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Deadline for registrations for the GRC on Diffraction Methods in Structural Biology is this Sunday.
by Edward Snell 16 Jun '16

16 Jun '16

Last chance to register for the Gordon Research Conference on Diffraction Methods in Structural Biology to be held at Bates College in Lewiston, Maine, July 17th-22nd 2016. The conference is themed around "Probing the structure and dynamics of macromolecules" and details of the program are at https://www.grc.org/programs.aspx?id=11655. The closing date for applications is this Sunday June 19th. Please join us in Maine this summer for the 40th anniversary of this meeting. Eddie Snell and Arwen Pearson Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

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Project Scientist positions for computational methods
by Nicholas Sauter 14 Jun '16

14 Jun '16

Two Project Scientist positions are available in my group in the *Molecular Biophysics and Integrated Bioimaging* <http://biosciences.lbl.gov/divisions/mbib/> (MBIB) Division at Lawrence Berkeley National Lab. *Bioimaging Project Scientist* Position Summary: We have an exciting opportunity for a Bioimaging Project Scientist who will apply neuromorphic computing techniques to structural biology problems in X-ray diffraction, CryoEM, and CryoET. This will be a cross-disciplinary effort between MBIB and the Computational Research (CRD) Division at Lawrence Berkeley National Laboratory. The research group will include investigators Nick Sauter (X-ray Crystallography), Karen Davies (CryoEM/ET), and Chao Yang (Scalable Solvers). Specific Responsibilities: - Investigate how to apply deep learning algorithms to specific data processing and data interpretation problems in structural biology. - Implement convolutional neural network (CNN) code on neuromorphic computing hardware such as the IBM TrueNorth chip. Example problems include the identification of positive diffraction events in X-ray free-electron laser diffraction, conformational classification in CryoEM single particle reconstruction, and the identification of 3D sections for CryoET subtomogram averaging. - Use tools such as MatConvNet, CAFFE, THEANO or TensorFlow to construct and train CNNs that can be used to optimally classify experimental data. Required Qualifications: - Research experience in Structural Biology, with expertise in allied fields such as Bioinformatics, Mathematics, Computer Science, or Engineering (Ph.D. + 3 years or equivalent) - Strong background in image analysis and machine learning, including neural networks. - Working knowledge of image classification and/or other image processing techniques. - Proficient programming skills in MATLAB and/or Python. - Working knowledge of performance optimization for scientific codes. *Algorithm Developer Project Scientist* Position Summary: We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov/> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Specific Responsibilities: - Continue work on the DIALS data integration suite. - Test new algorithms for optimally characterizing and merging data from serial crystallography experiments. - Analyze anomalous scattering from metalloenzymes using XFEL diffraction. - Investigate whether diffuse scattering can reveal correlated atomic motions in crystals. Required Qualifications: - Expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. - Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. - We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to Nick Sauter, nksauter(a)lbl.gov*. *Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82554. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

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Post-doctoral position in Structural Biology
by Dhirendra K Simanshu 14 Jun '16

14 Jun '16

A post-doctoral position ( structural biology) is available in the RAS initiative at Frederick National Laboratory for Cancer Research (operated by Leidos Biomedical Research for NCI) . Please visit the link below for more details and instructions on how to apply: http://jobs.leidos.com/ShowJob/Id/861827/Post-Doctoral-Fellow-629153-(NCI)/ *JOB DESCRIPTION* The structural biology group in the RAS initiative focuses on structural analysis of KRAS mutants and biologically relevant KRAS activator/effector complexes in support of drug discovery efforts and to further understand the biochemistry of RAS proteins. We are looking for a highly motivated post-doctoral fellow to join our group. Highly motivated candidates who recently obtained a Ph.D. with a strong background in biochemistry, biophysics and structural biology are encouraged to apply. This post-doc will work closely with the protein production group and carry out structural studies on oncogenic KRAS complexed with effectors, GAPs, regulators and small molecules. We use X-ray crystallography, NMR, molecular modeling, and other biophysical techniques for structural characterization. The candidate will be expected to be able to participate in experimental design and to independently conduct experiments in a priority-driven environment. The candidate should have the ability to act both independently and as a part of the RAS team in pursuit of specific research goals and objectives. The structural biology group in the RAS initiative works very closely with the biochemistry and biophysics group, and is well equipped with crystallization robotics, in-house X-ray generator, and has regular access to the synchrotron beamline at Argonne. *Qualifications:* BASIC QUALIFICATIONS - Possession of a doctoral degree from an accredited college/university according to the Council for Higher Education Accreditation (CHEA) in a field related to structural biology, biochemistry, biophysics or computational biology - Foreign degrees must be evaluated for U.S. equivalency - Demonstrated proficiency in protein biochemical and biophysical characterization - Ability to act both independently and as a part of the RAS team in pursuit of specific research goals and objectives - Ability to conduct experiments and evaluate results independently - Experience in crystallization and structure determination of protein-ligand and protein-protein complexes PREFERRED QUALIFICATIONS - Experience working with small GTPases or RAS-related effector proteins and Knowledge of molecular dynamics simulations and protein-ligand docking.

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Diffraction Methods in Structural Biology GRC - Last chance to register
by Edward Snell 11 Jun '16

11 Jun '16

Dear Colleagues, The registration deadline for this year's Diffraction Methods in Structural Biology GRC (17-22nd July 2016) held in Maine, USA is rapidly approaching (19th June). This year will be the 40th Anniversary of this GRC and we have a cracking program (or programme) for you (http://www.grc.org/programs.aspx?id=11655) including talks on new beamlines and sources, as well as presentations of many new tools (experimental and computational) for getting more information out of your data. There is also the traditional Thursday morning session (for which talks are selected from posters at the meeting itself) that will feature the latest and most exciting developments in diffraction methods So if you have something really cool you'd like to present, there is still time to apply! If that wasn't enough to tempt you, the main meeting will be preceded by a 2 day Gordon Research Seminar (16-17th July, http://www.grc.org/programs.aspx?id=16486) arranged *by* students and postdocs *for* students and postdocs. We strongly encourage and invite students and postdocs to attend and then come to the full meeting immediately afterward. We look forward to seeing you in July. Best wishes Eddie Snell & Arwen Pearson Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

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Fall 2016 MicroED workshop at Janelia Research Campus
by Hattne, Johan 09 Jun '16

09 Jun '16

The second installment of the MicroED workshop will be held at Janelia Research Campus (Ashburn, VA) November 13-16, 2016, hosted by Tamir Gonen. MicroED is a cryo-EM method that uses electron diffraction to facilitate structure determination from sub-micron sized 3D crystals of biological material. MicroED uses equipment and procedures that are standard on many cryo-EM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To encourage the widespread use of MicroED we are offering this workshop to teach microscopists how to perform the technique and adopt it at their own institutions. The first MicroED workshop was held in February of 2016 and was heavily oversubscribed. For this reason we are offering a second workshop. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Space in the course is limited. The application deadline is August 1, 2016 (11:59 PM EDT). For more details and to apply, visit https://www.janelia.org/you-janelia/conferences/microed-workshop-1. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

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twinning detection
by Ursula Schulze-Gahmen 07 Jun '16

07 Jun '16

I have an extremely low resolution data set to 6.5 A. The data were collected on a Pilatus detector, indexed and further processed in XDS, space group P321. Pointless determines spacegroup to P3221 or P3121 and L-test shows no twinning. Phenix X-triage indicates twinning, but the twin fraction varies enormously depending on the method used: Britton analysis 0.337, H-test 0.260, ML 0.022. The UCLA twin server also thinks that data are twinned. How do I evaluate which information is right? Also, I think I found a molecular replacement solution that is correct using these twinned data. Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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GPU acceleration of phenix.real_space_refine?
by Oliver Clarke 03 Jun '16

03 Jun '16

Hi all, phenix.real_space_refine takes a very long time to run on large systems when using any of the more computationally expensive options (e.g. morphing). I was wondering if there has been any consideration towards optimizing this code (and maybe that of phenix.map_to_model) for GPU acceleration? There is somewhat of a shift occuring in the EM community towards using GPU workstations for data processing - if we could use already purchased capabilities to accelerate model refinement as well that would be a huge bonus. I saw a discussion on the bb from a while back concerning the same question applied to phenix.refine, and the conclusion was that in that case the benefits would be minimal, but I'm not sure whether the same applies to real space operations. Cheers, Oli. PS has there been any consideration of including an option to allow users to supply two half maps at run time, one "work" and one "test" map for cross validation purposes? It is possible to do this with two separate runs right now but having the option integrated would be wonderful.

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phenix.real_space_refine GUI
by Pavel Afonine 02 Jun '16

02 Jun '16

Hi Phenix users, since I had to answer this very same question off-list three times in past 48 hours, I thought I post this for future reference... Yes, thanks *Billy* there is a GUI for phenix.real_space_refine (tool to refine atomic models against maps, such as cryo-EM maps)! To give it a try, you need: 1) Get the latest nightly build, dev-2427 for instance: http://phenix-online.org/download/nightly_builds.cgi 2) Enable alpha-test programs in Phenix GUI. To do this: -- start Phenix GUI; -- go to Preferences and tick "Enable alpha-test programs and features" box; -- restart the GUI (close down, then start again); -- phenix.real_space_refine will be available in Refinement section on the right (Real-space refinement [alpha]). Note, it has a very handy feature to see/explore/edit secondary-structure restraints graphically. Also note that *this is alpha-test version meaning that glitches are not unexpected*! However your feedback will help to improve it, so please let us know should you encounter problems, have suggestions or found bug(s)! All the best, Pavel

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r-free flag cell constant mismatch
by wtempel 02 Jun '16

02 Jun '16

Dear Phenix experts, our project involves crystals *A* and *B*, which are nearly isomorphous and of a protein’s complexes with two different small molecules, respectively. *A* diffracts better than *B*. The r-free flag from *A* was “attached” to *B*‘s input reflections with the CCP4 cad command and is still associated to *B*‘s slightly different cell dimensions. Would/should this be reason enough for refine to throw an error? The error message suggests changing the refinement.input.symmetry_safety_check setting. Can this setting be changed in the GUI? Thank you. Wolfram Tempel

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Berkeley Server Downtime (6/3/2016)
by Billy Poon 02 Jun '16

02 Jun '16

Dear all, On Friday, June 3, our servers will be shutdown starting at 6:30 am Pacific for scheduled maintenance in our building (7 - 8 am). This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) We expect that the servers will be available by 8:30 am Pacific at the latest. Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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