- phenixbb - phenix-online.org

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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.Trash_UID error message
by Michael Weyand 23 Mar '16

23 Mar '16

Dear experts, our Phenix installation suffers on a nasty error message concerning permission problems on /data/.Trash_UID (/data is our mount point of a NFS share) when deleting a certain job from the history. Of course, no user has write access to the top folder / mount point! And I know that is might be an OS problem with NFS mounted disks (well known for Ubuntu systems). But we have an openSuSE with KDE, not GNOME. I also checked the Phenix preferences for an option, but was not successful. Is there any way to get rid of this message or better to say not deleting to .Trash folder? Thanks in advance, Michael

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Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016
by Sanishvili, Ruslan 23 Mar '16

23 Mar '16

Dear Colleagues, This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago. All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. >From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed here: http://www.ccp4.ac.uk/schools/APS-school/publications.php Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Tuesday, February 23, 2016 7:48 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive 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, along with commercial/industrial researchers 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 or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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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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Re: [phenixbb] 7th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 08 Mar '16

08 Mar '16

Second announcement 7th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. May 16 - May 20, 2016 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/15 Application deadline: April 1, 2016 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 1, 2016. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Wrong stereochemical restraint of Hyp
by YANG HAI 07 Mar '16

07 Mar '16

Dear Phenix Developers, I was refining a structure containing L-hydroproline (HYP) and it looks like that the dictionary for HYP in Phenix has the wrong stereochemical restraint. I modeled as L-hydroxylproline (trans) but the phenix.refine always flipped the hydroxyl group and ended up as L-allo-hydroxylproline (cis). I created a .cif file and the issue is resolved, but it would be nice if the restraint can be fixed in the next version of Phenix. Thanks a lot Yang Hai Department of Chemistry, University of Pennsylvnia

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Constrained groups for occupancy refinment
by Jan Abendroth 07 Mar '16

07 Mar '16

Hi all, I have a case where a residue is in two alternative conformations for chain A and chain B. This residue (Arg 62) happens to be close to its NCS mate, such that only conformations A for both chains or only conformations B can take place at the same time. I tried to follow guidance from the CNG newsletter 2015/07 and set up the constrained groups as shown below. However, the refinement crashes with an AtomSelectionError. Any ideas what I could have done differently? Cheers, Jan refinement { refine { occupancies { constrained_group { selection = chain A and resseq 62 and altloc A or \ chain B and resseq 62 and altloc A or selection = chain A and resseq 62 and altloc B or \ chain B and resseq 62 and altloc B or } } } } -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

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Phenix omit maps
by wtempel 04 Mar '16

04 Mar '16

Hello all, is the output of phenix.maps with maps.omit.selection=(resname LIG) equivalent to removal of LIG atoms from coordinates and subsequent map calculation with an empty maps.omit.selection? What, if any, measures of bias removal are applied in the process of map calculation, absent any explicit efforts by the user to modify coordinates? Thank you, Wolfram Tempel

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