[ccp4bb] Announcement of the crystallographic school in Thailand

[Sanishvili, Ruslan]

Dear Colleagues,
We are delighted to announce the 2nd edition of the crystallographic school in 
Thailand, SEA COAST - SouthEast Asian Crystallographic Overview And Systematic 
Training.
The workshop will take place on January 21 - 29, 2020, at the King Mongkut's 
University of Technology Thonburi (KMUTT), in Bangkok, Thailand.

The school will cover all aspects of macromolecular crystallography and many 
popular software programs, such as CCP4, Global Phasing, Phenix, SHELX, 
ARCIMBOLDO, ARP/wARP, Auto-Rickshaw, Coot, DIALS, MOSFLM, PISA, Phaser, XDS 
etc. will be taught by the developers and other lead experts.

The course is designed for graduate students, postdoctoral researchers, and 
more established young scientists both from academia and industry. The workshop 
is mainly intended for researchers from the South-east Asian region, but 
applications from elsewhere will be strongly considered as well.

On-line applications are now being accepted until November 30, 2019. Total of 
30 applicants will be selected for participation.
For the school program, the list of confirmed speakers, application process and 
other details please visit the school website http://seacoast.kmutt.ac.th/

With any questions, please contact Leela Ruckthong 
(leela@mail.kmutt.ac.th) or Ruslan 
(Nukri) Sanishvili nu...@anl.gov
We hope to see you in Bangkok in January!
Leela, Garib, Ronan and Nukri


Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov




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Re: [ccp4bb] coiled coil molecular replacement

[Kay Diederichs]

Hi Tommi,

Arcimboldo is a good program for that - see 
http://scripts.iucr.org/cgi-bin/paper?cb5097

HTH

Kay

On Mon, 7 Oct 2019 21:33:44 +, Kajander, Tommi A 
 wrote:

>Hello, 
>
>We have a bit tricky case of coiled coil protein with good data (2.05Å) for 
>dimeric coiled coil (dimer in AU)  - looks like AMPLE might be a way
>to solve such cases, if you know other good programs please suggest (Better 
>yet if there is a clear how-to manual)
>
>Some technical tips on usage for generation of fragments for AMPLE would be of 
>help, not completely on top of that… (running the QUARK server, the real 
>sequence is bit over 200 aa so not sure what is the best approach here? 
>Rosetta? any how-to for that.. well i am running Robetta fragments too). 
>
>with AMPLE can I do this with the online server or better run locally (need 
>Rosetta installed I take it?)
>
>Suppose I could try Rosetta-MR also, but to my recollection that requires some 
>kind of a phaser hit first to be improved, and i dont think I am there.
>
>Thanks for any comments,
>
>Best,
>Tommi 
>
>
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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[ccp4bb] coiled coil molecular replacement

[Kajander, Tommi A]

Hello, 

We have a bit tricky case of coiled coil protein with good data (2.05Å) for 
dimeric coiled coil (dimer in AU)  - looks like AMPLE might be a way
to solve such cases, if you know other good programs please suggest (Better yet 
if there is a clear how-to manual)

Some technical tips on usage for generation of fragments for AMPLE would be of 
help, not completely on top of that… (running the QUARK server, the real 
sequence is bit over 200 aa so not sure what is the best approach here? 
Rosetta? any how-to for that.. well i am running Robetta fragments too). 

with AMPLE can I do this with the online server or better run locally (need 
Rosetta installed I take it?)

Suppose I could try Rosetta-MR also, but to my recollection that requires some 
kind of a phaser hit first to be improved, and i dont think I am there.

Thanks for any comments,

Best,
Tommi 






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Re: [ccp4bb] Shelx and debian 10

[Tim Gruene]

Dear Bernhard,

as Peter mentioned, you need to reboot the system with the kernel parameter 
vsyscall=emulate. On Debian, you edit the file

/etc/default/grub 

and modify the value of 
GRUB_CMDLINE_LINUX_DEFAULT="quiet vsyscall=emulate"

(default here is GRUB_CMDLINE_LINUX_DEFAULT="quiet")

Once saved,you run the command 'update-grub' and reboot the system.

@Peter: are you sure that without 'vsyscall=emulate' linux binaries need to be 
dynamically linked? I would be very surprised if the linux kernel would 
disable statically linked binaries. I rather think that the vanilla versions 
of shelx c/d/e (from shelx.uni-goettingen.de) are compiled with an obsolete 
compiler / obsolete compiler options. 

Best regards,
Tim


On Monday, October 7, 2019 5:53:44 PM CEST Peter Keller wrote:
> Dear Bernhard,
> 
> We had this issue drawn to our attention last year by an early adopter
> of Debian 10 while it was still in testing. I thought that it was a bug,
> and submitted a report accordingly here:
> . I was told
> that it is not a bug, but a feature ;-)
> 
> If you are able, you could try setting the kernel parameter
> vsyscall=emulate. In the longer term, SHELXC/D/E will have to be rebuilt
> to support systems where the vsyscall has been disabled. This means they
> have to be dynamic executables that include the following in the output
> of 'ldd':
> 
> % ldd /bin/bash
>  linux-vdso.so.1 (0x7fff50952000)
>  
> 
> All current distros use vDSO, so this shouldn't cause portability
> problems by itself, but handling dynamic executables can be trickier
> than static ones.
> 
> For a little more background, see 
> 
> Finally, you have my commiserations: although this change has been a
> long time coming, it hasn't attracted a lot of attention. It was bound
> to catch users of static executables by surprise.
> 
> Regards,
> 
> Peter.
> 
> On 07/10/2019 16:05, Bernhard Rupp wrote:
> > Hi Fellows,
> > 
> > we updated to Debian 10 on the local workshop computers, and reinstalled
> > 
> > Coot and ccp4. All fine.
> > 
> > Problem: Shelxc/d/e/  does not run, and
> > 
> > the call exits immediately sans any message.
> > 
> > This holds for the binaries included in ccp4 as well as for those from
> > the SHELX site.
> > 
> > The executables from CCP4 and SHELX site – same file size, probably
> > same - run fine under Debian 9.
> > 
> > I suspect a library problem.
> > 
> > Does some kind soul have CDE binaries for Debian 10 to share?
> > 
> > Many thx in advance, BR
> > 
> > --
> > --
> > 
> > Bernhard Rupp
> > 
> > Department of Genetics and Pharmacology
> > 
> > Institute of Genetic Epidemiology
> > 
> > Medical University Innsbruck
> > 
> > Schöpfstrasse 41
> > 
> > A 6020 Innsbruck – Austria
> > 
> > +43 (676) 571-0536
> > 
> > bernhard.r...@i-med.ac.at
> > 
> > --
> > --
> > 
> > k.k. Hofkristallamt
> > 
> > San Diego, CA 92084
> > 
> > 001 (925) 209-7429
> > 
> > b...@ruppweb.org
> > 
> > b...@hofkristallamt.org
> > 
> > http://www.ruppweb.org/
> > 
> > ---
> > 
> > 
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] Beam Time for Macromolecular Crystallography at CHESS: Rapid Access Available for Fall 2019

[Aaron Finke]

Dear CCP4bb Users,

The new and fully-upgraded macromolecular crystallography beamline at CHESS, 
FlexX, is now accepting Rapid Access proposals for the Fall 2019 run. Rapid 
Access ensures fast proposal review turnaround (two weeks or less) for access 
to slots still available for this run. Please include the words "RAPID ACCESS" 
in the proposal title when submitting for rapid turnaround.

SPRING 2020 RUN: The regular proposal deadline for the Spring 2020 run is Oct. 
28, 2019.

The FlexX station (beamline ID7B2) is the all-new macromolecular 
crystallography station at CHESS. The recently completed CHESS upgrade has 
considerably improved our capabilities in order to meet the the stringent 
demands of every user. Current capabilities include:
* undulator source with multilayer monochromator for high flux. 7-14 keV energy 
range. Standard beam sizes available: 100 x 100 um (H x V FWHM) and 10 x 10 um 
microbeam.
* single-axis goniostat, PILATUS3 6M detector, BAM2 automounter accepting 
Unipucks
* remote data collection with on-site CHESS staff scientist support
* we welcome "non-standard" experiments! The staff at CHESS is more than happy 
to work with users who want to perform experiments beyond standard rotation 
cryocrystallography. Interested in trying serial crystallography for 
room-temperature data collection, or microcrystals? High-pressure cryocooling 
for reduced mosaicity? High-pressure crystallography with a diamond anvil cell? 
We can accommodate your needs and more!

Interested? Learn how to submit a proposal here: 
https://www.chess.cornell.edu/users/new-user-guide

Feel free to contact me with any questions!

Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu




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Re: [ccp4bb] Shelx and debian 10

[Peter Keller]

Dear Bernhard,

We had this issue drawn to our attention last year by an early adopter 
of Debian 10 while it was still in testing. I thought that it was a bug, 
and submitted a report accordingly here: 
. I was told 
that it is not a bug, but a feature ;-)


If you are able, you could try setting the kernel parameter 
vsyscall=emulate. In the longer term, SHELXC/D/E will have to be rebuilt 
to support systems where the vsyscall has been disabled. This means they 
have to be dynamic executables that include the following in the output 
of 'ldd':


% ldd /bin/bash
    linux-vdso.so.1 (0x7fff50952000)
    

All current distros use vDSO, so this shouldn't cause portability 
problems by itself, but handling dynamic executables can be trickier 
than static ones.


For a little more background, see 

Finally, you have my commiserations: although this change has been a 
long time coming, it hasn't attracted a lot of attention. It was bound 
to catch users of static executables by surprise.


Regards,

Peter.


On 07/10/2019 16:05, Bernhard Rupp wrote:


Hi Fellows,

we updated to Debian 10 on the local workshop computers, and reinstalled

Coot and ccp4. All fine.

Problem: Shelxc/d/e/  does not run, and

the call exits immediately sans any message.

This holds for the binaries included in ccp4 as well as for those from 
the SHELX site.


The executables from CCP4 and SHELX site – same file size, probably 
same - run fine under Debian 9.


I suspect a library problem.

Does some kind soul have CDE binaries for Debian 10 to share?

Many thx in advance, BR



Bernhard Rupp

Department of Genetics and Pharmacology

Institute of Genetic Epidemiology

Medical University Innsbruck

Schöpfstrasse 41

A 6020 Innsbruck – Austria

+43 (676) 571-0536

bernhard.r...@i-med.ac.at



k.k. Hofkristallamt

San Diego, CA 92084

001 (925) 209-7429

b...@ruppweb.org

b...@hofkristallamt.org

http://www.ruppweb.org/

---




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--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom




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[ccp4bb] Shelx and debian 10

[Bernhard Rupp]

Hi Fellows,

 

we updated to Debian 10 on the local workshop computers, and reinstalled

Coot and ccp4. All fine. 

 

Problem: Shelxc/d/e/  does not run, and

the call exits immediately sans any message.

 

This holds for the binaries included in ccp4 as well as for those from the
SHELX site.

The executables from CCP4 and SHELX site – same file size, probably same -
run fine under Debian 9.

 

I suspect a library problem.

 

Does some kind soul have CDE binaries for Debian 10 to share? 

 

Many thx in advance, BR

 




Bernhard Rupp

Department of Genetics and Pharmacology

Institute of Genetic Epidemiology 

Medical University Innsbruck

Schöpfstrasse 41

A 6020 Innsbruck – Austria

+43 (676) 571-0536

bernhard.r...@i-med.ac.at




k.k. Hofkristallamt

San Diego, CA 92084

001 (925) 209-7429

b...@ruppweb.org

b...@hofkristallamt.org

http://www.ruppweb.org/

---

 




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[ccp4bb] PSDI 2019 meeting programme now live

[Debreczeni, Judit]

Dear all,

there are still a couple of weeks to register to this year's Protein Structure 
Determination in Industry meeting -- registration closes 28th October. We have 
a dazzling lineup of speakers this year -- please see the list at the end of 
this message or the full agenda on the website:
https://psdi2019.org/programme/

The meeting will be held at the Wellcome Genome Campus, Hinxton, 
Cambridgeshire, UK. There are still a few places available at the pre-meeting 
workshops which will take place on Sunday the 3rd of November. Scientific 
sessions and exhibition will be held on Monday the 4th and Tuesday the 5th of 
November, with a conference dinner in central Cambridge on the 4th.

Exhibitors/sponsors: there is still one exhibition stand up for grabs, along 
with a few other sponsorship options:
https://psdi2019.org/exhibition-sponsorship/

This year's meeting is organised by AstraZeneca, supported by Hg3 Conferences.

We are looking forward to seeing you at the PSDI in November!

Judit

---


Pre-meeting workshops (3rd Nov):

1. hot and new biophysical techniques :Chris Nortcliffe (Sciex), Abhay Kotecha 
(ThermoFisher), Michal Bista (AstraZeneca)
2. Cutting edge synchrotrons: Isabel Moraes (NPL), Justyna Wojdula (SLS), Robin 
Owen (Diamond), Eva Crosas (DESY), Thomas Scheider (EMBL), Valentin 
Borshchevskiy (MIPT)
3. cyoEM model building: Colin Palmer (CCPEM), Paul Emsley (MRC-LMB), Ana 
Casanal (MRC-LMB)



Main meeting (4-5 Nov):

keynote speaker: Richard Henderson

Drug discovery case studies: Rob van Montfort (ICR), Armin Ruf (Roche), Alexey 
Rak (Sanofi), Karl Edman (AstraZeneca), Dennis Fiegen (BI), Phil Day(Astex), 
Djordje Musil (Merck), Martina Schaefer (Bayer), Derek Ogg (Peak Proteins), Tom 
Cesca (UCB)

cryoEM: Kasim Sader (ThermoFisher), Celine Be (Novartis), Taiana Maia de 
Oliveira (AstraZeneca), Stacey Southall (Sosei Heptares), Radu Aricescu 
(MRC-LMB)

Integrative structural biology: Tamir Gonen (UCLA), Chun-wa Chung (GSK), Chris 
Nortcliffe (Sciex), Paul Erbel (Novartis)

New modalities: degraders: Gerd Bader (BI), Marcus Hartmann (MPI), Eric Fischer 
(Harvard)



Judit Debreczeni
Associate Principal Scientist
SBF, Discovery Sciences
AstraZeneca

AstraZeneca
Darwin (310) Building
Cambridge Science Park
Milton Road
Cambridge
CB4 0WG
UK



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[ccp4bb] Dorothy Hodgkin: a discussion of her life and work

[Peter Keller]

Dear all,

Last week, there was a broadcast of a discussion of Dorothy Hodgkin's 
life and work on BBC Radio 4. For those of you outside the UK or who 
missed it, it can be listened to or downloaded here: 
. As far as I can tell, there 
are no geographical restrictions, and it can be accessed from anywhere.


One of the panellists was Prof. Judith Howard, whom some of you know.

Regards,

Peter.

--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom




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[ccp4bb] Two Research Technician positions available in Berger team, Max Planck Centre for Minimal Biology, University of Bristol, UK

[kapil gupta]

Dear CCP4bb and CCPEM members,
Do you enjoy molecular biology and protein biochemistry and keen to work in
a vibrant, international environment?

Berger group is hiring! Two Research Technician positions are available in
the Berger team in the Max Planck Centre for Minimal Biology in Bristol.

The Berger group studies the structure, mechanism and cellular assembly of
eukaryotic multiprotein assemblies in transcription regulation and develops
enabling technologies for DNA transfer, genome engineering and multigene
expression in eukaryotic cells, tissues and organisms.

We are seeking up to two highly-skilled Research Technicians to actively
participate in the ambitious research projects in our laboratory in the new
Max Planck Centre for Minimal Biology at Bristol University. You will
engage in designing and preparing multigene DNA constructs and utilize and
further develop our award-winning MultiBac system for protein complex
production and gene therapy applications. Outstanding applicants have a
strong background in molecular biology and protein biochemistry. Experience
in eukaryotic cell culture, baculovirus expression and/or a structural
biology background is highly desirable.

Showing a high level of organization and independence, you will maintain
the molecular biology and protein purification infrastructure including
ordering of consumables and assist in operating the MultiBac platform in
the eukaryotic expression facility. Moreover, you will archive and manage
plasmid, baculovirus and protein stocks vital to the laboratory.

You will actively embrace the responsibility of managing technology
platforms underpinning all research in the Berger lab.

For informal enquiries please contact Imre Berger, +44 117 394 1857,
imre.ber...@bristol.ac.uk or Christiane Berger-Schaffitzel, +44 117 394
1869, christiane.berger-schaffit...@bristol.ac.uk.

 Join us and have fun !


Closing date for applications is *20th October 2019.  *


For details follow link:

https://www.jobs.ac.uk/job/BVR397/research-technicians-2-posts
(Dr. Kapil Gupta on Behalf of)

*Imre Berger PhD HDR FRSB*
Chair in Biochemistry and University Research Fellow

Wellcome Trust Senior Investigator

Founding Director, Max Planck Centre for Minimal Biology

Director, BrisSynBio Centre

Co-Director, Bristol Biodesign Institute BBI


School of Biochemistry,  Faculty of Life Sciences and

BrisSynBio, an EPSRC/BBSRC Centre for Synthetic Biology

University of Bristol

https://maxplanck-minimalbiology.bristol.ac.uk/

http://www.bristol.ac.uk/brissynbio

http://www.bris.ac.uk/biomedical-sciences/ 


[image: image.png]


A top 5 UK university with leading employers (2015)
A top 5 UK university for research (2014 REF)
A world top 50 university (QS Ranking 2019)

-- 
With Best Regards
Dr. Kapil Gupta, PhD
School of Biochemistry
University of Bristol
Bristol, United Kingdom
http://www.bris.ac.uk/biochemistry/people/kapil-k-gupta/index.html




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[ccp4bb] PhD and postdoc position - Structural Biology Methods development at Wuerzburg University

[Andrea Thorn]

Dear colleagues,

for two projects in structural biology methods development, we are
looking for a

PHD CANDIDATE (m/f/d)

and a

POSTDOCTORAL RESEARCHER (m/f/d)

The Thorn Laboratory the Rudolf Virchow Center at the University of
Wuerzburg  develops new methods for macromolecular X-ray crystallography
and Cryo-EM. In these exciting projects you will improve how well we
understand, measure and model macromolecular crystal structures using
practical experiments and big data analyses. We are looking for
candidates with skills in data analysis and programming. Any previous
experiences in crystallography, molecular biology, machine learning,
image or statistical analysis are also a bonus. You should be a good
communicator. For the PhD project, we offer a 36-month full- or
part-time position, embedded in the Würzburg Graduate School for Life
Sciences (GSLS); for the postdoctoral position, we offer a 30-month
full- or part-time position with a competitive salary as well as career
and family support. Women are particularly encouraged to apply.

For more details, see:
https://www.uni-wuerzburg.de/fileadmin/4302/2019/Stellenanzeige_PhD_Thorn_September_2019_final_Auslage.pdf
https://www.uni-wuerzburg.de/fileadmin/4302/2019/Stellenanzeige_PostdocThorn_Sep_2019_final_Auslage.pdf

If you have any questions, please email me: andrea.th...@uni-wuerzburg.de.

Best wishes,



Andrea Thorn.

_

Dr. Andrea Thorn
group leader
Rudolf Virchow Center for Experimental Biomedicine
University of Wuerzburg
Josef-Schneider-Str. 2
97080 Wuerzburg
Germany

andrea.th...@uni-wuerzburg.de
https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/



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