Re: [ccp4bb] detectors on home sources
Thanks so much for the generous replies I received so far both on and offline. By the way we visited the three top vendors and saw the systems in operation. We were slightly handicapped since at startup we don't yet have crystals and had to rely on standards, but the applications scientists were all very helpful. We are considering sealed tube sources, CCDs, etc., and we have an ample set of contacts with experience on these systems to advise us. But I should say that the purpose of my message was not to compare systems. This would be sensitive to do online anyway. The issue is the reliability in a home lab as has been well stated below, specifically for the newer components. Nothing like a satisfied customer to reassure on that point (or to warn about potential problems), and that's what I'm looking for with regard to the new detectors especially. Many thanks again. Fareed On Tue, Apr 30, 2013 at 11:44 PM, mjvdwo...@netscape.net wrote: I second this opinion. At the end of next week our Pilatus 200K will be delivered. Soon after that I will be able to report on its characterist ics. But really, Boaz nailed it: reliability and service are very important. It does not matter how good something is on paper if you cannot keep it running. And with this e-mail I think it is clear what my recommendation was to our department and I am pleased that the recommendation was followed. Exactly as Boaz suggests, it was based in significant part on consideration of reliability and quality of service. It is to be noted that reliability of instruments and quality of service could vary from region to region, that is, good service in the US may and may not translate to good service elsewhere. It would be good to do a regional poll for this. Having said all this, it is my impression that the newer technology has fewer moving parts and therefore should be expected to be more reliable. But I don't know that for sure, please ask again in 3-5 years. :-) Mark -Original Message- From: Boaz Shaanan bshaa...@exchange.bgu.ac.il To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Tue, Apr 30, 2013 2:53 pm Subject: Re: [ccp4bb] detectors on home sources One of the main things (if not THE main thing) to worry about when investing in such expensive equipment is long-time reliability and quality of service in your place. Nothing is more frustrating than seeing your wonderful and expensive equipment standing idle for long periods because of lack of service. This may mean quite often taking compromises and going perhaps not for the front-line state-of-art piece of equipment but rather for the sturdy, hard-working equipment. It worked for us very well. My 2p advice. Boaz *Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710* ** ** * * -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Fareed Aboul-Ela [faboul...@zewailcity.edu.eg] *Sent:* Tuesday, April 30, 2013 10:00 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] detectors on home sources I'm involved in advising my institute on an X-ray home source for a core facility. The vendors are offering some new configurations. Whatever the claimed advantages/disadvantages, I'm hesitant to make a decision without consulting someone with direct experience with them. In particular, has anyone had any experience with using the photon100 CMOS detector being offered by Bruker, or the pilatus 200K detector being offered by Rigaku? I'd also appreciate hearing from anyone with experience with the latest Bruker microfocus rotating anode generator (called the Turbo or TXS)? Many thanks for sharing your experiences. Fareed Aboul-ela Associate Professor Zewail University Zewail City of Science and Technology Giza, Egypt faboul...@zewailcity.edu.eg
[ccp4bb] The Second CCP4/OIST School on computational macromolecular crystallography
Dear Colleagues, we are pleased to announce the second CCP4 structure solution school at the Okinawa Institute of Science and Technology (OIST), Okinawa. All details can be found at http://www.ccp4.ac.uk/schools/OIST-2013/index.php Title: CCP4 school: From data processing to structure refinement and beyond Dates: November 4 to 8, 2013 Site: Okinawa Institute of Science and Technology, Okinawa, Japan The school content: Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is 7 September. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/OIST-2013/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation costs outside Okinawa. Lodging will be provided at the OIST Guest House Seaside House. The workshop will also cover the expenses for all meals and refreshments. Fadel Samatay, Charles Ballard, Matthais Wolf -- Scanned by iCritical.
[ccp4bb] ECM28 and the Bragg 100 year anniversary
Dear Colleagues The 28th European Crystallography Meeting will be held in Warwick University Arts Centre from 25th to 29th August 2013. The Programme and Abstract submission guidelines (deadline 31st May) are at: http://ecm28.ecanews.org/ Early Bird registration closes on 6th May. For each of the 40 Microsymposia, 3 talks will be chosen from the submitted Abstracts. There will be a special Bragg Symposium on the first morning and a Bragg Exhibition. Do plan to come and bring your students: the meeting promises to be a real celebration of 100 years of crystallography! Best wishes Elspeth Professor Elspeth F. Garman, Director Systems Biology Programme, Doctoral Training Centre. Postal address: Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Tel: (44)-1865-613297 South Parks Road, FAX: (44)-1865-613201 OXFORD, OX1 3QU, U.K. E-mail: elspeth.gar...@bioch.ox.ac.ukmailto:elspeth.gar...@bioch.ox.ac.uk http://lmb.bioch.ox.ac.uk/www/garman/gindex.html - The University of Oxford's Doctoral Training Centre has three available programmes for October 2013 entry: Life Sciences Interface Doctoral Training Centre; Systems Biology Doctoral Training Centre; and Systems Approaches to Biomedical Science Industrial Doctorate Centre. To find out more, visit: http://www.dtc.ox.ac.uk/
[ccp4bb] Young Crystallographers satellite meeting @ ECM28
Dear Colleagues Further to the ECM28, the British Young Crystallographers and European Young Crystallographers have also organised a Young Crystallographers satellite meeting prior to the opening ceremony on 25th August. Registration only costs £15 and includes coffee, lunch and a plenary lecture by Dr Birger Dittrich. The meeting will allow younger scientists to present their research either as an oral or poster presentation in a more relaxed environment. There are also a number of bursaries available for younger scientists. Registration for both the ECM and Satellite meeting can be done on the ECM28 website: http://ecm28.ecanews.org/registration/ Early bird registration is available until 6th May 2013. Best wishes, Geoffrey, on behalf of the YCG committee - Geoffrey Masuyer, PhD Research Officer, Structural Molecular Biology Department of Biology Biochemistry University of Bath, UK
[ccp4bb] DNS Group Leader/Manager – Structural Biology – Crystallography
Position: Group Leader/Manager – Structural Biology – Crystallography Client:Dart NeuroScience LLC (DNS) is a privately held Delaware Limited Liability Company with offices in San Diego, CA. DNS will discover new technologies and develop new therapies to help maintain cognitive vitality throughout life. www.dartneuroscience.com DNS is seeking a group leader with a strong background in macromolecular crystallography. Reporting to the director of structural biology, the successful candidate will be responsible to establish and manage the crystallography team within the group. The candidate should have expert knowledge of the state-of-the-art crystallization and structure determination equipment and processes necessary to produce high-quality crystal structures and to support structure-guided drug design. Major responsibilities will include independent hands-on experimental work and leading a team of scientists and research associates to support high-throughput crystallization, X-ray data collection, structure determination and refinement of high-quality protein structures originating from different protein families including membrane proteins. The candidate will be required to give scientific expert advice to group members and have frequent interactions with the molecular biologists, protein production team and protein chemists in the group to provide ideas on new protein boundary designs, incorporation of mutations that alter protein function and stability and on new ideas to improve protein expression and purification yields, crystallizability and diffraction quality of protein crystals. The candidate will also interact closely with computational and medicinal chemists in the company to propose new ideas for structure-based combinatorial libraries, inhibitor design, or variants of existing compounds that may be useful in advancing project goals. Good communication skills, leadership skills, project and sample management experience overseeing multiple projects in parallel as well as capacity for strategic thinking are required. Requirements Responsibilities: · Ph.D. in life science with thesis. · 8+ years of relevant experience in protein crystallography and structure-guided drug design. Preferably 1+ year of industrial supervisory experience of Ph.D. scientists and research associates. · Proven hands-on experience in high-throughput crystallization, synchrotron data collection, structure determination, structure refinement, structure-based drug design and fragment-based drug discovery. · Familiar with all major crystallography software packages (HKL, CCP4, COOT, Pymol). · Expert knowledge in the scientific principles and concepts of protein crystallography including state-of-the-art high-throughput crystallization, phasing (MAD/SAD/MR), density modification, model building, refinement and structure validation. · Knowledge in other areas of structural biology (protein chemistry and crystallography) and membrane protein crystallography is desirable. · Inter-disciplinary knowledge of drug discovery (enzymology, cellular pharmacology, DMPK) is a plus. · Demonstrated independent thought/creativity in science. · Excellent collaboration, communication (oral and written) and multitasking skills and able to present work formally to Scientific Research Committees. Opportunity: DNS offers competitive salaries and a great benefits package including incentive bonuses, healthcare, vision, dental, long-term disability, life insurance and a 401(k) retirement savings plan. For Additional Information Contact: Bill Domann, The Domann Organization, Inc. Cell: 415 726 9704 Office: 858 756 227 Email: b...@domann.net Jovanna Bost Market Development Business Relations The Domann Organization-Life Science Leadership Retained Search Services since 1988 www.domann.net jb...@domann.net
[ccp4bb] DNS Group Leader/Manager – Structural Biology – Protein Chemistry
Position: Group Leader/Manager – Structural Biology – Protein Chemistry Client: Dart NeuroScience LLC (DNS) is a privately held Delaware Limited Liability Company with offices in San Diego, CA. DNS will discover new technologies and develop new therapies to help maintain cognitive vitality throughout life. www.dartneuroscience.com DNS is seeking a group leader with extensive experience in the development and implementation of protein purification processes for macromolecular crystallography studies. Reporting to the director of structural biology, the successful candidate will be responsible to establish and manage the protein purification team within the group. The candidate should have excellent knowledge of the state-of-the-art protein purification equipment and processes necessary to create and mentor others in establishing purification procedures that reproducibly lead to the generation of crystallization-grade protein in quantity and quality suitable for structural studies. Major responsibilities will include independent hands-on experimental work and leading a team of scientists and research associates to support large scale protein purifications of proteins recombinantly expressed in either prokaryotic or eukaryotic (baculovirus and mammalian cells) systems and originating from different protein families including membrane proteins. The candidate will be required to provide scientific expert advice to group members and have frequent interactions with the molecular biologists, protein production facility and crystallographers in the group. The candidate will be required to provide feedback to team members to maximize protein yields and quality that will lead to successful crystallization enabling 3D structure determination. Good communication skills, leadership skills, project and sample management experience overseeing multiple projects in parallel as well as capacity for strategic thinking are required. Requirements Responsibilities: · Ph.D. in life science with thesis. · 8+ years of relevant experience in protein purification and biophysical characterization of proteins originating from different protein families for crystallization and 3D-structure determination. · Preferably 1+ year of industrial supervisory experience of Ph.D. scientists and research associates. · Proven hands-on experience in different protein purification methods (e.g. affinity, size-exclusion, ion-exchange, isoelectric focusing chromatography) and biochemical/biophysical characterization techniques (e.g., Western blot, light scattering, calorimetry, analytical ultracentrifugation, DLS, thermal melting, protein MS, protein NMR). · Expert knowledge in the scientific principles and concepts of protein chemistry and good understanding of the protein quality requirements for crystallization purposes preferably demonstrated through peer-reviewed publications. · Knowledge in membrane protein chemistry and other areas of structural biology (molecular biology and crystallography) is desirable. · Inter-disciplinary knowledge of drug discovery (enzymology, cellular pharmacology, DMPK) is a plus. · Demonstrated independent thought/creativity in science. Excellent collaboration, communication (oral and written) and multitasking skills and able to present work formally to Scientific Research Committees. Opportunity: DNS offers competitive salaries and a great benefits package including incentive bonuses, healthcare, vision, dental, long-term disability, life insurance and a 401(k) retirement savings plan. For Additional Information Contact: Bill Domann, The Domann Organization, Inc. Cell: 415 726 9704 Office: 858 756 227 Email: b...@domann.net Jovanna Bost Market Development Business Relations The Domann Organization-Life Science Leadership Retained Search Services since 1988 www.domann.net jb...@domann.net
[ccp4bb] DNS Group Leader/Manager – Structural Biology – Protein Production
Position: Group Leader/Manager – Structural Biology – Protein Production Client: Dart NeuroScience LLC (DNS) is a privately held Delaware Limited Liability Company with offices in San Diego, CA. DNS will discover new technologies and develop new therapies to help maintain cognitive vitality throughout life. www.dartneuroscience.com DNS is seeking a group leader with extensive experience in large-scale protein production for macromolecular crystallography studies. Reporting to the director of structural biology, the successful candidate will be responsible to establish and manage the large-scale protein production facility within the group. The candidate should have excellent knowledge of the state-of-the-art equipment and processes to perform large-scale recombinant expression in both prokaryotic and eukaryotic (baculovirus and mammalian cells) systems of proteins originating from various protein families to produce milligram-quantities of material suitable for structural studies and/or other drug discovery purposes. Major responsibilities will include independent hands-on experimental work in addition to guiding a team of scientists and research associates to ensure the optimal operation of the large-scale protein production platform to organize workload according to research priorities and to support successful protein crystallization. The candidate will be required to provide scientific expert advice to group members and have frequent interactions with the molecular biologists, protein chemists and crystallographers in the group on new ideas to enhance productivity and to improve protein expression and purification yields. Good communication skills, leadership skills, project and sample management experience overseeing multiple projects in parallel as well as capacity for strategic thinking are required. Requirements Responsibilities: · Ph.D. in life science with thesis. · 8+ years of relevant experience in recombinant large-scale protein expression to support structural studies. Preferably 1+ year of industrial supervisory experience of Ph.D. scientists and research associates. · Proven hands-on experience in large-scale scale recombinant prokaryotic and eukaryotic (baculovirus and mammalian cells) protein production, protein purification and biochemical/biophysical screening techniques for protein characterization (e.g. western blot, calorimetry, analytical ultracentrifugation, DLS, thermal melting, protein MS, protein NMR). · Expert knowledge in large-scale protein production platforms, recombinant protein expression and protein analysis techniques preferably demonstrated through peer-reviewed publications. · Knowledge in other areas of structural biology (protein chemistry and crystallography) is desirable. · Inter-disciplinary knowledge of drug discovery (enzymology, cellular pharmacology, DMPK) is a plus. · Demonstrated independent thought/creativity in science. · Excellent collaboration, communication (oral and written) and multitasking skills and able to present work formally to Scientific Research Committees. Opportunity: DNS offers competitive salaries and a great benefits package including incentive bonuses, healthcare, vision, dental, long-term disability, life insurance and a 401(k) retirement savings plan. For Additional Information Contact: Bill Domann, The Domann Organization, Inc. Cell: 415 726 9704 Office: 858 756 227 Email: b...@domann.net Jovanna Bost Market Development Business Relations The Domann Organization-Life Science Leadership Retained Search Services since 1988 www.domann.net jb...@domann.net
[ccp4bb] showing electron density on an ipad
Hello all, So, I find an ipad is a wonderful device for teaching (any tablet really - but I'm partial to the ipad). I can project it in a classroom, run pymol and a few other chemistry/biochemistry things, and really get the students interested in these subjects easily. I actually don't have a laptop - and our classrooms are such that there are computers connected to the projectors but they have standard University software packages installed on them. It would be very helpful if I could just display electron density using an ipad. The pymol app will load a map (it is an option) - but when I take a map from my linux machines it doesn't work. Any thoughts here? Has anybody done this Thanks Dave
Re: [ccp4bb] showing electron density on an ipad
Dear Dave I have found the Molsoft ICM browser useful for showing students structures. There is a freely distributed version available for both ipad and android. I have not used it for maps but I believe it can display them. SGC Oxford originally showed me this software and have great examples displaying their structures on their web site and in their PLoS articles. Sorry but I have not used the ipad version - I think you have to pay a nominal fee for that. All the best Martyn From: David Roberts drobe...@depauw.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 1 May 2013, 20:56 Subject: [ccp4bb] showing electron density on an ipad Hello all, So, I find an ipad is a wonderful device for teaching (any tablet really - but I'm partial to the ipad). I can project it in a classroom, run pymol and a few other chemistry/biochemistry things, and really get the students interested in these subjects easily. I actually don't have a laptop - and our classrooms are such that there are computers connected to the projectors but they have standard University software packages installed on them. It would be very helpful if I could just display electron density using an ipad. The pymol app will load a map (it is an option) - but when I take a map from my linux machines it doesn't work. Any thoughts here? Has anybody done this Thanks Dave
Re: [ccp4bb] showing electron density on an ipad
Imolview and ndkmol are excellent apps on android to show structures. Padayatti On May 1, 2013 3:56 PM, David Roberts drobe...@depauw.edu wrote: Hello all, So, I find an ipad is a wonderful device for teaching (any tablet really - but I'm partial to the ipad). I can project it in a classroom, run pymol and a few other chemistry/biochemistry things, and really get the students interested in these subjects easily. I actually don't have a laptop - and our classrooms are such that there are computers connected to the projectors but they have standard University software packages installed on them. It would be very helpful if I could just display electron density using an ipad. The pymol app will load a map (it is an option) - but when I take a map from my linux machines it doesn't work. Any thoughts here? Has anybody done this Thanks Dave
