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The 2016 Diffraction Methods in Structural Biology Gordon Research Conference
by Edward Snell 22 Mar '16

22 Mar '16

Dear All, This is not Phenix related but we do see a lot of representation from Phenix developers and users at this conference. The 2016 Diffraction Methods in Structural Biology Gordon Research Conference (GRC) will be held at Bates College in Maine from July 17,to July 22nd 2016 - immediately before the American Crystallography Association Annual Meeting. The theme of this year's conference is "Probing the Structure and Dynamics of Macromolecules" and the conference celebrates its 40 year anniversary. Current details are available at https://www.grc.org/programs.aspx?id=11655. Program details are below, it promises to be an exciting. Arwen Pearson (co-chair) and I would like to invite you to consider attending the conference. Topics to be covered include new instruments and opportunities on the horizon, methods to improve maps and models, complementary approaches, resolving dynamics, the interplay between XFEL and synchrotron, new diffraction developments, and structure beyond Bragg diffraction. Many of the worlds experts in these areas will be at the meeting and we encourage the participation of every level of expertise to cross-pollinate the field. We will also have an opportunity for selected poster presenters to present talks at the meeting. Applications for the conference are now being accepted and will continue to be accepted until we are full. >From a personal perspective this is probably one of the best meetings for those interested in the nuts and bolts of diffraction methods. It is also a unique opportunity to meet many of the key members of the field. It is a friendly and productive conference, and an exciting one in terms of getting a preview of the future. We encourage you to attend, take part in great science, and also interact in a less formal social and sometimes sporting atmosphere. This will also be the second year that a related Gordon Research Seminar (GRS) is run. This is a meeting organized for and by post-docs and graduate students. Drs. Rike Mueller-Werkmeister and Bradely Hintze are organizing this with details at https://www.grc.org/programs.aspx?id=16486. We strongly encourage laboratories with an interest in Diffraction Methods in Structural Biology to support their students in attending both the GRS and the GRC with the GRS serving as a useful introduction to the larger conference. We are still raising funds for the GRS and GRC, in particular to enable younger scientists to attend. We are grateful and thank those who have supported us so far, and also those that are in the process of doing so. We are actively looking for further sponsorship. Summer is a full time for meetings but this is going to be a very worthwhile one. Please pass this onto interested colleagues. Thanks, Eddie and Arwen Sunday 17th of July Keynote Session: Structure and Dynamics Discussion Leader: Elspeth Garman (University of Oxford, United Kingdom) * Carrie Wilmot (University of Minnesota, USA) MauG Catalysis: A Tale of Ferryl Heme, Radicals and Long-Distance Hopping * Joseph Ferrara (Rigaku Americas Corporation, USA) A special talk to look back over 40 years of this GRC and describe the developments in the field since the first Diffraction Methods Meeting. Monday 18th July New Instruments and Opportunities Discussion Leader: Sean McSweeny (NSLS-II, USA) * Armin Wagner (Diamond Light Source, United Kingdom) In-Vacuum Long-Wavelength Crystallography - First Results * Matthew Bowler (Synchrotron Crystallography Group, France) Fully Automatic Characterization and Data Collection: A New Tool for Structural Biologist * Marjolein Thunnissen (MAX IV Laboratory, Sweden) Possibilities for Structural and Dynamical Studies on Proteins at MAX IV * Esko Oskanen (European Spallation Source, Sweden) Structural Biology with Neutrons - Opportunities at the European Spallation Source * William Graves (Arizona State University) Electron Diffraction as a Method to Produce a Tabletop XFEL Improving Maps and Models Discussion Leader: Airlie McCoy (University of Cambridge, United Kingdom) * Elspeth Garman (University of Oxford, United Kingdom) Unambiguous Metal Identification and Accurate Stoichiometric Measurements in Proteins * Frank Von Delft (Structural Genomics Consortium, United Kingdom) PANDDA: A Multi-Dataset Method for Electron Density Signal Extraction of Superposed States such as Low-Occupancy Ligands * James Fraser (University of California, San Francisco, USA) Birth of the Cool: Multitemperature X-Ray Crystallography to Reveal Protein Conformational Heterogeneity * Paul Adams (Lawrence Berkeley Laboratory, USA) New Tools for Interpretation of Cryo-EM Maps Tuesday 19th of July Structural Biology Requires Multiple Methods Discussion Leader: Nozomi Ando (Princeton University, USA) * Allison Edwards (Bragg Institute, Australia) Neutron Diffraction from Protein Crystals * Neil Ranson (University of Leeds, United Kingdom) Experiences and Results Using the New Direct Electron Detectors for CryoEM * Saikrishnan Kayarat (Indian Institute of Science Education and Research, India) Mechanism of a Motor-Driven Endonuclease: Combining Structural and Single-Molecule Approaches * Nikolai Skrynnikov (Purdue University) Motions of Protein Molecules Within the Crystalline Lattice * Sarah Bowman (MIT) What Can Spectroscopic Techniques Tell You About Your Crystal Dynamically Resolved Methods Discussion Leader: Carrie Wilmot (University of Minnesota, USA) * Thomas Barends (Max-Planck Institute for Medical Research, Germany) Ultrafast Functional Motions in Myoglobin Probed by Serial Femtosecond Crystallography * Henrike Muller-Werkmeister (University of Toronto, Canada) Time-Resolved S(F)X Studies with a Fixed Target * Gergely Katona (University of Gothenburg, Sweden) An Interleaved Data Recording Method for Studying the Non-Thermal Effect of Terahertz Radiation on Protein Crystals * Petra Fromme (Arizona State University, USA) Time-Resolved Femtosecond Crystallography: Towards Molecular Movies of Biomolecules 'In Action' Wednesday 20th July Hybridization of Synchrotron and XFEL Approaches Discussion Leader: Aina Cohen (SSRL, USA) * Elizabeth Baxter (SLAC National Accelerator Laboratory, USA) Alternative Methods for High Throughput Data Collection * Manfred Burghammer (ESRF, France) Recent Developments in Serial Micro-/Nano-Beam Diffraction X-Ray Techniques at ID13, ESRF * Helen Ginn (University of Oxford, United Kingdom) Development of Methods in XFEL Analysis * Thomas White (CFEL, Germany) Advances in Data Processing for Serial Femtosecond Crystallography * Allen Orville (Diamond Light Source, UK) Dynamic Structural Biology: Awakened and Enabled by New Sources and Complementary Methods Developments in Diffraction Methods Discussion Leader: Nadia Zatsepin (Arizona State University) * Isabel Uson (ICREA and the Spanish Research Council, Spain) Arcimboldo on Tour * Kartik Ayyer (CFEL, Germany) Coherent Diffractive Imaging as a Structure Determination Tool for Disordered Crystals * Andrea Thorne (MRC Laboratory of Molecular Biology, United Kingdom) Developments in Diffraction Data Analysis Thursday 21st July Selected Poster Presentations: New Cool Methods and Hot New Structures Discussion Leader: James Fraser (University of California, San Francisco, USA) Nine posters selected from the meeting for presentation. Structural and Dynamical Information Beyond Bragg Discussion Leader: James Holton (Advanced Light Source, USA) * Michael Wall (Los Alamos National Laboratory, USA) Probing Protein Structural Dynamics Using Diffuse X-Ray Scattering * Robert Rambo (Diamond Light Source Ltd, United Kingdom) A Real-Space Modelling Algorithm for SAXS Using Information Theory and Computational Geometry * Nozomi Ando (Princeton University, USA) Untangling Protein Allostery 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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Denver ACA meeting abstract and travel award deadline March 31!
by Terwilliger, Thomas Charles 22 Mar '16

22 Mar '16

Hi Phenix users! It's time to sign up for the Denver ACA meeting! The meeting will be held Friday, July 22nd - Tuesday, July 26th, 2016 in Denver, Colorado. The abstract and travel award deadline is March 31. You can go to: http://www.amercrystalassn.org/ to register and apply for Young Scientist Travel awards! The transactions symposium will highlight Structural Dynamics across the disciplines represented by the ACA. The rest of the meeting will reflect the wide reach of crystallographic research with sessions on sources, methods, and results. These include opportunities from new and improved instrumentation, single/multiple crystal, powder and solution methods, and hot structural results. There will be sessions highlighting those results requiring complementary techniques including cryo-electromicroscopy. Invited speakers include this year's awardees: Jason Benedict (Etter Award), Axel Brunger (Trueblood Award), Elspeth Garman (Fankuchen Award) and Benno Schoenborn (Bau Award). The meeting will include a strong educational component forearly career scientists with specific talks designed to introduce research areas in addition to presenting results. Related evening sessions include amixer, career fair, career development, and diversity in the laboratory.The conference will end with a closing banquet and the award of poster prizes for the best presentations. DEADLINES: Abstract - March 31 Young Scientist Travel Grant - March 31 Early Registration - May 31 Hotel Reservations - June 28 All the best, Tom T Tom Terwilliger 2016 ACA President

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Error when using phenix.pdbtoos to show model statistics
by luzuok 18 Mar '16

18 Mar '16

Dear developers, Following http://www.phenix-online.org/download/documentation/cci_apps/pdbtools.html When typing phenix.pdbtools Mymodel.pdb --show-adp-statistics I got the following error: pdbtools.py: error: no such option: --show-adp-statistics Does this option belong to old version of pdbtools? My Phenix version is 1.10. Best wishes! Lu -- 卢作焜南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

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Set up phenix and rosetta for phenix.rosetta_refine
by Yonglin Hu 17 Mar '16

17 Mar '16

Hello List, I would like to perform phenix.rosetta_refine on a structure. I understand that to use this program, I need to set up phenix and rosetta installations separated from those used in MR_Rosetta. I installed the most recent phenix and rosetta and followed the online documents, but when I tried to run "rosetta.build_phenix_interface", the program failed immediately with the following error messages: False scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git Done. (0.0 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/usr/local/rosetta-refine/rosetta/main/source/SConstruct", line 172: main() File "/usr/local/rosetta-refine/rosetta/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/usr/local/rosetta-refine/rosetta/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/usr/local/rosetta-refine/phenix-dev-2328/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd) These messages are not very informative and I don't know what to do next. Any help will be greatly appreciated. Yonglin Hu

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on b-factor refine
by Smith Liu 15 Mar '16

15 Mar '16

Dear All, I just read a paper on phenix refine, which contains content "B-factor refinement (two groups per residue) ". Here the "two groups per residue" should be accomplished by the phenix command line rather than the GUI, right? And if right, will you please let me know the command for "two groups per residue" for B-factor refine? Smith

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Real space difference maps?
by Oliver Clarke 15 Mar '16

15 Mar '16

Hello, is there any possibility of (or current plan for) including the capacity in a future PHENIX release to calculate a residual map automatically after phenix.real_space refine, (i.e. simulating a map from the model incorporating corrections for B-factor variation and calculating a difference map with the experimental map)? This would be very convenient when building into EM maps. Cheers, Oli

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Postdoc position available at LBNL
by Peter Zwart 14 Mar '16

14 Mar '16

Berkeley Lab's Molecular Biophysics and Integrated Bioimaging Division is looking for a Computational Biologist to work on the development of computational and experimental methodologies for Fluctuation X-ray Scattering (FXS; *http://bit.ly/1W6SONZ* <http://bit.ly/1W6SONZ>) and associated biophysical techniques, such as SAXS/WAXS and Single Particle diffraction. The candidate will be involved in the development and expansion of the underlying theory of FXS, either as a standalone technique or in a hybrid capacity, and will aid in its practical deployment. For details, have a look here: https://lbl.taleo.net/careersection/jobdetail.ftl?job=82189&lang=en#.Vubva0… Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Staff Scientist Berkeley Center for Structural Biology, Science lead Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -----------------------------------------------------------------

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phenix autosol
by Vandna Kukshal 13 Mar '16

13 Mar '16

Hi , I am solving a structure using selenium SAD using autosol. Autosol gave me nice solution but many loop and side chain density is missing. autosol gave me many different output MTZ files . for building further in coot which MTZ file i should use and for refinement in phenix refinement which MTZ file i should use . I tried doing refinement with .sca file it gave me increase Rfree afte single cycle of refinement . thanks for your suggestions. -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110

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Feature request: multi-stage refinement protocols from the GUI?
by Tristan Croll 11 Mar '16

11 Mar '16

Hi all, I'm personally a big fan of the Phenix GUI, in particular for its automated record keeping for different runs. One thing I really wish it had, though, is the option to define more complex refinement scenarios as a single run. An example of what I'm talking about is the following protocol that has been working very well for me on a 3.6 Å strucutre: - ~6 rounds of refinement of TLS, a single group B-factor and occupancies (the latter for a very small set of residues, mostly low-occupancy lead ions) with positions fixed - ~8 rounds of TLS and individual B-factor refinement, still with positions fixed and with no further occupancy refinement - ~8 rounds of TLS, B-factor and position refinement with torsion-angle restraints to the starting model - ~8 rounds of position refinement with no restraints other than standard stereochemistry and metal bonds. I know that all of this could be scripted quite easily from the command line, but it would be fantastic to be able to queue up such a protocol as a single continuous job in the GUI. Best regards, Tristan

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Re: [phenixbb] Fluorescence group of eYFP
by miyatake 08 Mar '16

08 Mar '16

Hello, now I found a solution like below; 1) make links using " Extensions > Modeling > Make Link " in Coot 2) Do Ready_Set using the PDB file, and you'll get cif and link.edits files 3) Delete all the lines which contain OXT in the cif file. 4) Involve the cif and link.edits files to the Phenix.refine job It will work well for the CR2 containing GFP proteins. Best, Miyatake On Tue, 08 Mar 2016 15:00:29 -0800 André Hoelz <hoelz(a)caltech.edu> wrote: > Have you found a solution that works now? I have noticed the same problem that the OXT atom is incorporated and no bond is formed. I would be grateful if you share your a solution. > > Sent from my BlackBerry 10 smartphone. > Original Message > From: miyatake > Sent: Monday, March 7, 2016 11:07 PM > To: Pavel Afonine > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Fluorescence group of eYFP > > Dear Pavel, > > Thank you for your e-mail. > > The bonds I want to connect are between CR2 and amino acids like below; > > C PHE A 64 N1 CR2 A 66 > C3 CR2 A 66 N LEU A 68 > > so I made links by the "make link" of Coot. > > Then I made .cif file by the Ready_Set, but I noticed > it always contained OTX terminator atom of CR2, so the CR2 connections > to the next amino acids were something wrong after refinement if I used the cif > as it was. > > Thus I deleted OTX in the cif file, and then in turn it went well. > > I wonder why the cif file contained OTX, is it something a bug? > > Thank you for your attention. > > Miyatake > > > > On Mon, 7 Mar 2016 08:40:21 -0800 > Pavel Afonine <pafonine(a)lbl.gov> wrote: > > > Hi Miyatake, > > > > could you please send me (and copy to Nigel) the PDB file (and any > > ligand CIF files you use) and tell what bonds you are expecting to have > > and that brake as result of refinement. > > > > Thanks, > > Pavel > > > > On 3/7/16 03:40, miyatake wrote: > > > Dear all, > > > > > > I'm trying to a mutant of eYFP, which has fluorescence group, > > > CR2. > > > > > > During the refinement, however, the bonds between the CR2 and other amino acids > > > were cleaved even I added the cif file created by the ReadySet. > > > > > > > > > Would some one give me suggestions to solve the problem? > > > > > > Miyatake > > > > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://phenix-online.org/mailman/listinfo/phenixbb > > > Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

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