[ccp4bb] Call for Stanford-SLAC CryoEM Center (S2C2) Applications

[Dunn, Lisa B.]

We would like to announce the full operation of two new Titan-Krios electron 
microscopes with high-throughput detectors (K3 and Falcon 4) dedicated to high 
resolution biological single particle data collection at the Stanford-SLAC 
CryoEM Center (S2C2) located in the new Arrillaga Science Center at SLAC, 
Stanford University. This increased capacity will allow more users, longer data 
collection sessions, and more sessions per project. We also offer cryoEM 
instruments for in-residence training in cryoEM using our other Titan-Krios or 
Talos-Arctica electron microscopes. We welcome anyone with an interest to apply 
for time at our facility for data collection and/or for in-depth training in 
high resolution cryoEM. A rapid turnaround on project application evaluation by 
our expert panel is in place. More information on the user and trainee project 
application can be found at  
https://cryoem.slac.stanford.edu/s2c2/project-requests and 
https://cryoem.slac.stanford.edu/s2c2/training/residence-training-program


Stay well and safe !

Wah Chiu, Director of Stanford-SLAC CryoEM Center




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Crystallographer position at Sosei Heptares

[Prakash Rucktooa]

Dear all,

We are currently seeking a talented crystallographer to join the
Biomolecular Structure group at our research facility (Granta Park,
Cambridge, UK), to work on GPCR structure determination to enable drug
discovery efforts.

The ideal candidate would hold a PhD in protein crystallography or a
related discipline and be familiar with the purification of proteins from
recombinant expression systems, setting up crystallisation experiments
including Lipidic Cubic Phase crystallisation, X-ray data collection, data
processing, structure solution and refinement of novel structures.

The successful candidate will join the Crystallography team headed by Dr.
Andrew Doré, and will be employed by Heptares Therapeutics Ltd, a UK wholly
owned subsidiary of Sosei Group Corporation.

We offer a competitive salary, commensurate with qualifications and
experience, and benefits package including pension and healthcare schemes.

Applications should include a covering letter, providing a short
description of the background to their interest in the role, with
curriculum vitae including the names and contact details for two referees.
Please apply through our on-line jobs portal with your application in pdf
format, quoting reference number 2020-6BMS.

The closing date for applications is 4th September 2020.

Strictly No Agencies

Please do not reply directly to this email and apply through our career
portal :
https://cezanneondemand.intervieweb.it/heptares/jobs/crystallographer_10269/en/


Kind regards,

Prakash RUCKTOOA



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] XFEL Computational Crystallographer Research Scientist at Berkeley Lab

[Nicholas Sauter]

Dear XFEL and Structural Biology Colleagues,

Please note that we have an open Research Scientist position in Berkeley
Lab’s *Molecular Biophysics and Integrated Bioimaging Division
.*  The successful candidate,
with a strong interest in high-performance computing and an intuitive feel  for
experimental data, will work on our two projects 1) the DIALS/cctbx.xfel
project aiming to utilize XFEL crystallographic diffraction and
spectroscopy for increasingly complex studies on metalloenzymes and other
macromolecular complexes, and 2) the Exascale Computing Project,
specifically my Data Analytics for X-ray Free Electron Lasers (XFELs) group,
seeking to support high data rate analysis for XFEL experiments, accounting
for advances in light sources and detectors.

The group’s work will include:


   - Photosystem II, discovering the sequence of redox events leading to
   the release of molecular oxygen, using a combination of
time-resolved crystallography
   and X-ray emission spectroscopy.
   https://doi.org/10.1038/s41586-018-0681-2
   - Examining the electronic environment of metalloenzyme catalytic
   metals, with detection based on anomalous scattering. Data processing will
   engage high-performance computing facilities to analyze experimental data.
https://doi.org/10.1107/S205979832418


Please have a look at our job posting at
https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=90604.  The posting
will be open till August 18.

Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Research technician Position in Vienna

[Kristina Djinovic Carugo]

**

*Research Technician Position in Djinovic Group*

*/Dept. of Structural and Computational Biology/*

*Max Perutz Labs, University of Vienna*

**

*Research technician position*is available in the 
*Djinovic-Carugo**laboratory* 
in 
the Department for Structural and Computational Biology, Max Perutz 
Laboratories of the University of Vienna, Austria.


*The Position *

You will provide specific technical support to a research projects 
related to structural biology of muscle Z-disk interactome, and assist 
in the lab on a variety of biochemical, biophysical and structural 
studies, including gene cloning, protein expression, purification, and 
characterization of purified protein by various biochemical and 
biophysical techniques. You are also expected to help with the 
management of the laboratory, together with lab-manager of the research 
group.


*The Candidate*

We are looking for a highly motivated candidate who is enthusiastic 
about working in an ambitious and multidisciplinary team and fits the 
following profile:


·Degree in Biochemistry, Chemistry, Molecular Biology, or a related 
field (MTA, CTA, B.Sc., M.Sc., Mag., DI)


·Excellent understanding of the theoretical and technical principles of 
conventional techniques in protein biochemistry and molecular biology, 
such as molecular cloning, protein expression and purification and 
biophysical characterization.


·Practical experience with molecular biology, molecular cloning 
techniques, protein purification, biochemistry is needed; experience in 
insect and/or mammalian cell culture is an asset. Experience with 
biophysical characterization and structure determination will be highly 
valued.


·High accuracy, reliability and excellent interpersonal and 
organizational skills are a requirement.


·She/He should be willing to acquire further skills and contribute to 
the development of new methods.


·The working language in Max Perutz labs is English, excellent command 
of English (spoken and written) is a must, German skills are an asset. 
Computer literacy and experience of using Microsoft Word, Excel and 
PowerPoint is essential.


*The Laboratory*

Djinovic Lab 
isinterested 
in the molecular mechanisms underlying the architecture and assembly of 
thestriated musclesarcomeres, in particular Z-discs. We use an 
integrative structural biology approach combining biophysical and 
high-resolution structural studies (macromolecular crystallography being 
the main technique) with lower resolution approaches (small-angle 
scattering, electron microscopy) combined with chemical cross-linking 
mass-spectrometry and NMR.


*The Institute*

The Department for Structural and Computational Biology 
is equipped with state-of-the-art 
instrumentation/facilities to carry out all steps from cloning, protein 
expression and purification, to X-ray diffraction, biomolecular NMR, as 
well as for a series of biophysical and optical spectroscopy techniques. 
The Department is part of the Max Perutz Labs 
, established by the University of 
Vienna and the Medical University of Vienna to provide an environment 
for excellent, internationally recognized research and education in the 
field of Molecular Biology. Dedicated to a mechanistic understanding of 
fundamental biomedical processes, scientists at the Max Perutz Labs aim 
to link breakthroughs in basic research to advances in human health. 
Perutz Labs are located on Vienna Campus Biocenter 
, which is the largest life sciences 
hub in Austria. Vienna Campus Biocenter offers access to excellent 
Scientific Core Facilities 
. Vienna is frequently 
ranked as the world’s best city to live in. It is a United Nations city 
with a large English-speaking community.


*The Offer*

We offer a challenging position in dynamic and multidisciplinary team 
and contribute to our research on fascinating Z-discs assembly within a 
highly international environment. This is a 30-35 h/week post for up to 
6 years, subject to successful evaluation after one year. The post is 
funded by the University of Vienna, and is available for *start in 
October 2020*. This position is remunerated with a minimum gross salary 
accordingto collective agreement of Univ. Vienna, 33.903,80 Euro for 40 
hours/year, definite salary depends on the previous experiences.


*Application details*: if you want to join an exciting project and 
become a member of our interdisciplinary team, please compile an 
application package containing:


·Letter of interest

·Your CV

·Contact details for two references

and submit your application to *Kristina Djinovic Carugo *(to /e-mail: 
*admin.v...@univie.ac.at*/) by *September 21^st , 2020. *Review of 
applications will begin immediate

Re: [ccp4bb] Advice on DNA negative staining

[Artem Evdokimov]

Hiya

*Half an hour in the library saves a month of research.* That's what my
late advisor Dr. Frolow used to say a lot and he was not wrong.

Erenpreisa J. 1981. Staining of DNA with uranlyacetate in hydrolyzed
ultrathin sections. Acta histochem 68(1): 22-26

there are several very clever methods, using depurination and various
chemical treatments (e.g. phenylhydrazine) followed by staining with
various heavy atoms (tungsten derivatives)

In general, shadowing with tungsten is a highly adequate method, see for
example gorgeous images of replicaiton forks here:

https://www.jbc.org/content/285/18/13349.full.pdf

Artem

- Cosmic Cats approve of this message


On Tue, Aug 4, 2020 at 7:11 AM Panne, Daniel (Prof.) <
daniel.pa...@leicester.ac.uk> wrote:

> Hi Meytal,
>
> 1. The concentration seems way too high at 254mg/ml. Typically 0.1-5mg/ml
> are used.
> 2. Uranyl ions react with phosphate groups resulting in positive stain.
> The resulting contrast is frequently poor.
> 3. Rotary shadowing can be used to enhance contrast.
>
> Best,
> Daniel
>
>
> On 4 Aug 2020, at 11:20, Marin van Heel <
> 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Dear Meytal,
>
> Suggestion: Apply a strong high-pass filter to the images before visually
> judging them!
>
> Marin
>
> On Tue, Aug 4, 2020 at 3:50 AM Meytal Galilee 
> wrote:
>
>> Hi Arunabh Athreya,
>> Sure (this is the linear 2200 b.p. at 175uM)
>> 
>>
>>
>>
>> Get Outlook for Android
>> 
>>
>>
>> --
>> *From:* Arunabh Athreya 
>> *Sent:* Tuesday, August 4, 2020, 12:54
>> *To:* CCP4BB@JISCMAIL.AC.UK; Meytal Galilee
>> *Subject:* Re: Advice on DNA negative staining
>>
>> Hi Meytal
>>
>> Do you have an EM image snapped from your negative staining sample?
>>
>> Get Outlook for Android
>> 
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Advice on DNA negative staining

[Panne, Daniel (Prof.)]

Hi Meytal,

1. The concentration seems way too high at 254mg/ml. Typically 0.1-5mg/ml are 
used.
2. Uranyl ions react with phosphate groups resulting in positive stain. The 
resulting contrast is frequently poor.
3. Rotary shadowing can be used to enhance contrast.

Best,
Daniel


On 4 Aug 2020, at 11:20, Marin van Heel 
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>
 wrote:


Dear Meytal,

Suggestion: Apply a strong high-pass filter to the images before visually 
judging them!

Marin

On Tue, Aug 4, 2020 at 3:50 AM Meytal Galilee 
mailto:meytal.gali...@gmail.com>> wrote:
Hi Arunabh Athreya,
Sure (this is the linear 2200 b.p. at 175uM)




Get Outlook for 
Android



From: Arunabh Athreya mailto:arun...@iisc.ac.in>>
Sent: Tuesday, August 4, 2020, 12:54
To: CCP4BB@JISCMAIL.AC.UK; Meytal Galilee
Subject: Re: Advice on DNA negative staining

Hi Meytal

Do you have an EM image snapped from your negative staining sample?

Get Outlook for 
Android





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Job advert for a structural biology/biophysics role in PROTAC drug discovery

[David Zollman (Staff)]

Dear all,



We have a particularly exciting job opportunity in our lab, the PROTAC drug 
discovery collaboration between the group of Prof Alessio Ciulli at the 
University of Dundee and Boehringer Ingelheim. Our group are world leaders in 
the field of PROTACs, which has rapidly become one of the hottest topics in 
drug discovery. We are looking to recruit one new team member to help expand 
our structural biology, protein production and biophysical efforts.

If you have relevant doctoral/post-doctoral experience and are interested in 
joining a highly motivated, dynamic, interdisciplinary group at the interface 
of academia and industry, the deadline for application is Sunday 30th August. 
The post is available to start on 1st September 2020 and is for 3 years. Salary 
will depend on experience, but the appointment will be at Grade 7 on the 
University's salary scale (between £32,817 - £40,322). The full job advert 
including details on how to apply can be found at 
https://ig5.i-grasp.com/fe/tpl_uod01.asp?newms=jj&id=104360&aid=14197



Best wishes,

David Zollman

The University of Dundee is a registered Scottish Charity, No: SC015096



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Two scientist / software developer positions on neutron diffraction at RAL

[David Waterman]

Dear all,

Please be reminded about the two posts advertised below. You can ignore the
closing date of 2nd August shown here - the first post has been adjusted to
close on the 9th August as well, to be in line with the other position.

Best wishes
-- David


On Thu, 23 Jul 2020 at 19:25, David Waterman  wrote:

> Dear all,
>
> The STFC Scientific Computing Department and ISIS neutron source are
> looking for two programmer scientists, who will develop the next generation
> of single-crystal neutron diffraction analysis software for the
> time-of-flight technique. The software will extend the DIALS data
> processing package and be made available within the Mantid framework.
>
> The two positions are closely related, and indeed the successful
> candidates will be expected to work together, and with others, in a
> cross-campus collaboration at the Rutherford Appleton Laboratory. Broadly,
> the ISIS post has a stronger focus on crystallographic algorithm
> development while the SCD post emphasises implementation of the software,
> but there is much overlap and a similar skillset is required. Those
> interested may prefer to apply for both positions! The posts are initially
> for 18 months.
>
> Please see here for further details and to apply:
>
> https://www.topcareer.jobs/Vacancy/irc254133_10766.aspx (closes 2nd
> August)
> https://www.topcareer.jobs/Vacancy/irc254236_10785.aspx (closes 9th
> August)
>
> Please feel free to contact david.water...@stfc.ac.uk or
> silvia.cape...@stfc.ac.uk if you have any questions.
>
> Best wishes
>
> -- David
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Help needed (input files)

[Eugene Osipov]

Fred,
you could use the Academic version of Desmond freely available here:
https://www.deshawresearch.com/resources_desmond.html
The only difference from the commercial version is absence of OPLS3e force
field but you still could use GPU.


вт, 4 авг. 2020 г. в 10:08, Fred Vellieux :

> Hello,
>
> I need to perform some MD calculations and then trajectories of some
> small molecules analyzed.
>
> What I have is
> 1. protein
> 2. cofactor (FAD)
> 3. small molecule (either single O2 atom or single Chlorine atom)
> 4. crystallographic waters
>
> The software I can access is either Gromacs (with yum install) or
> perhaps Desmond.
>
> I have tried and tried to get this to run (for 6 months perhaps), to no
> avail. The input files located on the web do not work on the version of
> Gromacs provided by the yum install command. The Maestro license
> (required in order to get Desmond to run) is too expensive.
>
> Is there a kind soul somewhere that would have suitable input files that
> would do all the above steps and who'd be willing to pass them on to me?
>
> What needs to be done is:
> add waters to the crystallographic waters in order to fill a box of
> suitable size
> generate parameter and topology files for each component separately
> merge these into global parameter and topology files for the system
> run initial Energy Minimization
> run M.D. simulations
> analize the trajectories of the small molecules.
>
> Thanks in advance.
>
> Fred.
>
> --
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>


-- 
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Help needed (input files)

[Fred Vellieux]

Hello,

I need to perform some MD calculations and then trajectories of some 
small molecules analyzed.


What I have is
1. protein
2. cofactor (FAD)
3. small molecule (either single O2 atom or single Chlorine atom)
4. crystallographic waters

The software I can access is either Gromacs (with yum install) or 
perhaps Desmond.


I have tried and tried to get this to run (for 6 months perhaps), to no 
avail. The input files located on the web do not work on the version of 
Gromacs provided by the yum install command. The Maestro license 
(required in order to get Desmond to run) is too expensive.


Is there a kind soul somewhere that would have suitable input files that 
would do all the above steps and who'd be willing to pass them on to me?


What needs to be done is:
add waters to the crystallographic waters in order to fill a box of 
suitable size

generate parameter and topology files for each component separately
merge these into global parameter and topology files for the system
run initial Energy Minimization
run M.D. simulations
analize the trajectories of the small molecules.

Thanks in advance.

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 available at 
https://www.jiscmail.ac.uk/policyandsecurity/