[ccp4bb] Picking water molecules at 4A structure.
Dear community, Recently we have been able to solve a crystal structure of a DNA/protein complex at 4A resolution. After almost the final cycles of model building and refinement (with R/Rfree of ~ 22/27) we could see some small water like densities...all throughout the complex. Now my query is, whether one should pick water molecules at this low resolutions or it is totally unscientific to do so? Many thanks in advance...!!! My best regards, Sudipta.
[ccp4bb] Submit your abstract for the ACA Annual meeting in Philadelphia July 25-29, 2015
Hi CCP4 users! You are invited to the ACA meeting in Philadelphia! Abstracts are still being accepted (see the invitation below). All the best, Tom T Tom Terwilliger Vice President, ACA Abstracts still being accepted ACA 2015 Meeting - July 25-29 Philadelphia, PA Is this email not displaying correctly? View it in your browserhttp://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881id=0f524b9d2ce=9b7bdbf1d3. [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/2a8238a9-d302-416a-a57a-8921e2bf993d.png] [http://www.amercrystalassn.org/2015-mtg-homepage]http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2bc286881id=da758196b0e=9b7bdbf1d3 ABSTRACT SUBMISSION DEADLINE IS EXTENDED ACA Annual Meeting • Philadelphia, PA • July 25 - 29, 2015 Submit abstract now to be considered for an oral presentation. Once all the lectures are scheduled, abstracts will continue to be accepted for poster presentations. [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/21952137-733c-49cc-86ee-8291f48bc1be.jpg] Exhibit Showhttp://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2bc286881id=02f4dedb66e=9b7bdbf1d3 First-time exhibitors receive 25% discount Discount rates for Not-for profits Corporate Members receive an additional discount Coffee breaks poster sessions held in the exhibit hall to offer multiple opportunities to reach your target audience Your website linked on the meeting page Free listing in ACA RefleXions and Program Show Guides Special sponsorships for Exhibitors only [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/d9f63f39-b8be-49a4-8601-5032c2c9a830.jpg] Call for Papers:http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2bc286881id=270701d41ce=9b7bdbf1d3 40% of talks selected from contributed abstracts No abstract submission fee Lower registration fees for members Sessions for students young scientists on career directions, reviewer practices more Full scientific program:www.AmerCrystalAssn.orghttp://amercrystalassn.us2.list-manage1.com/track/click?u=3e43dd9d1724b97d2bc286881id=fd4ad5115fe=9b7bdbf1d3 [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/961e8c70-86c1-4ea2-8688-6b3bee6654e1.png] Registrationhttp://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2bc286881id=a00d1142b3e=9b7bdbf1d3: Join or pay membership dues and save on Registration fees Corporate Members receive advertising and exhibiting discounts Early bird rates until May 31 Online registration now openhttp://amercrystalassn.us2.list-manage2.com/track/click?u=3e43dd9d1724b97d2bc286881id=14cb125f04e=9b7bdbf1d3 follow on TwitterTwitter%20Account%20not%20yet%20Authorized | friend on Facebook | forward to a friendhttp://us2.forward-to-friend.com/forward?u=3e43dd9d1724b97d2bc286881id=0f524b9d2ce=9b7bdbf1d3 Copyright © 2014, AmericanCrystallographicAssn. All rights reserved. Our mailing address is: a...@hwi.buffalo.edumailto:a...@hwi.buffalo.edu ACA, PO Box 96, Buffalo, NY 14205 [Email Marketing Powered by MailChimp]http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletterutm_medium=emailutm_campaign=monkey_rewardsaid=3e43dd9d1724b97d2bc286881afl=1 unsubscribe from this listhttp://amercrystalassn.us2.list-manage.com/unsubscribe?u=3e43dd9d1724b97d2bc286881id=a9c22ea74ce=9b7bdbf1d3c=0f524b9d2c | update subscription preferenceshttp://amercrystalassn.us2.list-manage.com/profile?u=3e43dd9d1724b97d2bc286881id=a9c22ea74ce=9b7bdbf1d3
Re: [ccp4bb] Picking water molecules at 4A structure.
At 4A, I wouldn't unless I had an exceptionally good reason to. There will always be some blobs, due to random noise and fourier ripples as well as due to an imperfect model. Unless a blob makes nice H-bonds to something else that is nicely ordered, I wouldn't model at water into it. If you can't see nice density for side chains then you probably aren't really seeing density for waters either. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago pr...@uchicago.edumailto:pr...@uchicago.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sudipta Bhattacharyya [sudiptabhattacharyya.iit...@gmail.com] Sent: Monday, April 13, 2015 1:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Picking water molecules at 4A structure. Dear community, Recently we have been able to solve a crystal structure of a DNA/protein complex at 4A resolution. After almost the final cycles of model building and refinement (with R/Rfree of ~ 22/27) we could see some small water like densities...all throughout the complex. Now my query is, whether one should pick water molecules at this low resolutions or it is totally unscientific to do so? Many thanks in advance...!!! My best regards, Sudipta.
[ccp4bb] Post-doc position - Cryo-electron microscopy - University of Minnesota
A post-doctoral scientist position is available at the University of Minnesota, USA. The successful candidate will study the cell entry mechanism of small-enveloped viruses using cryo-EM and cryo-ET methods. The project focuses on understanding the oligomerizational and organizational changes of the type-II fusion proteins during low-pH triggered membrane fusion. Candidates are expected to have a strong background in either of molecular virology, protein structure determination, cryo-EM data collection, cryo-ET data collection and image-processing. The successful candidate will be involved in the specimen preparation and development of necessary computational algorithms to facilitate image analysis. Other expectations include high self-motivation, well-organized working style, good team work ethics, preparation of research papers and presentations at professional conferences. Scientists recruited will work in state-of-the-art facilities and will join a strongly interactive, collaborative and collegial research environment. Minneapolis is a dynamic and progressive city with outstanding cultural attractions and a high standard of living. Qualified applicants are invited to submit a cover letter, current CV and the contact information for three references to Dr. Wei Zhang (zhang...@umn.edu).
Re: [ccp4bb] Picking water molecules at 4A structure.
Now my query is, whether one should pick water molecules at this low resolutions or it is totally unscientific to do so? Your question is justified in intent, but ill phrased. The question you are faced with is “How plausible would the assignment of a given electron density reconstruction feature as a water molecule be?” The answer depends on observational evidence and chemical plausibility. You have the most knowledge about your protein complex and should have some knowledge about chemical plausibility of your proposal. (a)A few questions to consider re. evidence: What is the noise level in your map? How do normal 2Fo-Fc densities compare to difference densities? Density shape? Other isolated mystery density of same levels somewhere? If your maps are excellent and low noise it is not impossible to see a very well bound water molecule at 4A. (b) Plausibility based on prior expectations: Was Mg in the cocktail? Being isoelectronic with HOH (and a favorite companion of DNA in crystallization), it might be a plausible candidate. Anything else heavier, perhaps? SO4, PO4? Perhaps any clues from anomalous data/ano diff maps? Fragments of PEGs? What does the refinement tell you? How did you refine? Does your protocol match the low resolution of the data? Even at the low resolution, do bond length and coordination support a discrete moiety? Distances, geometry, B-factors? If everything points in your favor, you can justify the proposition of a discrete moiety. Your scientific credibility depends on how well your proposition is supported by reasoning from (a) and (b) – probably with heavy emphasis on (b) as you are poorly determined – and not whether you are ultimately right or not. Although I doubt that a water molecule without biological relevance assigned to it has any effect on global refinement stats nor on your career, you can always invoke the rule of parsimony for your model – no explanation is better than an unsupported one. “I don’t know” is a perfectly scientific answer. LGBR
[ccp4bb] CCP4 Scientific Programmer Position at CCP4 Core Group
Dear All, This is a repeat announcement of an opening in CCP4 core Group for the Scientific Programmer Position. The post is for 3 years and will be allocated in the Research Complex at Harwell, Rutherford-Appleton Laboratory, in some 17 miles south from Oxford, United Kingdom. Job advert and link for on-line applications follow below in this post. If this does not apply to you, please pass this e-mail on your colleagues and friends who may be interested in this exciting opportunity. Many thanks, Eugene Krissinel. CCP4 Scientific Programmer*STFC - The Science and Technology Facilities Council* Location:DidcotSalary:£28,384 to £29,566 per annum plus excellent benefits Hours:Full TimeContract Type:Contract / Temporary Placed on:12th March 2015 Closes:22nd April 2015Job Ref:IRC180113 *About Us: *The Science and Technology Facilities Council is a world-leading multi-disciplinary science organisation, and our goal is to deliver economic, societal, scientific and international benefits to the UK and its people – and more broadly to the world. CCP4 is a large and well-established project, hosted by STFC, with the aim of developing and maintaining state of the art structure solution and analysis software for protein crystallography. The CCP4 Software Suite is one of the most comprehensive and most widely used in its field. *About The Role: *Applications are invited for a CCP4 Scientific Programmer to work in the core CCP4 team. You will assist CCP4 developer’s teams in RAL, University of York and University of Newcastle in the roll-out of CCP4i2, CCP4’s new graphical front end, to end users with subsequent activities on its further development, improvement and increasing functionality. *This is a complex activity, which will include, but is not limited to, the following tasks:* - Develop and maintain the CCP4 release branch related to CCP4i2 and the corresponding development environment. This includes the maintenance of BZR repositories; accommodation of all relevant modifications and additions to the Suite; builds, tests and dynamic updates required for CCP4i2 development and releases - Learn CCP4i2 structure and code for being able to optimise and adopt it as necessary, and introduce new features - Work in close collaboration with CCP4 developers in both UK and overseas on various aspects of CCP4i2 development You will work closely with other members of the core team and there is frequent contact with collaborating scientists, code developers and users. The CCP4 team contribute to several major development projects, and you may be involved in these as appropriate. *About You**You will have the following:* - Degree in numerate science subject or computer science - Good communication skills in English, verbal and written - Experience of software development in both Python and C++ - Ability to analyse and solve problems independently - Ability to collaborate with colleagues at remote sites Knowledge of protein crystallography, as well as practical experience of both unix-based and Windows operating systems, is beneficial but not essential, as all relevant training and introduction will be provided. Candidates with good aesthetic taste for GUI design are particularly welcome. *Benefits: *An excellent index linked pension scheme, 30 days leave allowance and flexi-time are offered. Full details of offered benefits can be found on STFC’s careers pages https://www.stfc.ac.uk/1895.aspx *How to apply: *Applications are handled by UK SBS; to apply please visit our job board at http://www.topcareer.jobs/Vacancy/irc180113_5225.aspx and submit your CV and cover letter. If you are unable to apply online please contact us by telephone on 01793 867000. For an informal discussion about this role please contact: Dr Eugene Krissinel at eugene.krissi...@stfc.ac.uk
[ccp4bb] crystal structures of enzymes with catalytic mutants
Hello, I have a dispute with a grant referee about the scientific relevance of structures of catalytically inactive enzymes including their complexes with substrates or analogues. I was looking through pdb and the keyword search did not get me far. Could you please tell me - which enzyme structure of catalytically inactive mutant was published first and when - which catalytically inactive enzyme structure in complex with substrate or part of it as a ligand was published first and when. help of the community is highly appreciated, best wishes, dusan Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com http://www.skype.com/
Re: [ccp4bb] Poor resolution
Dera Prerana, Without more information, we cannot help. What have you done, what have you not done, 3.0Å where, etc... Except to say that 3.0Å is not poor at all, often that's all you can get and that's fine. What type of biological or chemical question are you trying to answer ? (we need more info in that sense too). Depending on the question, 3.0Å is enough, and you can refine and get your structure using more or less standard methods. Cheers, Jose. Jose Antonio Cuesta-Seijo, PhD Carlsberg Laboratory Gamle Carlsberg Vej 10 DK-1799 Copenhagen V Denmark Tlf +45 3327 5332 Email josea.cuesta.se...@carlsberglab.dkmailto:josea.cuesta.se...@carlsberglab.dk From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Prerana G. Sent: Saturday, April 11, 2015 3:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Poor resolution Dear all, I am working on a 40kDa protein. The size and diffraction pattern of the protein crystal seems to be fine but I am getting poor resolution (3.0 Å). How can I increase the resolution? Regards, Prerana
[ccp4bb] CCP-EM Spring Symposium
CCP-EM are proud to announce the inaugural 'CCP-EM Spring Symposium'. This two day conference will be held at the site of the new National UK Electron Bio-Imaging Facility on the Harwell Campus, Oxfordshire on the 28-29th May 2015. The theme of the conference is a celebration of the upcoming facility, the initial alpha release of the CCP-EM software suite (see http://www.ccpem.ac.uk/ for further information), as well as the exciting developments in electron microscopy and tomography. Confirmed speakers include: John Briggs (EMBL) Richard Henderson (MRC-LMB) Juha Huiskonen (STRUBI) Lori Passmore (MRC-LMB) Pavel Plevka (CEITEC) Neil Ranson (University of Leeds) Alan Roseman (University of Manchester) Helen Saibil (Birkbeck) Martyn Winn (STFC) For more information and registration details please see: https://eventbooking.stfc.ac.uk/news-events/ccpem-symposium-266 Best wishes, Tom and the rest of the CCP-EM team. -- Dr Tom Burnley, PhD CCP-EM Science and Technology Facilities Council (STFC) The Research Complex At Harwell Rutherford Appleton Laboratory, R92 OX11 0FA 01235 56 7871
Re: [ccp4bb] crystal structures of enzymes with catalytic mutants
Hi Dusan, I tried OCA (http://oca.weizmann.ac.il/oca-bin/ocamain) and entered the keywords: inactive enzyme substrate complex. I got five hits, including mutants (pdf here attached). Best, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-964 University of Lorraine, Nancy School of Science and Technology and School of Medicine 9, Avenue de la Foret de Haye 54500 Vandoeuvre-les-Nancy, France Tel. (direct) : +33 (0)3.83.68.32.73 Tel. (secretary) : +33 (0)3.83.68.32.92 Cell. : +33 (0)6 11 35 69 09 Fax. : +33 (0)3.83.68.32.79 Email : Nadir.Mrabet at univ-lorraine.fr - Le 13 Avr 15, à 10:51, dusan turk dusan.t...@ijs.si a écrit : Hello, I have a dispute with a grant referee about the scientific relevance of structures of catalytically inactive enzymes including their complexes with substrates or analogues. I was looking through pdb and the keyword search did not get me far. Could you please tell me - which enzyme structure of catalytically inactive mutant was published first and when - which catalytically inactive enzyme structure in complex with substrate or part of it as a ligand was published first and when. help of the community is highly appreciated, best wishes, dusan Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com OCA Query Results.pdf Description: Adobe PDF document
[ccp4bb] Senior Scientist position at the Paul Scherrer Institute
For a joint position at the Laboratory of Biomolecular Research and the Swiss Light Source of the Paul Scherrer Institute (PSI) we are looking for a Senior Scientist with interest in free electron laser science. You will work on the implementation and development of injector systems for the serial injection of microcrystals. Within an interdisciplinary team of scientists you will support PSI efforts in time-resolved serial crystallography of light-triggered membrane proteins at SwissFEL and other free electron lasers. Further information under: http://www.psi.ch/pa/offenestellen/1033 Best Regards, Joerg *** Dr. Jörg Standfuss Group Leader Biomolecular Research Paul Scherrer Institute 5232 Villigen PSI Switzerland
