular Biology

•  Proficiency in protein recombinant expression and purification and/or in 
RNA synthesis and purification

•  Practical experience in a biochemical laboratory

•  Experience in some of the biophysical techniques mentioned above

•  Skills in analysing data

•  Ability to analyse information and communicate effectively

•  Ability to access and organise resources successfully

•  Knowledge of the protected characteristics of the Equality Act 2010, and 
how to actively ensure in day-to-day activity in own area that those with 
protected characteristics are treated equally and fairly


===
Klaus Fütterer, PhD
Reader in Structural Biology


School of Biosciences
LES CollegeEmail: 
k.futte...@bham.ac.uk
University of Birmingham Phone: +44 - 121 - 414 5895
Birmingham, B15 2TT, UK(voice mail messages will 
forward to my email inbox)

My normal working hours are Mon - Fri 8.30 - 5.30 pm.


===



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[ccp4bb] REMINDER: Bioinformatician position at PDBe - closing 4th November

[David Armstrong]

A reminder of our exciting opportunity for a bioinformatician interested 
in structural biological data and functional annotations to work within 
the Protein Data Bank in Europe Team (PDBe) at the European 
Bioinformatics Institute (EMBL-EBI).


The work includes standardising post translational modification 
information within the PDB archive in collaboration with wwPDB partners, 
plus integration and display of *post-translational modifications and 
proteomics data* on the PDBe and PDBe-KB web pages. This is a 
collaboration with the PRIDE data resource at EMBL-EBI and Juri 
Rappsibler team at the University of Edinburgh to facilitate deposition 
of cross-linking data during PDB structure deposition.


The closing date for this post is *4th November 2021*.

For more information on the position, please visit:
https://www.embl.org/jobs/position/EBI01913

Kind regards,
David

--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544




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