[ccp4bb] Research Fellow opportunity in the Rossjohn Lab, Monash University, Australia.

[Jennifer Huynh]

Research Fellow opportunity in the Rossjohn Lab!Prof. Jamie Rossjohn, FRS, NHMRC Investigator Fellow, is seeking research fellows to join the research group at Monash Biomedicine Discovery Institute, Clayton campus, Melbourne, Australia. The selected candidates will work in the field of T cell recognition specifically working on gamma delta T cells. The Rossjohn Laboratory, as part of a broad collaborative network that includes lead national and international researchers, has provided profound insight into T-cell immunology, specifically defining the basis of key immune recognition events by T-cells. The laboratory has notably pioneered our understanding of lipid-based immunity by the innate Natural Killer T-cells (NKT) and the role of MAIT cells in recognizing vitamin B metabolites. For more details on the research themes, fellowships awarded and publication outputs see, https://rossjohnlab.com/Applicants should hold a PhD in Biochemistry, Molecular Biology, Structural Biology or Immunology with an interest in T cell recognition, Protein Chemistry, Crystallography or Immune Cell Biology. Experience in a number of the following areas would be an advantage:1) Molecular Biology: site-directed mutagenesis2) Protein Biochemistry- production, purification and analysis: E. coli, yeast, insect cells and/or mammalian _expression_ systems (including cell culture techniques), chromatography, crystallography, proteomics3) Cellular Immunology: tissue culture and flow cytometry;4) Technologies: SPR, SAXS, Cryo-EMCandidates with a promising track record in the relevant areas and a proven publication record in international journals are encouraged to apply. Appointment will be made at a level appropriate to the successful applicant’s qualifications, experience and in accordance with classification standards for Level A.Salary range: Level A $94,970 -$101,944 plus 17% superannuation Duration:   1 year in the first instance   Location:   Clayton CampusPlease direct all enquiries to Jennifer Huynh:  jennifer.hu...@monash.eduJENNIFER HUYNH                Project Manager Office of Prof. Jamie Rossjohn, FAA FAHMS FLSW FMedSci FRSNHMRC Investigator FellowDepartment of Biochemistry & Molecular Biology/ Monash Biomedicine Discovery InstituteMonash UniversityClayton VIC 3800AustraliaW: https://rossjohnlab.com/Twitter: @RossjohnLabFacebook: theRossjohnLab

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[ccp4bb] Post-doc position in protein crystallography and drug discovery at the City of Hope

[Jeff Perry]

A post-doctoral position in protein crystallography and drug discovery is 
available in the Perry laboratory at the City of Hope Medical Center in Los 
Angeles, California. The project is focused on hits-to-leads studies against a 
novel diabetes therapeutic target for both type 1 and type 2 forms of the 
disease. This is a collaborative effort between three research groups at the 
City of Hope and is funded by a City of Hope grant for drug development.

The research will involve protein expression, purification, and protein 
crystallography studies to determine co-crystal structures of small 
molecule:protein target complexes, in addition to fragment-based drug discovery 
approaches. Biophysical methods including thermal shift assays and isothermal 
calorimetry will also be employed. 

A PhD in biochemistry or related discipline with a strong background in protein 
crystallography is required. 

Kindly send your cover letter and CV to me at: jpe...@coh.org

informal enquiries are also welcome.
 
Jeff Perry, Ph.D.
Assistant Professor,
MDET, City of Hope Medical Center,
Biomedical Research Center,
1218 S. Fifth Avenue,
Monrovia, CA 91016
cityofhope.org/jeff-perry-lab



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Re: [ccp4bb] [Sender Not Verified] Re: [ccp4bb] To Trim or Not to To Trim

[Robbie Joosten]

Hi Markus,

Just to make sure that things are clear: PDB-REDO adds missing side chains 
(that is a design choice) and it also adds missing loops if, and only if, there 
is a homologous template, there is sufficient density (although the criteria 
are rather forgiving), and the geometry of the loop stays okay upon real-space 
refinement. We do not build termini.

Your water example is a very nice one, this also happens for main chain atoms 
unfortunately. So unlike building parts of the protein that are chemically 
attached, please be careful with building waters. Only build ones that you are 
sure are waters. If you know that it is something else, but you don’t know 
what, please don’t build anything. I actually encourage students to build 
waters by hand. It is really simple and fast in Coot and it takes though a tour 
of you structure model enabling you to spot other issues.

HTH,
Robbie

From: CCP4 bulletin board  On Behalf Of Rudolph, Markus
Sent: Tuesday, March 14, 2023 15:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [Sender Not Verified] Re: [ccp4bb] To Trim or Not to To 
Trim

Hello Adrian,

Provided a crystal contains the intact protein, as measured by mass 
spectrometry of a washed and dissolved crystal, leaving out side-chains makes 
little sense, even if some of them are destroyed by X-rays during data 
collection. I realize that most of the time, no such analysis is done on 
crystals, but if you assume all residues are there, then they must fit into the 
asymmetric unit. This includes N- and C-terminal residues, loops, and any 
side-chains without density. If side-chains won't fit, e.g. by crashing into 
symmetry neighbors, then the main-chain trace is very likely wrong. Thus, 
placing side-chains in a model is a good test for a correct main-chain trace. I 
understand many protein architects out there omit the terminal extensions and 
longer loops, and so do I. pdb_redo will automatically complete a model, so one 
could say - don't bother, as a user I'll retrieve the re-refined model from 
there. This is not my personal choice of model building, but a practical option 
from the viewpoint of downstream users. Sometimes, however, I see models where 
side-chains are truncated but the little density still present for the 
side-chain is interpreted by water (see image attached, in which case the water 
comes from a symmetry-related position). If one says "don't build what you 
don't see but build what the data tell you", a well-intended but 
mis-interpreted water molecule may occupy the density belonging to a truncated 
side-chain. I as a user would be confused by this, especially when using such 
models for ligand binding studies where water is important. In our SBDD 
projects, we always take B-values into account, and we welcome complete models 
or we complete and re-refine them ourselves. So yes, my 12 points go to the 
"let the B-factors take care of it” song. But really, I'm thankful for _any_ 
published structure, even with sup-optimal parameterization, experienced 
structural biologists can deal with that and communicate the information to 
their collaborators.


...which brings up the other evergreen, whether the PDB should be more strict 
about ...



Best wishes,
Markus



On Fri, Mar 10, 2023 at 5:33 PM Goldman, Adrian 
mailto:adrian.gold...@helsinki.fi>> wrote:
Maybe simplest just to trim it back. I do worry that the presence of a wrong 
conformation will lead to inaccurate vdw clashes that could negatively affect 
other atoms.

Sent from my iPhone

> On 10 Mar 2023, at 18:25, Phil Jeffrey 
> mailto:pjeff...@princeton.edu>> wrote:
>
> On 3/10/23 4:05 AM, Julia Griese wrote:
>> Hi all,
>> My impression has been that the most common approach these days is to “let 
>> the B-factors take care of it”, but I might be wrong. Maybe it’s time to run 
>> another poll?
>> Personally, I call any other approach R-factor cosmetics. The goal in model 
>> building is not to achieve the lowest possible R-factors, it’s to build the 
>> most physically meaningful, most likely to be correct, model.
>
> And I could call your approach "model cosmetics".
>
> If you can't see the side-chain, you don't know where it is and you probably 
> don't even know where the centroid of the distribution is. Only in the case 
> of very short side-chains with few rotamers can you make a reasonable volume 
> approximation to where the side-chain is and "let the B-factors" smear out 
> the density to cover a range of the projected conformations.
>
> For longer side-chains, if you put it in a single conformation, you are very 
> likely NOT coming close to correctly modeling the actual distribution of the 
> conformations.  So let's circle back on "most likely to be correct model" and 
> ask what we *actually* know about where the atoms are.
>
> Put your disordered Arg in with 10 alternate conformations, each with a 
> refined relative occupancy, and then let the B-factors smear that lot out, 
> and that's your better 

[ccp4bb] Upcoming SSRL Macromolecular Crystallography Proposal Deadlines

[Dunn, Lisa B.]

Dear All,



The next two deadlines for submitting Standard or Block Allocation Group (BAG) 
proposals for macromolecular crystallography (MC) beam time at the Stanford 
Synchrotron Radiation Lightsource (SSRL) are April 1, 2023 (for access 
beginning in May 2023) and July 1, 2023 (for access beginning fall 2023).  
Please visit our website and user 
guide to learn more 
about our beamline parameters, new developments and guidelines.



New or inexperienced users are welcome to contact one of our crystallography 
group leaders, Aina Cohen and Mike 
Soltis to discuss their proposals ahead of 
submission.  For administrative details related to access requirements, please 
contact Lisa Dunn.



If you are not currently a user of our facility the first step is to register 
in our user portal to submit a proposal. 
 Once your registration is accepted the next steps include:

  *   Log into the user portal and select the SSRL tab
  *   Click on Proposals Pull-Down Menu and Select "Submit SSRL PX Proposal"
  *   Select the radio button for "Macromolecular Crystallography Standard 
Proposal" or "MC Block Allocation Group (BAG)"


Note: Submitting a Rapid Access proposal is another option and can be submitted 
at any time. This proposal type is intended for short-term usage until a 
standard proposal can be submitted and reviewed.



Please reference proposal submittal 
guidelines
 for more information.



Best regards,

Lisa Dunn

SSRL User Services

SLAC National Accelerator Laboratory




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Re: [ccp4bb] anomalous data usage

[Boaz Shaanan]

Hi Ian,
The file that aimless/ccp4i produces is exactly as you describe. I noticed the 
weird output from aimless/ccp4i2 and hence don't use.
Cheers,
Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Mar 13, 2023 21:40, Ian Tickle  wrote:

Hi Gottfried

AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default.

Cheers

-- Ian


On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried 
mailto:p...@uni-greifswald.de>> wrote:
Dear all,
  I have a few questions handling (non) anomalous data:
By default aimless seems to produce Iplus and Iminus columns. Can I force it to 
(also) create an Imean column?
What does refmac do, when it gets Iplus and Iminus (and their sigmas) as input. 
Does it take only one of them or does it calculate and use Imean?
Greetings
  Gottfried



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[ccp4bb] PhD studentship in physics and structural biology of protein self-assembly at the University of Edinburgh

[Owen Davies]

Dear colleagues,

I would like to advertise an EPSRC-funded studentship that is available in my 
lab at the University of Edinburgh:

"The physics and structural biology of supramolecular protein self-assembly in 
meiotic chromosome synapsis"

One of the largest protein structures in the cell is the synaptonemal complex 
(SC), which synapses together homologous chromosomes to facilitate their 
recombination during meiosis. This project aims to uncover the physics of how 
the SC is formed through self-assembly of its protein components. This will 
involve a wide range of biochemical, biophysical, structural biology, 
computational and theoretical modelling methods. The laboratory-based methods 
include recombinant protein expression and purification, light and X-ray 
scattering, X-ray crystallography, cryo-EM and cryo-ET, which will include data 
collection at the Diamond Light Source synchrotron facility 
(www.diamond.ac.uk).
 Computational and theoretical methods include AI-based structural modelling, 
molecular dynamics, and building and simulating mathematical models of 
bio-assemblies, which will be performed in collaboration with the Institute for 
Condensed Matter and Complex Systems 
(https://www.ph.ed.ac.uk/icmcs).

This PhD provides an excellent opportunity for a student with a 
biochemical/structural biology, computational or physics background to engage 
in cutting-edge research into the physics of life.

For more information, please see:

https://www.findaphd.com/phds/project/the-physics-and-structural-biology-of-supramolecular-protein-self-assembly-in-meiotic-chromosome-synapsis/?p156057

To apply, please follow the 'institution website' link at the above address and 
complete the application form.

Application deadline: 31st March

Best wishes,

Owen.

Dr Owen Davies
Wellcome Senior Research Fellow
Institute of Cell Biology
University of Edinburgh
Michael Swann Building
Max Born Crescent
Edinburgh EH9 3BF
United Kingdom
The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh 
Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.



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