- phenixbb - phenix-online.org

The Hitchhiker’s Guide to the Biomolecular Galaxy symposium - May 11-12th 2016
by Noinaj, Nicholas 02 Apr '16

02 Apr '16

Dear PHENIXbb, I would like to bring to your attention our upcoming symposium (May 11-12) hosted here at Purdue University for students and postdocs. There will also be a Career Session on May 10th for students and postdocs only. More information is listed below and can also be accessed on our website: Symposium Website: https://purduegalaxy.science.purdue.edu/ Symposium Flyer: https://purduegalaxy.science.purdue.edu/images/2016/hg2bg_logo_Flyer_new.jpg Registration (including breakfast and lunch for both days and a T-shirt!) and abstract submission are completely FREE! And now, we are offering at least 10 travel grants (up to $150 each) for students and postdocs who are within driving distance of Purdue. Please forward this to anyone you think might be interested. Thanks in advance! Cheers, Nick Nicholas Noinaj 240 S. Martin Jischke Dr. Hockmeyer Building of Structural Biology, Rm 333 Dept. of Biological Sciences, Purdue Univ. West Lafayette, IN 47907 765-496-0061 (office) 765-496-0059 (wetlab) nnoinaj(a)purdue.edu ++++++++ Greetings all from Purdue! We would like to cordially invite you, your colleagues, students, postdocs and staff to our upcoming symposium hosted here at Purdue University, West Lafayette campus. The name of the symposium is: The Hitchhiker’s Guide to the Biomolecular Galaxy symposium May 11-12, 2016 ARMS 1010, Purdue University The symposium will highlight research from students and postdocs from neighboring institutions and from many departments here at Purdue including Biological Sciences, Medicinal Chemistry and Molecular Pharmacology, Chemistry, Biochemistry, and Physics and Astronomy. The keynote speaker will be Dr. Peter Kwong from NIAID/NIH who will talk about his work on ‘Multi-dimensional searching and the coordinates of effective HIV-1 and RSV vaccines’. In addition to the keynote address, the symposium will include six scientific sessions covering the following topics: Disease, Pathogenesis and Therapeutics; Biosynthesis and Catalysis; Biophysical Methods and Emerging Techniques; Macromolecular Assemblies and Complexes; and Disorder and Conformational Plasticity. There will also be opportunities for discussion and interactions during catered breaks, a poster session, and a reception. And back by popular demand, a Career Session will also be hosted on the evening of May 10th at the Lafayette Brewing Company for students and postdocs and will include a panel representing industry, academia, and government. Registration and abstract submission are both FREE. Undergraduates, graduates, and postdocs are encouraged to submit abstracts for poster or oral presentations. Prizes for best posters (undergrad ($100), grad ($150), and postdoc($150)) and oral presentations (grad ($200) and postdoc ($200)) will also be awarded at the close of the symposium. REGISTER NOW for the HG2BG symposium!!! The deadline is quickly approaching!!! Click link below to Register (Abstract submission NOT required!): https://purdue.qualtrics.com/jfe/form/SV_eeZ2HT409liD27z Just LOOK at ALL the FREE stuff you get with registration: Just a 1-click, 1-minute process FREE registration fees! FREE abstracts submission! FREE attendance to the Career Session which includes food and drinks at Lafayette Brewing Company! FREE HG2BG symposium T-shirt! FREE chance to win either a poster/oral presentation prize ($100-$200 each)! FREE food and drinks at the poster presentations/reception! FREE breakfast for both days of the symposium! FREE lunch for both days of the symposium! FREE travel grants for up to $150 each for registrants from neighboring institutions (10 available)! FREE attendance to all poster and oral presentations, including talk by Peter Kwong! We look forward to your participation and another successful symposium! On behalf of the organizing committee: Satarupa Bhaduri (Biological Sciences) Chen Chen (Medicinal Chemistry and Molecular Pharmacology) Samantha Lee (Biochemistry) Ngango Yvon Rugema (Chemistry) Phillip Rushton (Biological Sciences/ PULSe) Valentyn Stadnytskyi (Physics and Astronomy) Dr. Nicholas Noinaj (Faculty advisor; Biological Sciences) A special thanks to our corporate sponsors: Millipore(Jim Henderson) Carl Zeiss Microscopy LLC (Sam Byerly) Molecular Dimensions (Issa Isaac) Qiagen (Andrew Fritts) Rigaku (Angela Criswell) TTP Labtech (Melanie Adams) Anatrace (Ed Pryor) Hinds Instruments (Connie Wimmer) Beckman Coulter (Jona Kristo) Mitegen (Ben Apker) Fisher Scientific (Keven Peterson) Sigma Aldrich (Rick Belcher)

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phenix.AmberPrep
by Liu, Jing-Yuan 01 Apr '16

01 Apr '16

Dear PHENIX Developers, I would like to perform phenix.refine using amber gradient. I installed AmberTools 15 and the newest version of Phenix by following the instruction found here http://www.phenix-online.org/documentation/reference/amber.html.<http://www.phenix-online.org/documentation/reference/amber.html> However, when I ran"phenix.AmberPrep", it complains "phenix.AmberPrep not found". In dead, I cannot find any binary named "phenix.AmberPrep". However, it looks to me that phenix is installed OK and so does AmberTools 15. I checked each step of my installation, I could not find anywhere is wrong. Can you please help me out? Thank you! Sincerely, Jing-Yuan

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Tautomer/protomer plugin for Phenix
by Lance Westerhoff 01 Apr '16

01 Apr '16

Hello All- A paper from our group just came out in ActaD which I think fellow phenix users should find interesting. The paper details a new module we have available which uses our QM/MM-based Phenix plugin to correctly refine and determine tautomer/protomer, rotamer, flip state, and binding mode using X-ray data and refinement. The paper is available for free, Open Access on ActaD’s website: http://scripts.iucr.org/cgi-bin/paper?S2059798316002837 If you would like to give it a try, please let me know. The software is available for free for pure non-profit academic research and for a reasonable fee for commercial/industrial efforts. For more information, please visit our product site: http://www.quantumbioinc.com/products/phenix_divcon Or fill out one of our on-line license agreements to gain access: http://www.quantumbioinc.com/products/software_licensing Thank you for your time and have a good weekend! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

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Berkeley Server Downtime (3/30/2016)
by Billy Poon 30 Mar '16

30 Mar '16

Dear all, On Wednesday, March 30, our servers will be shutdown starting at 7:00 am Pacific for scheduled maintenance in our server room. 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 5 pm 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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autosol error
by Schnicker, Nicholas J 30 Mar '16

30 Mar '16

Hi, I have tried using Autosol through the Phenix GUI and it starts to run and then crashes with the following error. I could use some help figuring out what I need to do to fix this? Your help is appreciated! Thanks Nick AssertionError : Traceback (most recent call last): File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/wizards/AutoSol.py", line 3492, in AutoSol_scale_and_analyze_mad verbose="") File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/run_solve.py", line 499, in __init__ raise AssertionError,error AssertionError: None of the solve versions worked Traceback: File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/cctbx_project/libtbx/thread_utils.py", line 236, in run return_value = self._target(self._args, self._kwargs, self._c) File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/cctbx_project/libtbx/runtime_utils.py", line 95, in __call__ result = self.target() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__ result = self.run() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/wizards/runtime.py", line 36, in run run_wizard = wizard_cmdline(args=list(self.args)) File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/wizard_command_line.py", line 564, in __init__ self.RunWizard() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "/software/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line

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Selenocysteine
by Shilpa Janarthanan 30 Mar '16

30 Mar '16

Hello, How to add an unnatural amino acid (say OCS) at a position in the sequence and view it in PyMol, provided the protein structure (PDB file) is given? Is it correct to make changes in the PDB file itself, if Yes, then how should I do it? Thank you. -- Shilpa J Bioinformatics Dept., SASTRA University.

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symmetry rejected as inconsistent by model_vs_data
by wtempel 29 Mar '16

29 Mar '16

Hello, phenix.model_vs_data_1.10.1-2155, along with printing to stderr: Sorry: Crystal symmetry mismatch between different files. prints these, and only these, lines to stdout: x251682_scaled3.mtz (36.692, 53.798, 108.063, 90, 84.258, 90) P 1 21 1 readySet.pdb (36.69, 53.8, 108.06, 90, 84.26, 90) P 1 21 1 Is this related to this code <http://cci.lbl.gov/cctbx_docs/cctbx/cctbx.crystal.html#cctbx.crystal.symmet…> ? Can I force phenix.model_vs_data to omit this isomorphism check and “run” with the reflection dimensions? Thank you. Wolfram

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BSR2016: 12th International Conference on Biology and Synchrotron Radiation
by Thomas Eriksson 29 Mar '16

29 Mar '16

The 12th International Conference on Biology and Synchrotron Radiation will be hosted by the SLAC National Accelerator Laboratory - August 21-24, 2016. The objective of the conference is to bring together the community of biologists and scientists involved in the methodological developments on synchrotron and X-ray laser sources to discuss the novel possibilities of these sources and to promote their applications to challenging biological problems. The scientific program for the 2016 BSR covers applications of diffraction, spectroscopy and imaging methods applied to the structural and time-resolved studies of biological macromolecules, complexes and cellular and sub-cellular structures. There will be a $500 early registration fee ($350 for students). To take advantage of the early fees, registration must be complete by June 30th. Full information about the meeting, scientific program, registration and abstract submission forms can be found at the conference web site: https://conf-slac.stanford.edu/bsr-2016/content/biology-and-synchrotron-rad… Ana -- ------------------------------------------- Ana Gonzalez <ana(a)slac.stanford.edu> Staff Scientist Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, MS 99 Menlo Park CA 94025 Phone: (650) 926 8682 Fax: (650) 926 3292 -------------------------------------------

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how to generate a set of alternative conformations ?
by cedric bauvois 29 Mar '16

29 Mar '16

Dear all, Is there a way with phenix, in a badly defined electron density area, to generate a set of different alternative conformations for a small protein fragment ? Thanks a lot in advance Cedric Bauvois

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iNEXT / X-rays (and more) notes
by Anastassis Perrakis 24 Mar '16

24 Mar '16

Dear all, I want to bring to everybody’s attention a few things about iNEXT Synchrotron Access proposals, as they seem to surface up often. - “BAG” proposals are possible, but only when under a common translational scientific theme; not simply based on lab proximity. - iNEXT funds complete projects, both beam time and travel; arguing that "we have beamtime, just give us travel money” will likely get your proposal rejected. - Please be clear to state that you have crystals and/or justify what the SAXS experiments are answering. Please keep in mind a specific difference from past schemes: you do not need to submit a separate proposal to the synchrotron site to get beam time! A successful iNEXT application will be received by the site(s) you apply for, and only safety data will be requested and a technical review will be done based on the existing application. We are looking forward receiving your applications for high-end synchrotron data collection, but also for : 1. Structural Audit (including crystallisation trials and SAXS: please advertise to your biochemistry colleagues!) 2. Macromolecular Interactions (Biophysics for quantitative characterising) 3. Cryo-EM sample optimisation (if you have negative stain images) 4. High-end NMR data collection 5. High-resolution EM (if you have good cryo conditions, and also for tomography and CLEM) … and more modalities to come soon! http://www.inext-eu.org/access/ <http://www.inext-eu.org/access/> On behalf of the iNEXT team, Tassos

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