Re: [ccp4bb] one metalloid making multiple covalent bonds - generating library

[Robbie Joosten]

Hi Thiyaga,

Rather than compounds, you should define LINKs. You can do this in the CCP4 
program jligand. You may also want to define angle restraints depending on your 
resolution. In Refmac you can do that as external restraints. A similar 
situation is described in this 
(http://journals.iucr.org/d/issues/2016/10/00/rr5124/rr5124.pdf) paper about 
zinc coordination.

Cheers,
Robbie

Sent from my Windows 10 phone

Van: S. Thiyagarajan
Verzonden: zaterdag 11 maart 2017 06:19
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] one metalloid making multiple covalent bonds - generating 
library

Dear Experts,
I have a metalloid complex in a structure I am solving, where a single ion 
makes 3 covalent bonds to 3 different cysteine residues, at a bond length of 
1.8 A. How to generate the monomer library for refinement?

Leaving it without the bonds makes the SG atoms go farther than the required 
bond length, building up positive density in the difference map at the right 
locations.

Even if I create one monomer with the metalloid bound to cysteine, other 2 
cysteines will have problems as the ion is shared by 3 residues.
Any help is appreciated.

regards
Thiyaga

==
Dr. S. Thiyagarajan
Faculty Scientist
Institute of Bioinformatics and Applied Biotechnology
Behind 3M and next to Arvind Mills
Electronics City Phase I
Bangalore 560100
Karnataka
Ph: +91-80-28528900 ext 124
Fax: +91-80-28528904
===

[ccp4bb] one metalloid making multiple covalent bonds - generating library

[S. Thiyagarajan]

Dear Experts,I have a metalloid complex in a structure I am solving, where a 
single ion makes 3 covalent bonds to 3 different cysteine residues, at a bond 
length of 1.8 A. How to generate the monomer library for refinement?
Leaving it without the bonds makes the SG atoms go farther than the required 
bond length, building up positive density in the difference map at the right 
locations.
Even if I create one monomer with the metalloid bound to cysteine, other 2 
cysteines will have problems as the ion is shared by 3 residues.Any help is 
appreciated.
regardsThiyaga
==
Dr. S. Thiyagarajan
Faculty Scientist
Institute of Bioinformatics and Applied Biotechnology
Behind 3M and next to Arvind Mills
Electronics City Phase I
Bangalore 560100
Karnataka
Ph: +91-80-28528900 ext 124
Fax: +91-80-28528904
=== 

Re: [ccp4bb] Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein

[Phil Jeffrey]

Tricky - perhaps this could be viewed as "anti-averaging" methodologically.

Use USF programs MAMA, IMP to generate a mask and optimize the NCS 
operator (or skip this step if you feel you know yours accurately)


Use CCP4's MAPROT to rotate the map of one monomer onto the other

Conceivably use USF program COMDEM to create the "difference map" 
assuming it will tolerate a weighting of -1.  Or perhaps MAPROT will 
take a negative scale. Or MAPMASK, or there's a range of map 
manipulation programs that can scale an input map, but I've never tried 
to invert one.  Unless you actually wanted Fourier coefficients it 
shouldn't be impossible to create a masked volume of the difference 
between two maps after rotating one of them.


Phil Jeffrey
Princeton

On 3/10/17 5:24 PM, Oleg Zadvornyy wrote:

Dear All,


We are working on a tetrameric protein containing 2 heterodimers which
are related to each other by 2 fold symmetry. There are difference at
the active site between the two heterodimers in the crystals, and we
would like to make a difference map to compare one heterodimer to the
other. I would really appreciate your advise and suggestions how to
perform this comparison.
Thank you,
Oleg

--
Oleg A. Zadvornyy, PhD

Institute of Biological Chemistry,
Washington State University

237 Clark Hall
Pullman, WA 99163

Tel:  (509)-335-9837
Lab: (509)-335-1958

[ccp4bb] Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein

[Oleg Zadvornyy]

Dear All,


We are working on a tetrameric protein containing 2 heterodimers which are
related to each other by 2 fold symmetry. There are difference at the
active site between the two heterodimers in the crystals, and we would like
to make a difference map to compare one heterodimer to the other. I would
really appreciate your advise and suggestions how to perform this
comparison.
Thank you,
Oleg

-- 
Oleg A. Zadvornyy, PhD

Institute of Biological Chemistry,
Washington State University

237 Clark Hall
Pullman, WA 99163

Tel:  (509)-335-9837
Lab: (509)-335-1958

[ccp4bb] Cold Spring Harbor Asia conference on Membrane Proteins: Structure & Function

[Martin Caffrey]

*Membrane Proteins: Structure & Function*

Suzhou, China.  May 15-19, 2017

Organized by:

*Martin Caffrey,* Trinity College Dublin, Ireland

*Nancy Carrasco,* Yale University, USA

*Tian-Le Xu,* Shanghai Jiao Tong University, China

*Ming Zhou,* Baylor College of Medicine, USA



We are pleased to announce the *Cold Spring Harbor Asia conference on*
*Membrane
Proteins: Structure & Function* which will be held in Suzhou, China,
located approximately 60 miles west of Shanghai. The conference will begin
at *7:00 pm on the evening of Monday May 15, and will conclude after lunch
on May 19, 2017.*

The conference will include up to eight oral sessions and four poster
sessions covering the latest findings across a range membrane protein
related topics. Many talks will be selected from submitted abstracts on the
basis of scientific merit and relevance. Social events throughout the
conference provide ample opportunity for informal interactions.

*Major Topics*

*1. Channels*


*2. Cryo-EM 3. Dynamics*

*4. Emerging techniques*

*5. Enzymes*

*6. Functional characterization*
* 7. Transmembrane signalling*

*8. Transporters*

*Speakers*


*Martin Caffrey,* Trinity College Dublin, IRELAND
*Nancy Carrasco,* Yale Unviersity, USA
*Yifan Cheng,* University of California San Francisco, USA
*James Chou,* Harvard Medical School/National Center for Protein Science,
USA/CHINA
*Henry Colecraft,* Coumbia University, USA
*Raimund Dutzler,* University of Zurich, SWITZERLAND
*Karen Fleming,* Johns Hopkins University, USA

*Xin Huang,* Amgen Inc., USA

*Andy Kruse,* Harvard Medical School, USA
*Edmund Kunji,* Medical Research Council, UNITED KINGDOM

*Zhenfeng Liu,* Institute of Biophysics, CAS, CHINA

*Zhi-Jie Liu,* ShanghaiTech University, CHINA
*Kaspar Locher,* ETH Zurich, SWITZERLAND

*Aashish Manglik,* Stanford University School of Medicine, USA
*Yasushi Okamura,* Osaka University, JAPAN
*Eduardo Perozo,* The University of Chicago, USA
*Scott Prosser,* University of Toronto Mississauga, CANADA
*Daniel Rosenbaum,* UT Southwestern Medical Center, USA
*Irina Serysheva,* UTHealth Medical School, USA
*Yigong Shi,* Tsinghua University, CHINA
*Roger Sunahara,* University of California, San Diego, USA
*Chris Tate,* MRC Laboratory of Molecular Biology, UNITED KINGDOM
*Kutti Vinothkumar,* MRC Laboratory of Molecular Biology, UNITED KINGDOM
*Tian-Le Xu,* Shanghai Jiao Tong University, CHINA
*Bailong Xiao,* Tsinghua University, CHINA
*Nieng Yan,* Tsinghua University, CHINA

*Jian Yang,* Kunming Institute of Zoology, CHINA

*Maojun Yang,* Tsinghua Univeristy, CHINA
*Ming Zhou,* Baylor College of Medicine, USA

We encourage abstracts to contain new and unpublished materials. Abstracts
must be submitted electronically by the abstract deadline. Selection of
material for oral and poster presentation will be made by the organizers.
Status (talk/poster) of abstracts will be posted on this web site as soon
as decisions have been made by the organizers.

*Fellowships *
We are eager to have as many young people as possible attend since they are
likely to benefit most from this meeting. A certain number of presentations
by graduate students and postdocs attending the conference will be selected
for fellowship (US $100-$500) awards. For more details, please visit
http://www.csh-asia.org/stipends.html



We look forward to seeing you at Suzhou in May, 2017.

Early Registration: 17 April 2017

Website: https://www.csh-asia.org/2017meetings/membrane.html



-- 
Martin Caffrey  martin.caff...@tcd.ie
Schools of Medicine and Biochemistry & Immunology
Trinity Biomedical Sciences Institute, Trinity College Dublin
Room 5.62,152-160 Pearse St., Dublin 2, D02 R590, Ireland
http://www.tcd.ie/Biochemistry/research/m_caffrey.php
phone: +353-(0)1-896-4253; mobile: +353-(0)86-818-7704

[ccp4bb] PDRA position available in Leeds

[Glyn Hemsworth]

Dear All,

Can I please bring the PDRA opportunity that is available here in Leeds once 
more to your attention as the deadline for applications - 21st March 2017 is 
approaching.

Funded by the BBSRC the position is available for an initial 2 year period, 
with the possibility of extending to 4 years. The position will suit someone 
interested in redox proteins, structural biology and biotechnology.

The full candidate brief can be downloaded from the following web address:

https://jobs.leeds.ac.uk/FBSMB1100

To apply for the position please register for an account on the Leeds website 
and submit a covering letter, together with a CV including details of at least 
two references.

Please feel free to get in touch with informal enquiries about the role. Thanks 
and best wishes,

Glyn

–
Glyn Hemsworth
Astbury Building, Room 10.107
Faculty of Biological Sciences,
University of Leeds, Leeds, LS2 9JT, UK
Tel: (+44) 0113 3434 349
Email: g.r.hemswo...@leeds.ac.uk

Research Fellow

Are you an ambitious researcher looking for your next challenge? Do you have an 
established background in Structural Biology, Biochemistry or Chemistry? Do you 
want to further your career in one of the UKs leading research intensive 
Universities?

You will investigate the structure and function of a range of proteins, and 
their complexes, as potential activators of a class of enzymes known as lytic 
polysaccharide monooxygenases (LPMOs), (find out more in this recent 
review).
 LPMOs have emerged as key enzymes in biomass conversion, both in nature and in 
the applied setting of a biorefinery. Using a combination of structural, 
biophysical, and biochemical methods we are seeking to characterise the 
molecular mechanisms used in nature to shuttle electrons to LPMOs. The 
knowledge gained from this research is of considerable interest from both a 
fundamental and applied standpoint and will ultimately be used in protein 
engineering approaches to produce more efficient enzyme systems to be used in 
the biorefinery.

Funded by the BBSRC, you will be based in the newly established laboratory of 
Dr Glyn Hemsworth in the Faculty of Biological Sciences and the Astbury Centre 
for Structural Molecular Biology. With the recent £17 million investment in the 
Astbury Biostructure lab to complement the already superb infrastructure for 
structural molecular biology, Leeds represents the perfect environment for you 
to learn new techniques whilst contributing vital knowledge towards realising 
the development of lignocellulosing biofuels as a more sustainable energy 
source for the future.

You should have, or be close to completing a PhD in Structural Biology, 
Biochemistry, Chemistry or a related discipline, where practical experience of 
cryo-electron microscopy or X-ray crystallography is essential. You will be 
expected to show enthusiasm for engaging in inter-disciplinary research and 
expanding your knowledge and expertise into new areas. Experience of studying 
protein-protein interactions would also be an advantage.

To explore the post further or for any queries you may have, please contact:

Glyn Hemsworth

Tel: 0113 343 4349, email: 
g.r.hemswo...@leeds.ac.uk


Location:   Leeds - Main Campus
Faculty/Service:Faculty of Biological Sciences
School/Institute:   School of Molecular & Cellular Biology
Category:   Research
Grade:  Grade 7
Salary: £32,004 to £38,183 p.a.
Contract Type:  Fixed Term (Fixed term for 2 years due to funding - optional 4 
years)
Closing Date:   Tuesday 21 March 2017
Reference:  FBSMB1100

[ccp4bb] refinement / modeling of partly mobile domain

[Kajander, Tommi A]

Any hints on what might work for modeliing a domain that seems to be there 
visible in part and parly not?

(half ofan Ig-domain) - presumably the other end of the domain has larger 
ensemble of coordinate
postions (attached from one end to other part of the same molecule and 
neighbors in the crystal - and not at the other end,
causing maybe kind of swinging of it/positional disorder) - any good ideas how 
to model this welcome...

including the _whole domain model_  seems to drop R-factors but cant see much 
additional density - maybe we just model the
missing part then for this structure if nothing else..

Thanks,
Tommi

Re: [ccp4bb] Vacancy: structural biologist with cryo-EM expertise at GSK closing date 24th March

[Anindito Sen]

Apologies to you All.

The email got copied to every one. In any case its a junk for rest of you. 
Kindly delete it, if you can.


Best Regards

Andy



Anindito Sen. Ph.D
> On Mar 10, 2017, at 9:17 PM, Vellieux Frédéric  
> wrote:
> 
> Hello,
> 
> I am not “Dr Chung” and I haven’t received anything from you. Sorry to 
> disappoint you.
>  
> Perhaps a “reply all” isn’t appropriate when replying to a ccp4bb message ? I 
> let you be the judge on that…
>  
> Fred.
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
> ] On Behalf Of Anindito Sen
> Sent: Friday, March 10, 2017 12:53 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Vacancy: structural biologist with cryo-EM expertise at 
> GSK closing date 24th March
>  
> Hello Dr. Chung,
>  
> It was nice talking to you. I have submitted the application online. However 
> I have not received any email conformation. In any case, I am attaching the 
> screenshot of my submission below.
>  
> Kindly acknowledge when you receive my application. 
>  
> Best Regards
>  
> Andy
>  
>  
>  
>  
> 
>  
> Anindito Sen. Ph.D
> Scientist and Application Specialist in Biological Sciences
> JEOL LTD.
> 13F, Ohtemachi Nomura Bldg.
> 2-1-1 Ohtemachi, Chiyoda-ku, Tokyo
> 100-0004
> Tel: +81-3-62623563
> Fax: +81-3-6262-3577
> 
> www.jeol.com 
>  
> On Mar 6, 2017, at 7:03 PM, Chun-wa Chung  > wrote:
>  
> Job-posting  - Seeking structural biologist with cryo-EM expertise at GSK
>  
> A vacancy for a structural biologist with cryo-EM expertise has opened up 
> within the UK structural and biophysical sciences group at GlaxoSmithKline 
> R Joining an experienced multi-disciplinary group, this is an exciting 
> opportunity for a motivated individual to complement and help shape our 
> current capabilities in the EM area. 
> This is a permanent, full-time position suitable for a PhD degree holder (or 
> equivalent).
> 
> To apply for this role and for further details, please click on the link 
> below (Vacancy no : WD106591) 
> https://careers.peopleclick.com/careerscp/client_gsk/external1931/gateway.do?functionName=viewFromLink=330903=en-us
>  
> 
> A full job description is also included at the end of this message.
> 
> Applications for this vacancy are to be made online by 24th MARCH
> Informal inquiries can be sent to  chun-wa.h.ch...@gsk.com 
> 
> Thank you for your interest,  
> 
> Chun-wa Chung
> 
> UK Head Structural & Biophysics  Sciences
> GlaxoSmithKline R
> Stevenage
> SG1 2NY
> Tel no: +44 1438 763342
> email : chun-wa.h.ch...@gsk.com 
>  
>  
>  
> Full Job Description (WD78277):
> GlaxoSmithKline is a world leading research-based pharmaceutical company. We 
> are focused around three core businesses: Pharmaceuticals, Vaccines and GSK 
> Consumer Healthcare. We have a significant global presence with commercial 
> operations in more than 150 countries, a network of 84 manufacturing sites in 
> 36 countries and large R centres in the UK, US,  Belgium and China.
> The UK Structural and Biophysical Sciences group is a multi-disciplinary 
> department within GSK R that provides molecular insights into drug 
> discovery for both small molecule and biopharmaceutical programs.
> 
> We currently have an exciting opportunity for a laboratory-based scientist 
> with expertise in state-of-the-art electron microscopy techniques to play an 
> influential and key role in the application and development of these methods 
> across small molecule and therapeutic protein programs. This individual will 
> have extensive experience in the sample preparation and optimisation 
> processes necessary to produce high-quality molecular images of protein 
> structure, including direct experience of Cryo-EM methodologies. Experience 
> of data analysis and interpretation is also expected. Being responsible for 
> delivering structural insights to support program teams and contributing to 
> the  wider protein structural and biophysical area by identifying and driving 
> forward improvements and innovations that advance drug discovery projects, 
> the individual must be a collaborative team player able to work successfully 
> with other scientists within the department and within diverse teams.
> 
> Key Responsibilities and Accountabilities: 
> • Design and perform technical experiments in the EM area (sample 
> preparation, optimisation and analysis).
> • Document and communicate scientific results clearly and promptly.
> • Provide strong scientific lead to shape EM strategy within structural 
> biology and across therapeutic discovery programs.
> • Build EM capabilities and infrastructure through interactions with the 
> 

Re: [ccp4bb] Vacancy: structural biologist with cryo-EM expertise at GSK closing date 24th March

[Anindito Sen]

Hello Dr. Chung,

It was nice talking to you. I have submitted the application online. However I 
have not received any email conformation. In any case, I am attaching the 
screenshot of my submission below.

Kindly acknowledge when you receive my application. 

Best Regards

Andy






Anindito Sen. Ph.D
Scientist and Application Specialist in Biological Sciences
JEOL LTD.
13F, Ohtemachi Nomura Bldg.
2-1-1 Ohtemachi, Chiyoda-ku, Tokyo
100-0004
Tel: +81-3-62623563
Fax: +81-3-6262-3577

www.jeol.com

> On Mar 6, 2017, at 7:03 PM, Chun-wa Chung  wrote:
> 
> Job-posting  - Seeking structural biologist with cryo-EM expertise at GSK
>  
> A vacancy for a structural biologist with cryo-EM expertise has opened up 
> within the UK structural and biophysical sciences group at GlaxoSmithKline 
> R Joining an experienced multi-disciplinary group, this is an exciting 
> opportunity for a motivated individual to complement and help shape our 
> current capabilities in the EM area. 
> This is a permanent, full-time position suitable for a PhD degree holder (or 
> equivalent).
> 
> To apply for this role and for further details, please click on the link 
> below (Vacancy no : WD106591) 
> https://careers.peopleclick.com/careerscp/client_gsk/external1931/gateway.do?functionName=viewFromLink=330903=en-us
>  
> 
> A full job description is also included at the end of this message.
> 
> Applications for this vacancy are to be made online by 24th MARCH
> Informal inquiries can be sent to  chun-wa.h.ch...@gsk.com 
> 
> Thank you for your interest,  
> 
> Chun-wa Chung
> 
> UK Head Structural & Biophysics  Sciences
> GlaxoSmithKline R
> Stevenage
> SG1 2NY
> Tel no: +44 1438 763342
> email : chun-wa.h.ch...@gsk.com 
>  
>  
>  
> Full Job Description (WD78277):
> GlaxoSmithKline is a world leading research-based pharmaceutical company. We 
> are focused around three core businesses: Pharmaceuticals, Vaccines and GSK 
> Consumer Healthcare. We have a significant global presence with commercial 
> operations in more than 150 countries, a network of 84 manufacturing sites in 
> 36 countries and large R centres in the UK, US,  Belgium and China.
> The UK Structural and Biophysical Sciences group is a multi-disciplinary 
> department within GSK R that provides molecular insights into drug 
> discovery for both small molecule and biopharmaceutical programs.
> 
> We currently have an exciting opportunity for a laboratory-based scientist 
> with expertise in state-of-the-art electron microscopy techniques to play an 
> influential and key role in the application and development of these methods 
> across small molecule and therapeutic protein programs. This individual will 
> have extensive experience in the sample preparation and optimisation 
> processes necessary to produce high-quality molecular images of protein 
> structure, including direct experience of Cryo-EM methodologies. Experience 
> of data analysis and interpretation is also expected. Being responsible for 
> delivering structural insights to support program teams and contributing to 
> the  wider protein structural and biophysical area by identifying and driving 
> forward improvements and innovations that advance drug discovery projects, 
> the individual must be a collaborative team player able to work successfully 
> with other scientists within the department and within diverse teams.
> 
> Key Responsibilities and Accountabilities: 
> • Design and perform technical experiments in the EM area (sample 
> preparation, optimisation and analysis).
> • Document and communicate scientific results clearly and promptly.
> • Provide strong scientific lead to shape EM strategy within structural 
> biology and across therapeutic discovery programs.
> • Build EM capabilities and infrastructure through interactions with the 
> internal and external scientific community.
> • Maintain scientific excellence and lead in a rapidly evolving area e.g. 
> through interactions such as the FEI/LMB/Pharm consortium.
> • Become an integral team member of multiple project teams.
> 
> Key Capabilities and Proficiency:
> 1. Technical expertise leading to Impact 
> Evidence of specific and in depth knowledge of transmission electron 
> microscopy used as a structural technique, especially single particle 
> cryo-EM. A track record of its application to address scientific problems 
> relevant to pharmaceutical research. 
> 2. Influence and Scientific awareness 
> Evidence of engagement with external scientific environment including the 
> ability to identify and pursue opportunities that advance capabilities within 
> own research area.
> 3. Team work 
> Demonstrable ability to both directly and indirectly influence and impact the 
> progression of programs of research and to work in 

Re: [ccp4bb] xdscc12 Expires

[Carlos CONTRERAS-MARTEL]

Hi Kay


Thank you very much ... xdscc12 is working now perfectly ... so xdsgui


Best

Carlos


On 03/10/17 09:27, Kay Diederichs wrote:

Hi Carlos,

sorry - the problem should be fixed now.; pls download a fresh copy.
Since I didn't find bugs for quite some time, the new binaries have no 
expiration date.

best wishes,

Kay

On Thu, 9 Mar 2017 21:18:12 +0100, Carlos CONTRERAS-MARTEL 
 wrote:


Hi CCP4BB

My XDSGUI is reporting :


xdscc12 -cdef -nbin 3 -t 1 XDS_ASCII.HKL > XDSCC12.LP
expired


So, downloaded again from the XDSWiKi link, but :


xdscc12/20170309> ./xdscc12.rhel6.64 -h
xdscc12 KD 2017-01-12. Academic use only; no redistribution. Expires
2016-12-31. -h option shows options.
Please cite Assmann, G., Brehm, W., Diederichs, K. (2016) J.Appl.Cryst.
49, 1021-1028
usage: xdscc12 -dmin  -dmax  -nbin  -mode <1 or
2> - FILE_NAME
dmax (default 999A), dmin (default 1A) and nbin (default 10) have the
usual meanings.
mode can be 1 (equal volumes of resolution shells) or 2 (increasing
volumes; default).
-t: total oscillation (degree) to batch fine-sliced frames into
other options can be combined (e.g. -def), and switch the following off:
-a: individual isomorphous summary values
-b: individual (Fisher-transformed) delta-CC1/2 values
-c: individual delta-CC1/2 reflection numbers
-d: individual anomalous summary values
-e: individual (Fisher-transformed) delta-CC1/2ano values
-f: individual delta-CC1/2ano reflection numbers
-w: weighting of intensities with their sigmas
-z: Fisher transformation of delta-CC1/2 values


it seems to me also be a expired version ...

Somebody know where I can find a newer-working version?


All the best


Carlos

--
  Carlos CONTRERAS MARTEL, Ph.D.
  (CR1 CNRS)

  carlos.contreras-mar...@ibs.fr

  "Bacterial Pathogenesis Group"
 Institut de Biologie Structurale
  UMR5075 CEA-CNRS-UGA

   IBS
   Campus EPN
   71, avenue des Martyrs
   CS 10090
   38044 Grenoble CEDEX 9
   FRANCE


  tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en



--
 Carlos CONTRERAS MARTEL, Ph.D.
 (CR1 CNRS)

 carlos.contreras-mar...@ibs.fr

 "Bacterial Pathogenesis Group"
Institut de Biologie Structurale
 UMR5075 CEA-CNRS-UGA

  IBS
  Campus EPN
  71, avenue des Martyrs
  CS 10090
  38044 Grenoble CEDEX 9
  FRANCE


 tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en

[ccp4bb] 2 year BBSRC funded PDRA position at the University of Liverpool, UK

[Antonyuk, Svetlana]

THE UNIVERSITY OF LIVERPOOL
FACULTY OF HEALTH AND LIFE SCIENCES
INSTITUTE OF INTEGRATIVE BIOLOGY
DEPARTMENT OF BIOCHEMISTRY
POSTDOCTORAL RESEARCH ASSOCIATE GRADE 7
£32,958 - £34,956 pa
An exciting opportunity has emerged in the Molecular 
Biophysics group to work on a BBSRC-supported 
project on structure-function-mechanism studies of Cu-nitrite reductase and 
membrane bound nitric oxide (NO) reductase and the role of metabolon complex 
formation in controlling levels of cytotoxic NO. The project will link 
crystallographic studies with techniques to probe factors that control delivery 
of electrons and protons to the active site of these enzymes. You will be 
responsible for using established molecular biology procedures underpinning the 
overexpression and purification of a number of enzymes and their mutants 
including membrane proteins and undertake crystallographic, spectroscopic and 
mechanistic aspects of the programme. You will have the opportunity to spend up 
to 4 weeks in the RIKEN laboratories in Japan as part of a collaborative 
programme alongside two PhD students working on membrane-bound nitric oxide 
reductases. You should have a PhD in the area of physics, chemistry, biological 
sciences or biophysics, with experience in protein crystallography and 
practical knowledge of molecular biology preferably with experience in membrane 
proteins. Excellent verbal and written communication skills are essential. The 
post is available for 2 years and the ability to commence immediately would be 
advantageous.

Job Ref: 006744 
Closing Date: 11 April 2017

For full details and to apply online, please visit: 
https://recruit.liverpool.ac.uk

Re: [ccp4bb] xdscc12 Expires

[Kay Diederichs]

Hi Carlos,

sorry - the problem should be fixed now.; pls download a fresh copy. 
Since I didn't find bugs for quite some time, the new binaries have no 
expiration date. 

best wishes,

Kay

On Thu, 9 Mar 2017 21:18:12 +0100, Carlos CONTRERAS-MARTEL 
 wrote:

>Hi CCP4BB
>
>My XDSGUI is reporting :
>
>
>xdscc12 -cdef -nbin 3 -t 1 XDS_ASCII.HKL > XDSCC12.LP
>expired
>
>
>So, downloaded again from the XDSWiKi link, but :
>
>
>xdscc12/20170309> ./xdscc12.rhel6.64 -h
>xdscc12 KD 2017-01-12. Academic use only; no redistribution. Expires
>2016-12-31. -h option shows options.
>Please cite Assmann, G., Brehm, W., Diederichs, K. (2016) J.Appl.Cryst.
>49, 1021-1028
>usage: xdscc12 -dmin  -dmax  -nbin  -mode <1 or
>2> - FILE_NAME
>dmax (default 999A), dmin (default 1A) and nbin (default 10) have the
>usual meanings.
>mode can be 1 (equal volumes of resolution shells) or 2 (increasing
>volumes; default).
>-t: total oscillation (degree) to batch fine-sliced frames into
>other options can be combined (e.g. -def), and switch the following off:
>-a: individual isomorphous summary values
>-b: individual (Fisher-transformed) delta-CC1/2 values
>-c: individual delta-CC1/2 reflection numbers
>-d: individual anomalous summary values
>-e: individual (Fisher-transformed) delta-CC1/2ano values
>-f: individual delta-CC1/2ano reflection numbers
>-w: weighting of intensities with their sigmas
>-z: Fisher transformation of delta-CC1/2 values
>
>
>it seems to me also be a expired version ...
>
>Somebody know where I can find a newer-working version?
>
>
>All the best
>
>
>Carlos
>
>--
>  Carlos CONTRERAS MARTEL, Ph.D.
>  (CR1 CNRS)
>
>  carlos.contreras-mar...@ibs.fr
>
>  "Bacterial Pathogenesis Group"
> Institut de Biologie Structurale
>  UMR5075 CEA-CNRS-UGA
>
>   IBS
>   Campus EPN
>   71, avenue des Martyrs
>   CS 10090
>   38044 Grenoble CEDEX 9
>   FRANCE
>
>
>  tel : (+33) (0)4 57 42 86 41
>
>http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
>http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en