[ccp4bb] Fwd: International Fellowship Program for Postdocs at Paul Scherrer Institut
Prof. Gebhard F.X. Schertler Head of Biology and Chemistry Paul Scherrer Institut Laboratory of Biomolecular Research, BMR OFLC 109 CH-5232 Villigen PSI gebhard.schert...@psi.ch phone +41 (0)56 310 4265 http://www.psi.ch/lbr/laboratory-of-biomolecular-research 15th International Retinal Protein Metting https://indico.psi.ch//event/icrp2012 Anfang der weitergeleiteten E-Mail: Von: PSI User Office useroff...@psi.ch 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: psifel...@psi.ch Paul Scherrer Institut, Human Resources, Miriam Zehnder, 5232 Villigen-PSI, Switzerland - To unsubscribe from this mailing list, please click the following link: https://duo.psi.ch/duo/change_mailing.php?CMD=UkVNOjU1MTI6MTMw -
[ccp4bb] Position for Structural Biology Computing Specialist at Harvard Medical School
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 http://core.sbgrid.org 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 http://sbgrid.org, 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 Systemhttps://sjobs.brassring.com/1033/ASP/TG/cim_jobdetail.asp?SID=^hH7dMHjmiaNUiq3l33ZH95QgBP8GnH2BkV9pAHrTb6H1o2hqnQrW0reB8DGBkhvhjobId=882942type=searchJobReqLang=1recordstart=1JobSiteId=5341JobSiteInfo=882942_5341GQId=0 . *For more information* about this position please contact Piotrek Slizs...@hkl.hms.harvard.edu with subject line: *26887BR.* (the position is renewable annually with no maximum number of terms) -- *Piotrek Sliz* Harvard Medical School Center for Molecular and Cellular Dynamics 250 Longwood Ave., Rm SGM130, Boston MA 02115 http://hkl.hms.harvard.edu e-mail: s...@hkl.hms.harvard.edu Voice: 617-432-5608, ext 70
[ccp4bb] off-topic: Verify3D
I recently acquired the source for Verify3D and have tried unsuccessfully to compile it. It seems to have been written with the SGI Irix F77 compiler in mind, and Ubuntu's gfortran doesn't seem to know what to do with it. Has anyone gotten it to compile on a Linux system, Ubuntu 11.04 in particular? Thanks. :) Eric Williams PhD candidate, Intelligent Systems Program University of Pittsburgh
[ccp4bb] Aspen Center for Physics workshop on Molecular Physics of Non-bonded Biomolecular Interactions
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 – MPrd, LLC - mplumme...@msn.commailto:mplumme...@msn.com Dr. Shing Ho – Dept. Biochemistry Colorado State University – shing...@colostate.edumailto:shing...@colostate.edu Dr. Anthony Rappe – Dept. Chemistry Colorado State University – ra...@lamar.coloradostate.edumailto:ra...@lamar.coloradostate.edu Please contact one of the above by June 29, 2012 to express an interest and a possible area of study. P. Shing Ho, Ph.D. Professor Chair Biochemistry Molecular Biology 1870 Campus Delivery Colorado State University Fort Collins, CO 80523-1870 970-491-0569 (phone)
[ccp4bb] lithium incorporation in refmac
Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. thanx in advance l -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] Are these xtal conditions worth optimizing?
Hi Christine, I would try to optimize both conditions, provided that you do not have contradicting information (like a diffraction pattern that shows a small lattice - salt). Have you tried an additive screen? Have you tried adding a detergent? My experience is mixed with things of that nature - sometimes you can get better looking crystals, sometimes not. And you should always keep in mind that looks and content (and subsequently diffraction quality) are two different matters. Once I was taught a rule that in the case of protein-DNA complexes, the quality of diffraction is inversely proportional to the prettiness of the crystals and then I proved that rule wrong with nice-looking crystals that did diffract well. But it is true that crystals do not need to be pretty to be useful. So by all means, please do test diffraction. Good luck. Mark -Original Message- From: Harman, Christine christine.har...@fda.hhs.gov To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Wed, Jun 6, 2012 3:53 pm Subject: [ccp4bb] Are these xtal conditions worth optimizing? Hi All, I have these very weird drops that I found from screening (please find pictures attached). I am not sure if they are worth optimizing. I am very interesting to know your opinions of what you think of thesedrops could be (are these what you call spherulites?). If you think these conditions are worth optimizing, I welcome any ideas on how to optimize. I have done some optimization and still get the same result which is many of these weird things growing throughoutthe drop and with no sharp edges, and sometimes a skin forms after 2weeks (with the sodium malonate conditions only). I have also opened the drop and poked around to see if it is phase separation and this things are definitely solid and slightly-very mushy. I haven't had a chance to check for diffraction, but will be very soon. Both of these drops contain the same protein preparation of a Fab/peptide complex @ ~5mg/mL in buffer containing 0.1M Sodium Acetate pH 5, 150mM NaCl. I appreciate any advice, thoughtsor comments that you could provide. Peace, Christine
Re: [ccp4bb] lithium incorporation in refmac
Hi You don't need a CIF file for elements or their ions, only for compounds. Li and Li+1 are already in the list of scattering factors ($CLIBD/atomsf.lib) as indeed are all the elements with their common ions. Are you sure you have the atom name in the right columns on the HETATM record (e.g. Li in 13-14 and LI1+ in 77-80)? Cheers -- Ian On 8 June 2012 19:35, Faisal Tarique faisaltari...@gmail.com wrote: Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. thanx in advance l -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] lithium incorporation in refmac
On Friday, June 08, 2012 11:35:25 am Faisal Tarique wrote: Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. If you see density, it might not be lithium :-) i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. LI is in the standard monomer dictionary. You don't have to do anything special. But given that it has no scattering power to speak of, you may have to add explicit restraints to hold it in place during refinement. LI appears in 41 PDB entries. You might want to inspect the density in some of them to get a feel for how it looks. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] off-topic: Verify3D
Eric, have you tried it with g77? - gfortran cannot handle certain IRIX extensions which are considered by the Gnu folks to be 'beyond the pale'! However according to the g77 man page: -fugly Specify that certain ugly constructs are to be quietly accepted. Same as: -fugly-args -fugly-assign -fugly-assumed -fugly-comma -fugly-complex -fugly-init -fugly-logint These constructs are considered inappropriate to use in new or well-maintained portable Fortran code, but widely used in old code. See section Distensions, for more information. Note: The `-fugly' option is likely to be removed in a future version. Implicitly enabling all the `-fugly-*' options is unlikely to be feasible, or sensible, in the future, so users should learn to specify only those `-fugly-*' options they really need for a particular source file. Cheers -- Ian On 8 June 2012 15:47, Eric Williams ericwilli...@pobox.com wrote: I recently acquired the source for Verify3D and have tried unsuccessfully to compile it. It seems to have been written with the SGI Irix F77 compiler in mind, and Ubuntu's gfortran doesn't seem to know what to do with it. Has anyone gotten it to compile on a Linux system, Ubuntu 11.04 in particular? Thanks. :) Eric Williams PhD candidate, Intelligent Systems Program University of Pittsburgh
Re: [ccp4bb] off-topic: Verify3D
I have received several very helpful responses off-list. I very grateful and extremely impressed with the prompt and friendly help I've received. Thank you. :) One of the responders supplied me with a newer version of the code, updated in 2003 to compile in Linux. Some further tweaks may be needed, but once everything compiles and runs properly, I'll let the list know (assuming anyone's interested). Thanks again. :) Eric On Fri, Jun 8, 2012 at 10:47 AM, Eric Williams ericwilli...@pobox.comwrote: I recently acquired the source for Verify3D and have tried unsuccessfully to compile it. It seems to have been written with the SGI Irix F77 compiler in mind, and Ubuntu's gfortran doesn't seem to know what to do with it. Has anyone gotten it to compile on a Linux system, Ubuntu 11.04 in particular? Thanks. :) Eric Williams PhD candidate, Intelligent Systems Program University of Pittsburgh
Re: [ccp4bb] lithium incorporation in refmac
thanx a lot... On Sat, Jun 9, 2012 at 12:23 AM, Ian Tickle ianj...@gmail.com wrote: Hi You don't need a CIF file for elements or their ions, only for compounds. Li and Li+1 are already in the list of scattering factors ($CLIBD/atomsf.lib) as indeed are all the elements with their common ions. Are you sure you have the atom name in the right columns on the HETATM record (e.g. Li in 13-14 and LI1+ in 77-80)? Cheers -- Ian On 8 June 2012 19:35, Faisal Tarique faisaltari...@gmail.com wrote: Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. thanx in advance l -- Regards Faisal School of Life Sciences JNU -- Regards Faisal School of Life Sciences JNU
