PhD position available at Umea University, Sweden

From: Uwe Sauer
Date: 29 June 2012 21:43


Dear All,

A full time PhD student position is available in the laboratory of
Uwe Sauer at the Chemical Biology Center at Umea University, Sweden.

The project focuses on proteins involved in oxygenic photosynthesis.
The successful candidate will determine 3D structures by X-ray
Crystallography and study interactions and stabilities by applying
Biochemical and Bioinformatics methods.

The highly motivated applicant should have previous experience in
macromolecular crystallography such as crystallization and structure
determination and should be proficient in cloning techniques, protein
molecular biology, and biochemistry methods. Enthusiasm, the ability to
integrate into a team, and a fluent command of English, both spoken and
written, are important. Knowledge of the Swedish language is an additional merit.

The applicant should have completed a MSc (or equivalent) degree in
Biophysics, Biochemistry or Molecular Biology.

The complete application, marked with reference number 313-632-12,
should be sent by e-mail to jobb@umu.se (state the reference number in
the subject field) or send by regular mail to the "Registrar, Umeå University, SE-901 87 Umeå, Sweden".
Closing date for the applications is August 15, 2012.

More detailed application instructions are available at :
http://www8.umu.se/umu/aktuellt/arkiv/lediga_tjanster/313-632-633-12.html

For further information about the project and the PhD position, please have a look at:
http://www.chemistry.umu.se/english/research/group-leaders/uwe-sauer/?languageId=1

For informal enquiries please contact uwe.sauerATchem.umu.se

I am looking forward to your application!

/Uwe Sauer


--
Dr. Uwe H. Sauer, Associate Professor

Postdoc position

From: Zheng, Lei
Date: 29 June 2012 21:34

One postdoctoral position funded by NIH is available immediately at the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Houston Medical School (http://www.uth.tmc.edu/cmb/). The fellow will focus on structural determination of important membrane proteins involved in lipid metabolism and signaling. The fellow will also work with other lipid experts in the center for structural and functional characterization. 

The ideal candidate should be a self-motivated individual and have a recent PhD degree in structural biology or biochemistry. Decent experiences with standard molecular biology technique, protein crystallization and structural determination approaches are expected.

The laboratory locates in the Texas Medical Center campus which provides an excellent environment for academia and research. The lab is fully equipped for protein x-ray crystallographic study, including a Graphon LCP crystallization robot, a Rigaku rotating anode X-ray home source and immediate access to the Berkeley ALS beamline 4.2.2 in the framework of the molecular biology consortium.

To apply or request further information, please contact: Dr. Lei Zheng (E-mail: lei.zhengATuth.tmc.edu). The application should include a current resume and the names and addresses of three referees.

Post doctoral vacancy in structural biology, Oxford (deadline 23.7.)

From: Juha Huiskonen
Date: 26 June 2012 10:28


Dear All,

I would like to draw your attention to a post doctoral vacancy in my group, located at the Division of Structural Biology (StruBi), University of Oxford.

Your role will be to study the structure of an enveloped virus using electron cryo-microscopy (cryo-EM).  Necessary training will be provided.  The project involves working only with non-hazardous materials, such as chemically inactivated viruses.

The position is funded by the Medical Research Council and is fixed-term until 30 June 2015 in the first instance.

Only applications received before 12.00 midday on 23 July 2012 will be considered.

Please quote reference 103398 on all correspondence.  You will be required to upload a CV and supporting statement as part of your online application.  The application form, full job description, and selection criteria are available at http://www.recruit.ox.ac.uk.

Please address all informal inquiries about the post directly to me.

Juha

--
Dr. Juha T. Huiskonen
Oxford Particle Imaging Centre
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive, Oxford OX3 7BN

[PyMOL] Structural biologist job

From: Bernhard Rupp (Hofkristallrat a.D.)
Date: 22 June 2012 05:32

FYI for the on-pymol readers.
BR

-----Original Message-----
From: H. Adam Steinberg 
Sent: Tuesday, June 12, 2012 4:22 AM
Subject: [PyMOL] Structural biologist job

Hi all,

A friend of mine is looking to hire a structural biologist. With the tight job market I though I would try and get this out to as many people as possible.


> I am looking to hire a PhD structural biologist to join the team I manage at Myriad Genetic Laboratories in Salt Lake City, Utah. Please forward/post/pin-up the attached pdf if you can think of anybody who might be interested, or if you can think of someone that might know someone who might be interested.
>
> Myriad Genetics is a great company to work for, with all the perks of a biotech company (employee stock option purchase plan, 401k company match, full benefits, etc). Myriad Genetics is nestled in the foothills of the Rocky Mountains with over 1,100 employees and growing. Salt Lake City is a great place to live both for the outdoorsy person, as well as the cultural arts type person. It s also a great place to raise a family.
>
> Please email all job inquiries to Dr. Julie Eggington.
>
> Thank you.
> Julie
>
> Myriad Genetics - Clinical Variant Specialist unofficial job posting
> 2012.pdf

 JOB OPENING:  Clinical Variant Specialist Requires Ph.D. in Biochemistry or related field, with emphasis in structural biology.

Location: Myriad Genetic Laboratories, Inc. Salt Lake City, UT. Full time position NOTE: This is an early, unofficial job posting.  Official job postings are found at www.myriad.com

Overview: Myriad Genetic Laboratories is a leading molecular diagnostic company based in Salt Lake City, Utah. Myriad offers predictive medicine tests that identify hereditary breast and ovarian cancer, hereditary colorectal and uterine cancer, and other hereditary cancer syndromes. DNA sequencing allows Myriad to detect these syndromes by identifying disease causing mutations in specific genes. However, not all genetic variants which are identified in DNA testing are disease causing. Initially, some variants are classified as "Genetic Variant of Uncertain Significance" until research shows whether or not the genetic variant is disease causing or benign. It is the role of Myriad's Variant Specialist Team to collect and analyze data so that these Genetic Variants of Uncertain Significance can be correctly classified in a clinical setting.

 The Variant Specialist Team is looking to hire an expert in structural biology.  Unlike traditional Scientist I/II positions in biotechnology, the Clinical Variant Specialist is not likely to pursue lab bench work, but will apply his/her skills to reviewing literature and using molecular modeling and bio-informatics approaches to assist in better understanding the effects of genetic mutations.  The Clinical Variant Specialist will work within a larger group of cross-disciplinary scientists and statisticians.  Additionally, the Clinical Variant Specialist will work with clinician customers to assist in scientific understanding and in the coordination of research studies.  Excellent communication skills are required.  Attendance at professional meetings and publication opportunities are fostered.  The clinical Variant Specialist will also work on a variety of projects across different non-science divisions within Myriad as a representative of the Variant Specialist Team.

Qualifications:
-Ph.D. in Biochemistry or a related field required, with emphasis in structural biology -Excellent written and verbal communication skills -Candidates with postdoctoral research experience or equivalent are preferred -Candidates with experience in protein-nucleic acid interactions and/or experience in cancer causing biological pathways are preferred

How to apply: -Applications are to be formally made through http://www.myriad.com/careers/ when the position officially posts (likely in July 2012).  The position may have a different title at time of posting.  Dr. Julie Eggington is seeking resumes early to screen candidates as soon as possible starting in June 2012.  To facilitate this, please email resumes and enquiries to Dr. Julie Eggington at jeggingtATmyriad.com with  Clinical Variant Specialist Job Opening  in the subject line.

About Myriad:  Myriad Genetics, Inc. (Nasdaq: MYGN) is a leading molecular diagnostic company dedicated to making a difference in patient s lives through the discovery and commercialization of transformative tests to assess a person s risk of developing disease, guide treatment decisions and assess risk of disease progression and recurrence.  With fiscal year 2011 revenue of over $400 million and more than 1,100 employees, Myriad is working on strategic directives, including new test introductions, companion diagnostics, and international expansion, to take advantage of significant growth opportunities to further the Company s mission. Thanks to the dedication of our employees, the Company is succeeding in making a difference by improving the quality of patient s lives and saving lives.  For more information on Myriad, please visit the Company s website at:  www.myriad.com

INVITATION: Murnau Conference 2012 on Structural Biology of Molecular Transport

From: Christine Bentz
Date: 21 June 2012 09:53

Dear colleagues,

this is to remind you that the Murnau Conference 2012 on Structural Biology of Molecular Transport will be taking place from 17-20 October. Online registration is NOW OPEN on a first come-first served basis (http://www.murnauconference.de/2012/registration.html).

 

We would be delighted to meet you at the conference. Please also spread the information amongst your colleagues to help us attract a broad audience and an interesting cross-section of the community. If you want the conference poster (PDF file) for your notice boards, please let us know.

 

Murnau Conference 2012 on Structural Biology of Molecular Transport

October 17–20, 2012 - Murnau/Germany

 

SESSIONS

I Channels and Transporters I: Transport through Membrane
II RNA, Nuclear and ER Transport / Nucleocytoplasmic Transport
III Endosomal / Synaptic Transport
IV Cytoskeleton and Cellular Motility
V Channels and Transporters II: Molecular Machines

 

PLENARY SPEAKERS

Marc Baldus (Utrecht)
Tamir Gonen (Seattle)
Reinhard Jahn (Göttingen)
Hartmut Michel (Frankfurt)
You Min Chook (Dallas)
Poul Nissen (Arhus)
Tom Pollard (New Haven)
Jim Rothman (Yale)
Mike Rosen (Dallas)
Helen Saibil (London)
Irmi Sinning (Heidelberg)
Daniela Stock (Darlinghurst)
Gerhard Wagner (Harvard)

 

BACKGROUND INFO

The Murnau Conference is an international meeting covering current issues in the wide field of modern structural biology. A clear goal of the conference, which will take place this year for the 4th time, is to bring together the most eminent scientists in the field with young researchers in a casual atmosphere in the heart of Europe. The first three meetings in the series took place in 2005 (Structural Biology of Molecular Recognition), 2007 (Structural Biology of Disease Mechanisms) and 2010 (Structural Biology of the Modern RNA World). Murnau is a picturesque small town located directly at lake Staffelsee in the Bavarian alpine upland between Munich and Garmisch-Partenkirchen. There will be an exciting social program including a typical Bavarian evening in a fashionable microbrewery and ample time for stimulating discussions with participants from all over the world.

 

Please contact us in case of further questions.

With best regards,

Prof. Dr. Dirk Heinz
in the name of the organization committee

 

www.murnauconference.de

murnauconference2012@gmail.com

 

--------------------------------------------------------

Murnau Conference 2012 -Office-

--------------------------------------------------------

 

 

Practical Membrane Protein Course in Brazil

From: Dr. Isabel De Moraes
Date: 21 June 2012 18:51


Dear All,

The Laboratório Nacional de Biociências (Campinas-Brazil) and The Membrane Protein Laboratory (MPL) at Diamond Light Source are organising a Practical course in Structure and Function of Membrane Proteins.

The goal of the course is to introduce PhD students and post-docs to the basic principles of membranes proteins and the methods for production, structure solving and analyses of these proteins.

The course will run at The Laboratório Nacional de Biociências, Campinas-Brazil

The official language is english.

The course suits attendees who are entirely new to the field as well as those who wish to acquire an in-depth understanding of the methodology.

The course will be limited to 20 people from Universities and Research Institutes from MERCOSUL.

Deadline for application: 30th June, 2012

For more information:
www2.lnbio.org.br/membraneproteinscourse


Best Wishes,
Isabel

-----------------------------------------------------------------------------------------
Dr. Isabel De Moraes, MRSC

negative difference density around sulphur and oxygen atoms

From: Chris Meier
Date: 4 April 2012 16:16


Dear all,
I am refining the X-ray structure of a protein:
Data to ~2A were collected at a latest-generation synchrotron.
The 2fo-Fc maps are crisp, the model of the protein is complete and I am reasonably happy with the stats (R below 20%, Rfree below 25% in Refmac 5.5).
However, I am seeing a lot of negative difference density,
especially around sulphur atoms (negative density around -9 sigma)
and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma).
Has anyone observed this before?
I have found CCP4bb postings discussing radiation damange of suplphur atoms
(e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ).
Can this also happen with oxygen atoms?
What would be an appropriate way to deal with this issue during refinement?
Suggestions greatly appreciated.
Thanks,
Chris


----------
From: Ian Tickle


Hi Chris

I would say there's something very wrong if you're seeing -6 sigma
difference peaks at O atoms.  I don't see how this can be explained by
radiation damage.  I for one have never seen that before in a
structure where there weren't other obvious issues (or maybe I just
haven't looked hard enough).

I would try refining it with a different program, e.g. Buster, or even
a different version of Refmac (I use 5.6.x routinely, but I see
there's a 5.7.x now - Garib will no doubt have an opinion on which is
the best one to use).  At least that will eliminate the software as
the origin of the problem: if it doesn't go away then we'll have to
think again.

Cheers

-- Ian

----------
From: Ian Tickle


PS you say the model is complete, but just as important how complete
is (are?) the data.

-- Ian

On 4 April 2012 16:16, Chris Meier  wrote:

----------
From: Roger Rowlett


Radiation damage induced loss of definition of disulfide bridges, side chain carboxylates, and certain histidine residues has been observed in synchrotron-irradiated protein crystals. For example, see Weik et al., PNAS 2000, 97, 623. I have also seen a recent paper where radiation damage of a bound protein ligand was apparently observed in a synchrotron beam.

I look forward to hearing from others how best to handle this in refinement.

Cheers,

_______________________________________
Roger S. Rowlett

----------
From: Jacob Keller

I look forward to hearing from others how best to handle this in refinement.

Dose-dependent occupancies (tau of an exponential decay function?) refined against unmerged data

JPK

*******************************************
Jacob Pearson Keller
*******************************************

----------
From: Scott Classen


Hello Chris,

Are you refining individual atomic B factors or grouped? Perhaps the B factors of the terminal atoms of the side chain are being restrained to too low of a B factor resulting in excessive negative density?

Scott

----------
From: Ian Tickle


The PNAS paper you refer to talks about a "loss of definition" of
exposed carboxyl O atoms, i.e. an increase in B factor, but presumably
if this is modelled properly then it shouldn't leave a big hole in the
difference map.  After all, the paper is not claiming that C-O bonds
are broken, only that there is "increased mobility" (or just as
likely, induced static disorder).  I'm wondering if this is related to
too-tight B-factor restraints.  I never use the default settings and
always use more relaxed ones: in particular I set the weights of B
factor restraints across angles to zero, IMO the across-bond
restraints are more than sufficient.  There has been a historical
obsession with getting B factors as low as possible (too-tight
restraints will certainly achieve this if that is your goal!), but
isn't the true goal of refinement to obtain the model which best
explains the data?

Cheers

-- Ian



----------
From: VAN RAAIJ , MARK JOHAN


apart from radation damage it could be a combination of:

- too tight restraints on the B-factors

- 9 sigma not being that much on a the e/A3 scale, i.e. your difference map is very flat (which is good) and the few peaks that remain stand out a lot, even if their absolute height is low...

Quoting Chris Meier:

Message

Mark J van Raaij

----------
From: Garib N Murshudov

Dear Chris

Could you please try later version of refmac then if the problem persists please let me know. Before making any suggestions it would be good to make sure that the problem is not related with particular software version (as Ian suggested)

regards

Garib

----------
From: Yuri Pompeu

could it be that the scattering table would be slightly different for the sulfur atoms at the collected wavelength?
Are they Cys or Met residues? if Cys is there a possibility of oxidation to the disulfides?

----------
From: Katherine Sippel <

On Wed, Apr 4, 2012 at 10:31 AM, Roger Rowlett  wrote:

 I have also seen a recent paper where radiation damage of a bound protein ligand was apparently observed in a synchrotron beam.

That was a manuscript were I would have happily given the coordinates and structure factors to the reviewers with my blessing. Learned a valuable lesson about adopting orphaned data sets though.

Cheers,
Katherine
 

----------
From: Sanishvili, Ruslan <

Hi Chris,

As has been suggested already, and seems quite plausible to me, it sounds like tell-tale signs of radiation damage.

To have little more substance behind this suspicion, some more experimental details could help:

What was the dose accumulated during data collection?

If the dose cannot be calculated, what was the beam intensity, frame exposure time, number of frames, total rotation of the crystal, crystal size, beam size? If the beam intensity is not known, the beamline and the attenuation factor used might be helpful.

 

What is the space group and how much data were collected? IF you have data with high multiplicity, you may be able to get rid of the latter parts of it maintaining completeness. This would reduce the effects of radiation damage if you are really dealing with it. Alternatively (but again with highly redundant data), you could try "zero dose extrapolation". Look up Kay Diederichs' and Dominika Borek's works on this.

 

Regards,

Nukri

Ruslan Sanishvili (Nukri), Ph.D.

----------
From: Eleanor Dodson


This could well be due to radiation damage - S are often affected, also Glu and Asp side chains. It is hard to know what to do since the effects are time related. If you have high redundancy maybe you could not use he later batches? Otherwise maybe just relax the B factor restraints and let them show the loss of atoms.. The trouble with that is that you have to relax all side-chain B restraints which may not be so appropriate for ILE say...
 Eleanor

On Apr 4 2012, Chris Meier wrote:

MessageDear all, I am refining the X-ray structure of a protein:Data to ~2A were collected at a latest-generation synchrotron.The 2fo-Fc maps are crisp, the model of the protein is complete and I am reasonably happy with the stats (R below 20%, Rfree below 25% in Refmac 5.5). However, I am seeing a lot of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms(e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ).Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks,Chris

--
Professor Eleanor Dodson

Post-doctoral position available

From: Jim Spencer, Cellular and Molecular Medicine
Date: 15 June 2012 09:31

Dear All,

A postdoctoral position is available in my lab to study the interactions of zinc-dependent (metallo) beta-lactamases with beta-lactam substrates and candidate inhibitors using both rapid kinetics and X-ray crystallography. The position will be offered for one year in the first instance but with a strong possibility of renewal.

Details of the post and application procedure are available at:

http://www.bris.ac.uk/boris/jobs/feeds/ads?ID=112771

or by informal enquiry to me.

Please note that, if interested, you will need to apply online through the link above.

Best wishes

Jim Spencer

-----

Faculty position in protein crystallography

From: Danny Huang
Date: 14 June 2012 13:42

Lecturer/Senior lecturer position in X-ray crystallography located at the Beatson Institute for Cancer Research.

The Beatson Institute for Cancer Research is committed to carry out world-class research into the biology of cancer and to help develop better treatments to improve the quality of life for cancer patients. In conjunction with the University of Glasgow, we are looking to make an appointment at a lecturer/senior lecturer level in structural biology. We would be interested to hear from successful and motivated scientists who would like to develop an independent research programme in this area and join our strong interdisciplinary research center. The ideal candidate should have an excellent publication track record and extensive experience in X-ray crystallography to complement our well-established X-ray crystallography platform. We will offer a generous startup package and research support that includes access to leading-edge facilities (including state-of-the art X-ray crystallography, DNA sequencing, IT and proteomics).

Further information on the Beatson's research activities, infrastructure and facilities is available on our website www.beatson.gla.ac.uk

If you are interested, please send your cv along with a one to two page statement of research interests and goals to Dr. Danny Huang, the Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland (email: d.huangATbeatson.gla.ac.uk).

X-FEL nanocrystallography SwissFEL

From: Schertler Gebhard
Date: 14 June 2012 22:34

UNIVERSITÄT BASEL - PAUL SCHERRER INSTITUTE

Professor in Nano-Diffraction

of Biological Specimens

The University of Basel and the Paul Scherrer Institute (PSI) in Switzerland invite applications for a Professor­ship in the area of Nano-Diffraction of Biological Speci­mens. We are considering applications at a tenure-track assistant or associate professor level. The position will be shared between the University of Basel and the PSI. It will be integrated into the research environment at the Biozentrum and the Swiss Nanosciences Institute (SNI) of the University of Basel and the Biology and Chemistry Department at PSI. The successful candi­date will be responsible for coordinating the design and operation of the biological end-station at the Swiss free electron laser (SwissFEL) at the PSI. The ideal candidate will develop a nano-diffraction setup for biomolecular samples (e.g. nanocrystals and suspensions of single particles, or viruses) for femto-second x-ray diffraction studies using free electron laser technology, and will have his/her own biological project of interest. The infrastructure of the Biomolecular Research Laboratory at PSI will support the research activities of the new professor. The successful candidate will contribute to undergraduate and postgraduate teaching at the Uni­versity of Basel and will engage in collaborative projects between the University of Basel and the PSI.

The University of Basel and the PSI offer an outstand­ing scientific environment and an attractive research endowment, and Switzerland provides a high standard of living and a superb cultural atmosphere. Applications, including CV, list of publications and a short research summary, should be sent by e-mail (pdf or zip) to Prof. Martin Spiess, Dean, Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland, to dekanat-philnatATunibas.ch. For informal enquiries please contact Prof. Henning Stahlberg (henning.stahlbergATunibas.ch,Or Prof. Gebhard Schertler (gebhard.schertlerATpsi.ch).

The deadline for receipt of applications is August 31, 2012. Applications from female candidates are particu­larly welcomed.

UNI

BASEL

PAUL SCHERRER INSTITUTE

ICCBM14 Workshop & Conference, Hunstville, Alabama

From: mesters
Date: 13 June 2012 12:43

We cordially invite you to participate in the 14th International Conference on the Crystallization of Biological Macromolecules (ICCBM14) on September 23-28, 2012. The conference will be held in Huntsville, the "Rocket City," in the beautiful state of Alabama. The meeting site will be at the Westin within the second largest research park in the U.S. nearby the NASA Marshall Space Flight Center, the Redstone Arsenal and the new HudsonAlpha Institute for Biotechnology.

The theme of the meeting will be synthetic design, engineering and strategies for macromolecular crystallization. Focus will be on the practical and theoretical basis of macromolecular crystallization involving synthetic biology, protein complexes, nucleic acids, membrane proteins and convection-free crystallization platforms.

A practical workshop will precede the main conference devoted to hands-on instruction on selected aspects of macromolecule production, synthetic biology engineering and crystal growth.

Lodging will be available at the Westin conference center as well as other convenient and affordable housing nearby the University of Alabama in Huntsville and Research Park.

Early registration deadline has been extended to July 14, 2012

Please visit the conference homepage at http://www.iccbm14.org

We look forward to seeing you in September 2012!

Joseph Ng and Marc Pusey, Co-chairs of ICCBM14

International Workshop on New Developments of Methods and Software for Protein Crystallography, August 24-27, 2012 Xi’An, China

Date: 12 June 2012 18:03



International Workshop on New Developments of Methods and Software for Protein Crystallography, August 24-27, 2012 Xi'An, China
Organizers: Commission on Biological Macromolecules, IUCr;
Chinese Crystallographic Society (CCrS) and
Northwestern Polytechnical University

Program Committee: HF Fan; XD Su; TC Terwilliger; BC Wang; RM Xu
and RG Zhang

http://cbmxian2012.ccrs.net.cn/ccrs.html, please register before July 15 …

This workshop is intended to reflect and summarize some important advances of protein crystallography in methodology and automation procedures, such as new ideas and implementations for protein crystallography with emphases on low-resolution phasing and futuristic methods for crystal, nano-crystal or non-crystal structure determination; Automatic, user-friendly pipeline developments; Future data acquisition and storage for structural biology, particularly at modern synchrotron sources. The workshop will also include topics in new methods in protein crystallizations, nano-liter robots, automatic data collection at third generation synchrotrons, new light sources, new detectors, new ideas and ways of diffraction data collection, processing and storage.

The workshop is also good for students and scientists in the early stage of their careers, it will provide platforms for young scientists and students to learn the recent advances and to exchange new ideas and results.  There will be poster and selected oral presentation sessions during the workshop, and abstract or full-paper book will be printed and published.  Travel sponsorship for students and postdocs will be provided by IUCr and the workshop. Please include a copy of your advisor's recommendation letter if you would like to apply for the IUCr travel grant.

Please finish and submit the registration form to xdsu@pku.edu.cn and ccrs@pku.edu.cn befor July 15 2012
Registration fees will be collected on-side: RMB 2000 (Ca. US$320)




Confirmed Speakers: (in alphabetic order)
Paul Adams (Lawrence Berkeley Laboratory, USA);
Gerard Bricogne (Global Phasing Ltd., Cambridge, UK);
Yuhui Dong (BSRF:Beijing Synchrotron Radiation Facilities, China);
Haifu Fan (Institute of Physics, Chinese Academy of Sciences, China);
Mitchell Guss (University of Sydney, Australia);
Kazuya Hasegawa (Spring-8, Japan);
Jianhua He (SSRF: Shanghai Synchrotron Radiation Facilities, China);
Wayne Hendrickson (Columbia University, HHMI, USA);
Zhijie Liu (Institute of Biophysics, CAS, China);
Santosh Panjikar (Australian Synchrotron, Australia);
Yigong Shi (Tsinghua University, China),
Xiao-Dong Su (Peking University, China)
Tom Terwilliger (Los Alamos National Laboratory, USA);
BC Wang (University of Georgia, USA);
Manfred Weiss (BESSY, EMBL, Germany);
Jian XU (Rigaku, USA); Kam Zhang (RIKEN, Japan);
Dachuan Yin (Northwestern Polytechnical University, China)

CBF raw images in iMOSFLM- error

From: Yuri Pompeu
Date: 11 April 2012 16:08


Hello everyone,

I am trying to process ###.cbf raw images (BNL X25) using the iMOSFLM utility and I get the following error message:
"Distance has refined to an unreasonable value"
This causes the program to freeze and  not open the rest of the frames.
Also it is not picking up the X and Y beam positions.
It looks to me like its just simply not reading the image file HEADER properly.
Anyone has encountered this before and has any ideas on how to get around/fix this?
Thanks a lot!
Yuri


----------
From: Harry


Hi Yuri

If you can put some of the images on our ftp site (instructions sent separately) we'll have a look. There was a problem a while ago when some Pilatus  detectors changed from writing the distance in metres to writing it in millimetres, but no-one told us until iMosflm started having problems.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH

----------
From: Harry Powell

Dear all

The problem was indeed the distance being written in mm rather than m, so some of our internal maths gave surprising results. This will be fixed in the next versions of iMosflm and Mosflm - barring finding any killer bugs I hope this will be released next week.

----------
From: Kip Guja

Thank you Harry for letting us know about this!

Could you please send an update to the list when the new
version is out? (I would also like to process images from
BNL x25 (Pilatus 6M), and I'm sure there are others in the
same boat).

Best wishes,
Kip

vacancy for Java Web Application Developer at Diamond

From: Martin Walsh
Date: 12 June 2012 09:57

Dear all, this new vacancy at Diamond may be of interest for some readers of this BB which is focused on further development of ISPyB at Diamond. Full details of the post can be found here:

 

http://www.diamond.ac.uk/Home/Jobs/Current/DIA0737_TH.html

 

Informal inquiries can be made to myself (martin.walshATdiamond.ac.uk ) or Alun Ashton (Alun.ashtonATdiamond.ac.uk)

 

Thanks

Martin

 

 

Aspen Center for Physics workshop on Molecular Physics of Non-bonded Biomolecular Interactions

From: Ho,Shing
Date: 8 June 2012 16:31

Announcement of a Workshop at the Aspen Center For Physics

"Molecular Physics of Non-Bonded Biomolecular Interactions"

Summer 2013

 

A proposal will be submitted to the Aspen Center for Physics (ACP) in Aspen Colorado to sponsor a three week workshop focusing on efficient computational approaches to enhance the understanding of non-bonded interactions in biological systems and assemblies.   The workshop will occur sometime during the last two weeks of June through the end of July of 2013 depending on space availability.  The purpose of this advertising statement is to find 40 Ph.D. scientists that may have interest in such a workshop.  However, no commitment is required at this time.  If the workshop is accepted, ACP will notify interested parties and put out a general invitation and application on their web site.

The purpose of the ACP is to provide an enriching and non-interrupted atmosphere for each person to work on an individual project while having time to exchange ideas with other attendees.  The workshop is partially funded by the National Science Foundation through significant reductions in housing costs.  There are no experimental facilities at ACP so all projects are computational in nature.  More information on the goals and costs of attending the workshop can be found on the ACP web site – aspenphsy.org.  

Formal presentations on individual work are not required.  However, short presentations are encouraged at the beginning of the workshop for introductions as to the expertise of each attendee.

The workshop is being organized by the following people who have interests, respectively, in modeling of protein folding, macromolecular structure through halogen bonds and force field development:

      Dr Mark Plummer – MPr&d, LLC  - mplummer65ATmsn.com

      Dr. Shing Ho – Dept. Biochemistry Colorado State University – shing.hoATcolostate.edu

      Dr. Anthony Rappe – Dept. Chemistry Colorado State University – rappeATlamar.coloradostate.edu

 

Please contact one of the above by June 29, 2012 to express an interest and a possible area of study.   

------------------------------------------------

Gordon Research Conference on Diffraction Methods - last chance

From: Ana Gonzalez
Date: 11 June 2012 04:12


The registration deadline for the Gordon conference on diffraction methods
in Structural Biology (15-20 July), is at the end of the week (June 17th).

This is you last chance to register and get some of the places left!!!

See the program and application information at:
http://www.grc.org/programs.aspx?year=2012&program=diffrac

Ana and Tassos
--

International Fellowship Program for Postdocs at Paul Scherrer Institut

Anfang der weitergeleiteten E-Mail:

Datum: 5. Juni 2012 09:14:02 MESZ

Betreff: International Fellowship Program for Postdocs at Paul Scherrer Institut

PSI-FELLOW/COFUND - International Fellowship Program for Postdocs

The Paul Scherrer Institute is the largest research centre for the natural and engineering sciences in Switzerland and a worldwide leading user laboratory. Its research activities are concentrated on the main topics structure of matter, energy and environmental research as well as human health.

In the framework of the international fellowship program 'PSI-FELLOW', PSI is offering scientists and engineers challenging opportunities in all main topics listed above. The program provides an excellent possibility for work, research and training to those who are interested in science and technology at the highest level.

PSI-FELLOW runs under COFUND (Marie Curie Action under the European Commission's 7th Framework Program). The goal is to submit a successful grant application for a subsequent research project at PSI. The application has to be made together with a senior scientist at PSI, who will act as the fellow's mentor. After a stringent selection process ensuring that the best candidates are selected each successful fellow is offered a 24 months contract.

Please find the job announcement for the following four grand thematic areas on http://www.psi.ch/pa/offenestellen/:
- Materials and Matter (index no. 0101-00)
- Human Health and Life-Sciences (index no. 0102-00)
- Energy & Environment (index no. 0103-00)
- Accelerator Concepts, beam characterization methods and detectors (index no. 0104-00)

Read more: http://www.psi.ch/psi-fellow/scientific-fields

** Tasks **
You will conduct your own research in the framework of the proposed project and in collaboration with your future team.

** Profile **
You hold a PhD degree in one of the PSI related scientific fields and a strong scientific background in the theme mentioned above. You have a publication record with at least one original accepted first author publication in press or published in a peer-reviewed journal.
The program is open for candidates from EC Member States, associated or third countries. Please read the eligibility criteria carefully: http://www.psi.ch/psi-fellow/eligibility-criteria.

** How to apply ? **
- Check the eligibility criteria: http://www.psi.ch/psi-fellow/eligibility-criteria
- Contact the mentor in your field of interest (http://www.psi.ch/psi-fellow/list-of-mentors-and-themes)
- Elaborate the written application (for more details about the proposal preparation and submission procedure please refer to the applicant guide and project template: http://www.psi.ch/psi-fellow/call-for-applications
- Register at http://www.psi.ch/pa/offenestellen/ and submit the application online

In case of questions please read the Frequently Asked Questions on http://www.psi.ch/psi-fellow/faq or contact: psifellow@psi.ch

Paul Scherrer Institut, Human Resources, Miriam Zehnder, 5232 Villigen-PSI, Switzerland

Membrane Protein Crystallography Postdoctoral Fellow, Caffrey Lab, Trinity College Dublin, Ireland

From: Martin Caffrey
Date: 10 June 2012 21:39

Postdoctoral Research Fellow – Macromolecular Crystallography

Membrane Structural and Functional Biology – Caffrey Lab

Trinity College Dublin, Ireland

Trinity College Dublin is inviting applications for the post of Postdoctoral Research Fellow in the Caffrey Membrane Structural and Functional Biology Research Group.  The major theme within the Group is structure and function of membrane proteins by crystallographic means.  Systems under investigation include human GPCRs, transducers, transporters, lipid metabolizing enzymes, respiratory complexes, and quorum sensing-related and biofilm forming membrane proteins of Pseudomonas aeruginosa.  Purified protein and in meso-grown crystals of several targets are already in hand.

Person Specification

- A Ph.D. in macromolecular X-ray crystallography
- Experience and demonstrated success with macromolecular crystallization
- Experience and demonstrated mastery of all of the computational aspects of crystal structure determination to include MR, MAD, SAD, MIR, and S/MIRAS
- Experience with low-resolution structure determination
- Experience and demonstrated mastery of the latest crystallographic software on UNIX-based operating systems to include the CCP4 suite, CNS, Phenix, Phaser, Sharp and other relevant packages
- Recent experience and demonstrated mastery of on-site data collection at a synchrotron X-ray source
- Availability and willingness to travel to synchrotrons and collaborators worldwide
- A commitment to quality and innovative research

The candidate should be a self-motivated individual who enjoys working as part of a collaborative, multidisciplinary team.  Strong leadership, communication and teaching skills are decided assets.  

Salary: based on experience

The closing date for receipt of applications is Tuesday, 19th June 2012.

Further information for applicants and application material are available online from: www.tcd.ie/vacancies

Postdoctoral Position at ICR, London, UK

From: Sebastian Guettler
Date: 11 June 2012 14:32


Postdoctoral Position at ICR, London, UK

We seek to appoint a Post-doctoral Training Fellow to the Divisions of Structural and Cancer Biology of the Institute of Cancer Research (ICR; http://www.icr.ac.uk) in London, UK, to a new team led by Dr. Sebastian Guettler. The successful applicant will undertake biochemical, crystallographic and functional studies on members of the ADP-ribosyltransferase (or "PARP") family of proteins and their regulators. Our goal is to gain insight into the control and cellular roles of these enzymes with a specific interest in ADP-ribosyltransferase-dependent signalling processes linked to cancer.

Research in the Divisions of Structural and Cancer Biology focuses on the functional, biochemical, and structural characterisation of cellular processes relevant to cancer and cancer therapy. The Division of Structural Biology, where the laboratory will be physically based, has managed facilities for protein crystallography (crystallisation robots, Bruker Microstar and CCD detector), cryo-electron microscopy (FEI Tecnai F20 and T12), and protein production with expertise in multi-subunit expression (insect cell, yeast and bacterial expression, including a 60-litre fermentor). The Division is also well equipped with instrumentation for biophysical analysis (e.g. ITC, fluorescence, multi-angle light scattering). The Division of Cancer Biology provides a state-of-the-art infrastructure for mammalian cell culture, imaging, mammalian genetics, chemical biology and proteomics.

Applicants should possess a PhD (or equivalent) in biochemistry or molecular biology and a sound knowledge of protein purification for structural analyses. Experience with recombinant DNA techniques, protein expression and purification as well as protein crystallography is essential. Experience in mammalian cell culture, enzymology or protein production in insect cells (MultiBac) would be of advantage.

Length of contract: 3 years in the first instance
Salary range: £27,536 to £33,852 p.a. inclusive (depending on previous post-doctoral experience)
Closing date: 6th of July 2012
Starting date of position: mid-October / early November 2012

For further details and instructions on how to apply, please refer to our online vacancy and recruitment site at http://www.icr.ac.uk/jobsearch, quoting job reference number 1257974 for this position.

While applications need to be placed via our online system, informal inquiries can be sent to Dr. Sebastian Guettler at sebastian.guettlerATicr.ac.uk.

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

bulk solvent treatment inside protein cavities

From: Allister Crow
Date: 16 April 2012 11:37

Board members,

I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins.

I am currently nearing the end of refinement of a protein structure at 2.8 A resolution.  I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps.  These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form.  In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied.

I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters).

My questions are therefore:

1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6?

2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities?

Best wishes, and thanks in advance for all your help,

- Allister Crow



----------
From: Garib N Murshudov

Dear Allister

Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site:

http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz

There is a mac version also.

regards

Garib

<bulk_solvent_inside_cavities.png>

Dr Garib N Murshudov

----------
From: Eleanor Dodson


Oh dear - this is the version of Refmac in the latest ccp4 release - can this be updated on the web site as soon as possible ?

Eleanor

----------
From: Keitaro Yamashita


Dear Garib,

Is there REFMAC option to output solvent mask information (e.g. Fmask
and PHImask in mtz to check with Coot)?

I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
But I'm not sure that FC_ALL = FC + FMASK is correct or not.

Keitaro

----------
From: Garib N Murshudov <

Yes there is. If you use command line (it is not available on the ccp4i yet).

If you run with command lines

refmac5 <all others like hklin, xyzin etc> mskout <mask file name> <<eof

all options you want

eof

Then there will be a map and you can visualise it using coot.

regards

Garib

----------
From: Garib N Murshudov

A follow up:

In the new version there is FC_ALL_LS, PHIC_ALL_LS

That should be FC_ALL_LS = FC + FMASK. 

I have not tried but if you can use vector difference map then it should be: FMASK = FC_ALL_LS - FC

But it is after scaling. If you write out mask map then it is just 0 1 map (0 inside protein and 1 outside), except values are not 0 1 but 0 and some constant

Regards

Garib

 

----------
From: Keitaro Yamashita


Dear Garib,

Thank you very much for your quick reply.

I tried mskout option and the output looked almost the same as the map
generated by FC_ALL - FC.

By the way, when mskout option is specified, refmac stops before CGMAT cycles.
Is there any way to do refinement with mskout option?

> I have not tried but if you can use vector difference map then it should be:
> FMASK = FC_ALL_LS - FC

What is FC_ALL in the new version?


Thanks,

----------
From: Garib N Murshudov

Dear Ketaro

At the moment mskout option is a signal that the program should stop. Obviously I can add an option to continue. However if you have mskout option it is likely that you want to check what is going on with the mask. If you want to compare starting and final mask then you could run refmac with mskout in the beginning and after refinement.

If you need it urgently then I can add continuation of refinement with mskout option.

FC_ALL is ML scaled FC+FMASK

Sometime it may be different from least-squares scaled FC+FMASK

regards

Garib

----------
From: Keitaro Yamashita

Dear Garib,

I think it is better if refmac outputs final solvent mask when mskout specified.
If one just wanted to calculate the mask, NCYC 0 should be specified.

I hope my suggestion would be accepted, but I'm not in a hurry.

> FC_ALL is ML scaled FC+FMASK
>
> Sometime it may be different from least-squares scaled FC+FMASK

For what purpose is FC_ALL_LS written?
Can I check something by comparing FC_ALLto FC_ALL_LS?

I found somewhat large difference between FC_ALL_LS map and FC_ALL
map in Se position.
I used SAD function.
What does it mean?


Cheers,

Keitaro

----------
From: Garib N Murshudov

On 16 Apr 2012, at 17:14, Keitaro Yamashita wrote:

Dear Garib,

I think it is better if refmac outputs final solvent mask when mskout specified.
If one just wanted to calculate the mask, NCYC 0 should be specified.

I hope my suggestion would be accepted, but I'm not in a hurry.

ok

FC_ALL is ML scaled FC+FMASK

Sometime it may be different from least-squares scaled FC+FMASK

For what purpose is FC_ALL_LS written?
Can I check something by comparing FC_ALLto FC_ALL_LS?

There could be some differences, as I said FC_ALL maximum likelihood scaled (they are used for map calculation) and FC_ALL_LS least-squares scaled (it is used for Rfactor calculations)

I found somewhat large difference between FC_ALL_LS map and FC_ALL
map in Se position.

Without data I could not say what might be going on.

----------
From: Dirk Kostrewa

Dear Allister Crow,

in cases like these, I would recommend to apply the Babinet bulk solvent correction instead of the mask bulk solvent correction as a control (Refmac5 -> Scaling -> Use Babinet scaling; uncheck "Calculcate the contribution from the solvent region"). The Babinet bulk solvent correction only uses two overall scaling factors and is usually simple, robust and, in my experience, does not show any local difference density artefacts. The mask bulk solvent correction is more powerful, but, depending on the project and the various mask radii for generating and shrinking the mask, could produce false positive or negative difference density. To exclude these cases, you can always calculate the Babinet bulk solvent correction as a control.

Best regards,

Dirk.

Am 16.04.12 12:37, schrieb Allister Crow:

--   

----------
From: Ed Pozharski

On Tue, 2012-04-17 at 11:08 +0200, Dirk Kostrewa wrote:
> The mask bulk solvent correction is more powerful

Just to note that sometimes Babinet solvent correction returns lower
Rfree and thus may be preferred to mask (assuming that the Rfree is the
only thing that matters).

Beginning with 5.6.0078, you can also optimize the bulk solvent mask
parameters

http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html#Bulk_solvent

This, imho, is not likely to remove the density artifacts, but is worth
a try.

--
"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs

Beamline scientist position at the HZB BESSY-II MX-beamlines (application reference: F 2012/7), deadline 30.06. 2012

From: Müller, Uwe
Date: 11 June 2012 10:37

The HZB MX-team is seeking a beamline scientist to support the operations of the three MX-beamlines at BESSY-II. The initial contract will run over a period of three years. Payment will be on the basis of germans TVöD-Bund salary scheme. 

HZB-MX is offering state-of-the-art MX-beamlines to the international user community and is actively developing the experimental capabilities of these stations. This includes the development of long wavelength phasing methods, the in situ crystal screening using the automation platform CATS, controlled crystal dehydration by the HC1c device and the utilization of the Pilatus 6M detector, which will soon be installed at BL14.1.

The successful candidate shall have a PhD in physics, biochemistry or chemistry and shall possess practical experiences in the field of X-ray crystallography, preferentially using synchrotron radiation. Furthermore proven experiences in software development i.e. using Python or other modern languages are a clear advantage.

HZB is encouraging the application of female scientists. Handicapped applicants with a comparable qualification are preferred.  

In case of further questions contact:

Dr. Uwe Mueller (e-mail: umueAThelmholtz-berlin.de), 

or

Dr. Manfred S. Weiss (e-mail: mswAThelmholtz-berlin.de), 

Applications including a CV, list of publications and contact information of two referees shall be sent until 30.06. 2012 electronically and as a single pdf-file stating the application reference: "F 2012/7" within the email header to: personalabteilungAThelmholtz-berlin.de)

We are looking forward for your applications.

Uwe Mueller & Manfred Weiss

Dr. Uwe Mueller
Soft Matter and Functional Materials
Macromolecular Crystallography (BESSY-MX) | Group leader
Elektronenspeicherring BESSY II

url: www.helmholtz-berlin.de/bessy-mx

Yeast plasmid DNA miniprep problem

From: Zhang, Zhen
Date: 12 April 2012 16:32

Sorry for the non-ccp4 question. I am having trouble to miniprep plasmid from yeast. The plasmid is pCTCON2 and the yeast strain is EBY100. I am using Zymoprep Yeast Plasmid Miniprep II kit. I grow the culture in SDCAA medium to OD0.3 and spin down 1.5ml cells. The pellet was resuspended in solution 1 supplemented with Zymolyase and was incubated for 1 hr. I followed the manual exactly for the rest steps. However, I have never been able to recover any plasmid. There is nothing or smear in the agarose gel and there is no colony after transformation to DH5alpha after one overnight incubation at 37. The existence of the plasmid in the yeast has been confirmed by the ability to grow in the nutrition deficient medium SDCAA and the expression of plasmid protein in SGCAA medium was observed by FACS. I am wondering if someone here can shine some light on this issue. Any thoughts or suggestions are welcome.

 

Thank you.

 

Zhen

 

----------
From: Philipp Ellinger

Hi Zhen,

I also had problems with low amounts of plasmid from yeast using 5 ml o/n cultures. But when increasing the culture volume it worked:

Large-scale (0.5–1 l for obtaining preparative plasmid amounts) overnight  yeast cultures were harvested, washed in cold water once, and then resuspended in Zymolyase incubation buffer (0.1 M sodium phosphate buffer pH 7.4, 2 mM DTT, and 5–10 mg/ml of Zymolyase with 1.2 M sorbitol). The yeast cell wall was digested for 30 min at 37°C, cells were then lysed by alkaline lysis as (described in: Singh MV, Weil PA. A method for plasmid purification directly from yeast. Anal Biochem.2002;307:13–17). 0.5–1 µl of this preparation was used to transform chemically competent E. coli.

Cheers Phil

very uninformative

From: Bernhard Rupp (Hofkristallrat a.D.)
Date: 4 April 2012 06:07

Ok Kevin,

 

thank you for your response. You got it, and that is good, and I am sure we'll hear from you again and that is

good too. But let me explain the Orcus (however, keep in mind, I am only a single contributor and almost

always do not represent the majority of CCP4BB users' opinions. So that alone should be some comfort).

 

The title of Orcus means that you have earned yourself a nickname. Nicknames are a brutal invention, common in Western

civilization, almost always addressing some personal idiosyncrasy, in general politically incorrect, but nevertheless they stick*).

 

So let me explain:

St. Orcus is the patron saint of trolls, hobgoblins and troglodytes, and the defender of off-topic posters and otherwise chastised

contributors (just like the Hofkristallrat sitting in his Hofkristallamt is the defender of structures collected from

real data. That is for example why I do not get invited to modelers' conferences. Everything has its price).

So you are now in the unique position to evaluate the orcness of a contribution – perhaps first by making sure that

your own contributions are not orcish - and exercise your right to identify any contributions you consider orcward.

 

Experiencing a new culture can be a confusing and upsetting experience. If I may offer some comforting example

relating to your blogs, and coming from a different planet myself, I once considered it a shocking calamity that

protein-ligand structures are published that do not contain a ligand. I have mellowed a lot since and prevented a few

cardiac events and assassination attempts by accepting the editorial indifference towards such orcward orcness. Maybe

you'll get there too, and maybe you'll become a Hofkristallamtsapprentice.

 

But let me tell you, if you are serious about correcting poor science, you've got to be ready to take a lot more flak

to get there than being beatified on the BB. Oh, and by the way, no academic career.   

 

Wingardium Leviosa!

 

Over and out, BRRRR

 

*) Like Kim Jong-il probably means something like Gold Upright Sun. Just to demonstrate how poor those things translate into reality….

 

PS: Orcward ligand orcs, the Amt is watching!

 

PPS: it is still ok to ride a trolley.

 

From: Kevin Jin 
Sent: Tuesday, April 03, 2012 5:23 PM

Thanks of your education. I got it.

 

By the way, what does Orcus mean here?

 

Regards,

 

Kevin

----------
From: Kevin Jin

Cool!  You are a good tutor for Greek culture.

 

Orcus blesses you.

 

^_^

--

Kevin Jin

Position for Structural Biology Computing Specialist at Harvard Medical School

From: Piotrek Sliz
Date: 8 June 2012 15:15

Job Opening:

Structural Biology Computing Specialist

Harvard Medical School

Longwood Ave, Boston, MA, 02115. USA.

The Center for Molecular and Cellular Dynamics Structural Biology Computing Center at Harvard Medical School provides research computing support to 25 structural biology laboratories in the Boston area. We design, implement and maintain a specialized computing infrastructure to support all phases of macromolecular structure determination by X-ray Crystallography, NMR and electron microscopy. The infrastructure includes storage to support data acquisition as well as Linux workstations and OSX research desktops for data processing. We also support specialized research instrumentation computers running the Windows operating system.  

The Structural Biology Computing Specialist position with the Research Computing Core at Harvard Medical School provides a unique opportunity to provide computing support to structural biology laboratories located at Harvard Medical School. Supported groups include laboratories of James Chou (NMR), Stephen Harrison, Piotr Sliz, Suzanne Walker, Tom Rapoport (X-ray Crystallography), Tom Walz, James Hogle (X-ray Crystallography and EM) as well as other groups occasionally utilizing structural biology techniques. You will work as a member of a multidisciplinary research and computing environment that integrates the Computing Core, a software consortium, research laboratories, and teaching initiatives. Your daily responsibilities will include system administration of Linux and OSX workstations and integration of the workstation with research computing services (e.g. storage, authentication, cluster/grid job submission, backups). The individual will be also responsible for support of the specialized structural biology computing workflows. This includes assistance with setting up molecular dynamics computations, assistance with setting up advanced structure determination and analysis pipelines, assistance with preparing macromolecular animations and publication figures and training users. Additional responsibilities will include assistance with software compilation, configuration and customization for cluster deployment including supporting structural biology HPC workflows on clusters and computing grids. Occasionally you might be also included in collaboration and research projects.

Basic Qualifications:

Degree in Computer Science/Bioinformatics; or MSc/PhD in Structural Biology; or equivalent combination of education plus relevant support and research experience.  5-7 years of structural biology research computing support experience.

Additional Qualifications:

Requires familiarity with python or other programming languages; familiarity with structural biology applications (e.g. Pymol, COOT, Schrodinger) and structure determination/analysis workflows; strong knowledge of Linux and OSX operating systems. The successful candidate will have excellent organizational skills and particular ability to work independently and prioritize work in an environment of multiple and conflicting interests. Proven project and/or program management skills. Excellent interpersonal and communications skills. Ability to work with discretion.

Apply to job:

Grade 58 position (http://employment.harvard.edu/benefits/compensation/)

Applications should be submitted through Harvard's Recruitment Management System.

For more information about this position please contact Piotrek Sliz with subject line: 26887BR.

(the position is renewable annually with no maximum number of terms)

--

Piotrek Sliz

zinc fingre

From: Rajesh kumar
Date: 3 April 2012 16:07

Dear All,

I am trying to crystallize a protein, so far I got no diffraction though I have large crystals.

It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only).

Is there a way if I could check using bioinformatic tools if  my protein has Zinc finger or zinc finger-like motif?  If so, is it possible assume it would bind some sort of DNA and could I check that as well?

I appreciate any suggestions to this BROAD question and some references would be helpful.

I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. 

I appreciate your time.

Thanks,

Rajesh

----------
From: Debasish Chattopadhyay

Read a book.

If you can't find a book then ask the all knowing Google.

 

----------
From: Rajesh kumar

Thanks...... I will.

---

----------
From: Pius Padayatti


Hi Rajesh,
First of all you did the right thing to ask people here about our doubts.
There is nothing wrong in asking questions.

The board is for asking questions realted to crystallography
(all aspects).

Padayatti

--
Pius S Padayatti,PhD,


----------
From: Debasish Chattopadhyay


Yes, Rajesh, I completely agree with Pius.  There is absolutely nothing wrong in asking a question on ccp4bb.
The suggestion 'read a book and search on-line information sources' is a good one on any subject.

----------
From: Peter Hsu


Hi Rajesh,

Have you looked at how well conserved these Cys/His residues are? Is the spacing similar to known zinc fingers? Might be good things to consider if you suspect a zinc finger in your protein, of course you probably know this already.

Best,
Peter

----------
From: Rajesh kumar

Dear All,

Thanks everyone for the suggestions. I did go to library to look up some chapters in books which gave me lot of information about conserved zinc finger domain. My protein  has Cx4C and Cx3C and with very large spacing, so I suspect it could be zinc finger like protein (though no software showed any indication) but I am looking forward to do some experiments to confirm this. I was looking for some examples other than known domains (TFIIS, LIM, ring finger ref:encyclopedia of Mol Biol and Mol Med vol 6) which have C2H2 or C3H but doesn't follow the rules zinc finger but still bind to DNA and has been crystallized. I guess I will do more reading.

Thanks again

Rajesh