[ccp4bb] postdoc position at the University of British Columbia, Vancouver.

[Filip Van Petegem]

Dear ccp4bb,


A position is available for a highly motivated and skilled Post-doctoral
Fellow (PDF) at the University of British Columbia in Vancouver, Canada.
The successful candidate will lead cryo-EM experiments to understand
potassium ion channel complex gating and drug regulation in the heart.
The position will be held within the Life Sciences Centre and Departments
of APT and Biochemistry and Molecular Biology at the University of British
Columbia (UBC), under the co-supervision of Dr. David Fedida and Dr. Filip
Van Petegem.



The successful applicant must have a Ph.D. in structural biology. Excellent
theoretical knowledge and practical skills in either X-ray crystallography
or cryo-EM are required. Familiarity with the production and purification
of membrane proteins is a major plus.  The position forms part of a
collaborative, multidisciplinary effort between the Fedida and Van Petegem
laboratories. As such, excellent oral and written English communication
skills, the proven ability to work and as part of a team, and strong
individual research productivity are essential.



Qualified Applicants should submit a cover letter including contact
information for three professional references, and a curriculum vitae
including a list of publications (*n.b.* do not include reprints).
Application materials should be combined into a single PDF document and
submitted via email to david.fed...@ubc.ca and filip.vanpete...@gmail.com



The position is available immediately. The appointment will be at the rank
of Postdoctoral Fellow with a salary commensurate with research experience,
plus benefits (see
https://hr.ubc.ca/benefits/eligibility-enrolment/eligibility-and-plan-cost/faculty-postdoctoral-fellows-employees-and
 ).



*Equity and diversity are essential to academic excellence. An open and
diverse community fosters the inclusion of voices that have been
underrepresented or discouraged. We encourage applications from members of
groups that have been marginalized on any grounds enumerated under the B.C.
Human Rights Code, including sex, sexual orientation, gender identity or
expression, racialization, disability, political belief, religion, marital
or family status, age, and/or status as a First Nation, Metis, Inuit, or
Indigenous person.*






-- 
Filip Van Petegem, PhD
Professor, Dept. of Biochemistry and Molecular Biology
The University of British Columbia
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3

phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/

Twitter: @FilipPetegem



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[ccp4bb] Course on X-ray, electron and neutron crystallography - summer 2021

[Lari Lehtiö]

Dear Colleagues,

We are organizing an Instruct-ERIC training course on X-ray, electron and 
neutron crystallography. The course is virtual, but it includes practicals and 
a possibility to collect data remotely at Diamond Light Source. Participants 
are selected based on applications while the lectures will be available for a 
wider audience. As the course is already at the end of June please forward this 
to the young researchers who could benefit from this opportunity. The deadline 
for the applications is 30th of May.

https://instruct-eric.eu/events/instruct-eric-course-on-macromolecular-x-ray-electron-and-neutron-crystallography

Best regards,

Lari

__
Lari Lehtiö, Professor
Faculty of Biochemistry and Molecular Medicine
P.O.Box 5400
FIN-90014 University of Oulu
Finland
https://www.oulu.fi/university/focusarea/lifelong-health/spearhead-projects/lehtio
https://twitter.com/LabLehtio
_



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[ccp4bb] Structural Biology faculty position, UConn Health Center (UCHC), assistant/associate professor

[Page,Rebecca]

UCONN Health

ASSISTANT/ASSOCIATE PROFESSOR - BASIC SCIENCES


The Department of Molecular Biology and Biophysics (MBB) at UConn Health, 
Farmington, CT, seeks exceptionally creative candidates for an early-to-mid 
career position (tenure-track Assistant or Associate Professor), who use 
molecular and translational approaches to elucidate the molecular basis of 
disease.



Research in MBB integrates multiple approaches to molecularly define the 
proteins and pathways affected in human disease. Our studies span the 
structural biology of cancer drug targets to the mechanistic interplay between 
viruses and human cells. We seek creative and innovative candidates whose 
research interests and accomplishments complement and further existing 
strengths in the department and the larger UConn Health research community. 
Ideal candidates will have a research program focused on molecular signaling 
(including but not limited to areas such as posttranslational modifications, 
DNA repair, protein ubiquitination, kinase/phosphatase signaling/regulation) 
and/or the structure, function and regulation of proteins involved in signaling 
processes. Programs that focus on the identification and development of 
translational outcomes, including probes that will allow for in-depth analysis 
of key biological pathways or novel drug-like molecules, are also of particular 
interest.



MBB and UConn Health provides a rich and diverse research environment and is 
deeply committed to the development and success of its incoming faculty. The 
UConn Health School of Medicine is home to 30 departments and institutes, 
including Cell Biology, Genetics and Genome Sciences, the Richard D. Berlin 
Center for Cell Analysis and Modeling, among others. It is also closely 
affiliated with The Jackson Laboratory, which is housed on the same campus. 
Candidates will also have access to 22 exceptional core facilities, including 
the CCAM Microscopy, NMR Structural Biology and Biophysics, High-Performance 
Computing, EM, MS, FACS and Histology core facilities. UConn Health also offers 
competitive salaries and excellent benefits.



Successful applications will have a PhD, MD or equivalent degree; a sustained 
record of exceptional scholarly success; and the promise of future innovative 
accomplishments via a proposed (early-career) or established (mid-career, 
including evidence of successful extramural grant writing) research programs 
that utilizes state-of-the-art molecular, genetic, cellular, biochemical, 
biophysical and/or structural methodologies. Candidates are also expected to be 
highly collaborative and integrate well with the growing number of researchers 
and physician scientists in the basic and clinical departments of UConn Health. 
Candidates with ongoing funded research are encouraged to apply.



Please visit https://jobs.uchc.edu/CSS_External/CSSPage_Welcome.asp and select 
'Molecular Biology and Biophysics' under 'department' (job number 2021-650).

?

To apply, interested individuals should submit a curriculum vitae, cover 
letter, statements of research plans (up to 3 pages) and teaching (up to 1 
page) and arrange for the submission of three letters of reference on 
letterhead with signature.



Questions regarding this position should be addressed to Wolfgang Peti, 
Department Head, Molecular Biology & Biophysics at 
p...@uchc.edu.



UConn Health is an affirmative action employer, in addition to an EEO and 
M/F/V/PWD/PV employer.




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[ccp4bb] Job Posting - Protein Scientists positions at Peak Proteins Ltd.

[Derek Ogg]

Dear Colleagues,
                   There are currently a number of job 
openings at Peak Proteins Ltd. for exceptional protein scientists 
including graduate level positions right up to Director.


If interested more information including job descriptions can be found 
here: https://peakproteins.com/join-us/


Peak Proteins is a vibrant contract research organisation (CRO) that 
provides research services to clients globally and is located on the 
Alderley Park site in Cheshire; only 18 miles from the heart of 
Manchester and has easy access to the Peak District, Snowdonia and Lake 
District national parks.



Derek J. Ogg
Chief Scientific Officer
___
Peak Proteins Ltd.
Alderley Park,
Macclesfield,
Cheshire,
SK10 4TJ.





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Re: [ccp4bb] sugestions on weak diffracting protein crystals

[Patrick Shaw Stewart]

Hi Deepak

In my opinion, rMMS microseeding, ie adding crushed seed crystals into *random
screens*, should be used routinely in most crystallization projects.  It
gives much more control, in particular you can control the number of
crystals per drop.

In a case like this, I would use it straight away - use the crystals that
you showed us to make a seed-stock.


  The protein is a DNA binding protein and I have crystallized and solved
> the structure of this protein with its DNA partner


All seed-stocks are not the same - one may work but another may not.  Or
one particular seed-stock may give crystals with a different unit cell or
space group.  Since you have a *family *of constructs, you should try
cross-seeding with all the other (related) crystals that you have.

At the beginning of the project, to keep the number of experiments down,
you can mix together several different seed-stocks.  However it is
recommended that you keep crystals where the main precipitant was PEG
separate from crystals where the main precipitant was salt.

https://doi.org/10.1107/S2053230X14012552
https://doi.org/10.1107/S0907444907007652


or google MMS or rMMS.

Good luck, Patrick


On Tue, May 18, 2021 at 11:19 AM Deepak Deepak 
wrote:

> Dear all,
>
> I have got multiple crystals (see picture 1) of a protein (8kDa) with a
> helical aromatic oligoamide foldamer (5kDa) but these crystals *diffract
> very poorly *(see the diffraction pattern in picture 2).
>
> I prepare a 1.3mM:1.3mM complex of protein: foldamer in 20mM Tris, pH 7.5
> buffer. Crystals grew in 3-5 days in sitting and hanging drop at 20 Deg C
> and 25 Deg C in the following conditions:
>
> *- 20% PEG 400, 0.1M MES pH 6.0*
> *-20% PEG 400, 0.1M Sodium Cacodylate pH 6.0*
>
> *Multiple cryo used were:*
> *-25%Glycerol in mother solution*
>  -30% glycerol in water
> *-30%PEG 400,*
> *-35% PEG 400*
> *-20% PEG 8000 + 40% PEG 400 mix*
>
> Kindly suggest some methods/modifications on how can I improve the
> resolution and get better-diffracting crystals. Please let me know if you
> need more information.
>
> Kind regards,
> Deepak
> Ph.D. Student
>
> PS: The protein is a DNA binding protein and I have crystallized and
> solved the structure of this protein with its DNA partner and now I
> crystallized it with our foldamers but diffraction is not good. There are
> multiple structures of the Protein+DNA complex in literature but *no
> apo-protein structure *as the protein needs a binding partner to
> crystallize. *We already have solution studies showing a good binding.*
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>


-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36



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[ccp4bb] Lectureship Position at University of Essex

[Prischi, Filippo]

Dear all,

We have a Lectureship position available in the School of Life Sciences at 
University of Essex. We encourage applicants with a skillset and research 
interest in structural biology, biochemistry, molecular biology and 
computational biology.
For more info and details on how to apply, please follow this link 
https://vacancies.essex.ac.uk/tlive_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=665656O0U2=9918109NEm=USA=IwAR1ZPrMHwNZ7LxF_2crDeQBPlg0dZ0ilzS9DfrqMWxE-kZ9NQd1VzOkCuoI

Kind Regards,
Filippo

~~
Dr Filippo Prischi
Senior Lecturer in Biochemistry
School of Life Sciences
University of Essex

T.  +44 (0)1206 873370
E.  fpris...@essex.ac.uk
► http://www.essex.ac.uk/bs/staff/profile.aspx?ID=4512



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[ccp4bb] The CBMS SAXS and MX workbenches

[Stojanoff, Vivian]

Dear Colleagues,

The Center for Biomolecular Structure (CBMS), at the National Synchrotron Light 
Source II,  invites you to participate in the BioMolecular Solution Scattering 
(SAXS/WAXS) and Macromolecular Crystallography (MX) workbenches.  Scheduled 
back-to-back, June 7 through 9, these virtual training workshops are aimed at 
researchers that would like to know more about forefront techniques and methods 
available at the CBMS structural biology beamlines.  Participants are 
encouraged to register for both workshops (https://www.bnl.gov/cbmsworkbench/). 
 If you would like to analyze your sample(s) as part of the workshop,  contact 
James Byrnes (jbyr...@bnl.gov) for SAXS/WAXS and Vivian Stojanoff 
(stoja...@bnl.gov) for MX samples no later than May 28, 2021.

Registration is FREE!  Early registration closes May 24;  Registration closes 
May 28.

https://www.bnl.gov/cbmsworkbench/
Center for BioMolecular Structure 
Workbenches
Scope. The BioMolecular Solution Scattering (SAXS/WAXS) and Macromolecular 
Crystallography (MX) workbenches span three days of virtual training classes 
aimed at researchers that would like to know more about forefront techniques 
and methods available to scientists at BNL’s Center for Biomolecular Structure 
(CBMS) structural biology beamlines.
www.bnl.gov


Kind regards,

The CBMS Team
-
Center for Biomolecular Structure
https://www.bnl.gov/nsls2/lifesciences/
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973




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[ccp4bb] postdoc position at Imperial College London

[Zhang, Xiaodong]

Dear all

There is a postdoc position available in my lab. For details and how to apply, 
please follow this link.

https://www.imperial.ac.uk/jobs/description/MED02162/research-associate-structural-biology

kind regards

Prof Xiaodong Zhang, Section of Structural Biology, Department of Infectious 
Disease, Imperial College London
Room 104, Sir Alexander Fleming Building, South Kensington, SW7 2AZ
xiaodong.zh...@imperial.ac.uk, (0) 207 
594 3151, http://www.imperial.ac.uk/people/xiaodong.zhang

PA - Ms Kasia Pearce, 
structuralbiolog...@imperial.ac.uk, 
(0) 207 594 2917





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Re: [ccp4bb] Shortest distance between side chains

[Eleanor Dodson]

Yes - contacts or distang gives you a list of distances. PISA a list of h
bonds and salt bridges - all with associated sym ops.
But none produce a complete table - PISA output prob the best.
Eleanor

distang gives you this sort of information but i guess it is far too
detailed?

 R  125 NA   R5 NH1  A  3.599 X,Y,Z   1.00
25.73

 R  125 NA   H  121 OA  3.493 X,Y,Z   1.00
26.73

 R  125 NA   A  122 CA  3.767 X,Y,Z   1.00
24.41

 R  125 NA   A  122 OA  3.199 X,Y,Z   1.00
24.69

 R  125 NA   W  123 CA  3.509 X,Y,Z   1.00
25.05

 R  125 CA   A   A  122 OA  3.926 X,Y,Z   1.00
26.28

 R  125 CB   A   A  122 OA  3.569 X,Y,Z   1.00
28.11

 R  125 NE   A   N  113 OD1  A  3.934 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
34.82

 R  125 CZ   A   N  113 OD1  A  3.360 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
35.77

 R  125 CZ   A   A  122 NA  3.964 X,Y,Z   1.00
31.89

 R  125 CZ   A   A  122 CA   A  3.631 X,Y,Z   1.00
32.07

 R  125 NH1  A   N  113 OD1  A  3.592 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
36.32

 R  125 NH1  A   A  122 CA   A  3.714 X,Y,Z   1.00
32.62

 R  125 NH1  A   A  122 CB   A  3.745 X,Y,Z   1.00
32.41

 R  125 NH2  A   N  113 CG   A  3.947 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
32.44

 R  125 NH2  A   N  113 OD1  A  3.274 -X+1/2,Y+1/2,-Z [0-1+1] 1.00
34.03



On Wed, 19 May 2021 at 10:19, Hari shankar <
465d10db143e-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Misha,
>
> There is a program in ccp4 called contacts that will give you this
> information. You can alter entry parameters to show you the relevant
> information.
>
> I think you can also try PISA server from EMBL-EBI.
>
> I reckon both these programs show you all distances and you may have to
> manually pick out the shortest ones.
>
> Regards
> Hari
>
> On Wednesday, May 19, 2021, 16:54, Isupov, Michail 
> wrote:
>
>
> Hi
>
> I am wondering if there  is a simple program that would convert a pdb file
> into a matrix that
>
> shows the smallest distance between all pairs of amino-acid side chains?
>
>  Thanks,
> Misha
>
> --
>
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>
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Re: [ccp4bb] Shortest distance between side chains

[Hari shankar]

Dear Misha,
There is a program in ccp4 called contacts that will give you this information. 
You can alter entry parameters to show you the relevant information.
I think you can also try PISA server from EMBL-EBI. 
I reckon both these programs show you all distances and you may have to 
manually pick out the shortest ones. 

Regards
Hari


On Wednesday, May 19, 2021, 16:54, Isupov, Michail  
wrote:

#yiv2028539353 P {margin-top:0;margin-bottom:0;}
Hi
I am wondering if there  is a simple program that would convert a pdb file into 
a matrix that
shows the smallest distance between all pairs of amino-acid side chains?
 Thanks,
Misha

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[ccp4bb] Shortest distance between side chains

[Isupov, Michail]

Hi

I am wondering if there  is a simple program that would convert a pdb file into 
a matrix that

shows the smallest distance between all pairs of amino-acid side chains?

 Thanks,
Misha



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