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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 12 Mar '16

12 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 09 Mar '16

09 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 05 Mar '16

05 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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iNEXT
by Anastassis Perrakis 03 Mar '16

03 Mar '16

Dear all, iNEXT is a Horizon2020 project aiming to allow international users transnational access to infrastructures for Structural Biology, with an emphasis on new users, and a focus on translational research projects in biomedicine, biotechnology and biomaterials. http://www.inext-eu.org For the first time, iNEXT offers coordinated access to NMR, EM, X-ray crystallography and biophysical methods. There are specific access routes for expert users and new users, and for the different techniques. These are becoming gradually available as the project proceeds, and you should expect regular updates. For now you can apply for access to some of the planned modalities, namely: Structural Audit: mail-in your protein sample for quality analysis including stability, dispersity, crystallisation and SAXS Cryo-EM sample optimisation: to move from negative stain to cryo-EM Macromolecular interactions: for accessing biophysical equipment and expertise to quantify macromolecular interactions Synchrotron data: for access to some of the best beamlines in Europe High-field NMR: or access to some of the most powerful NMR machines in Europe High-resolution EM: : for access to some of the best microscopes in Europe For more details please see: http://www.inext-eu.org/access/ with best regards from the iNEXT team, Tassos Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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Remove distant restraint between two atoms
by Blankenfeldt, Wulf 03 Mar '16

03 Mar '16

Dear all, I would like to unrestrain the distance between two atoms in a ligand – how can I do this? I found instructions for writing a remove_restraints_selections.params file in the phenix.refine manual, but it does not seem to address bond distances. Thank you in advance, Wulf ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Rwork Rfree gap by bust and phenix
by Zheng Zhou 03 Mar '16

03 Mar '16

Dear phenix experts, I have sent the question to the buster discussion board one week ago. I think I'd better consult this problem on the active phenix discussion board. I recently solved a P1 crystal structure, 6 fold NCS at 1.6 angstrom resolution. I used lattice symmetry to generate test set in phenix. The phenix.refine gave me Rwork/Rfree = 0.1828/0.2081. There are pieces of positive and negative density for the compounds. So I tried buster refinement with autoncs, TLS. The density for the compounds are much improved, no obvious positive density. However, It generated Rwork/Rfree = 0.1801/0.1912. I also find similar R factor examples at the similar resolution in the buster wiki: https://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample4chawa… Would the small gap between Rwrok and Rfree be an issue? I have not deposited buster refined PDB yet, would this acceptable? Any reference to help if any reviewer questions about the small gap? Thanks for your advice in advance. Best, Zheng

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Re: [phenixbb] phenix.elbow with GAMESS
by Dyda 02 Mar '16

02 Mar '16

Dear Nigel, I agree, but pdb is what I have. I should think that the quality of the input should not impact whether .cif is output or not. The end of .gam: COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ CR 24.0 0.1912339815 -0.0759848760 -0.0714344444 O 8.0 2.3234578345 -0.2357845497 -0.1508067587 O 8.0 -0.7105232282 0.0098034893 1.8036685126 O 8.0 1.2076867850 -0.3346443692 -1.7335283981 O 8.0 -0.5260639033 1.7906968578 0.3539796904 O 8.0 0.9068338690 -1.9599479901 -0.6296444533 O 8.0 -1.9397708185 -0.1141525894 0.1891144601 C 6.0 2.8515146213 -0.0055174102 1.1989521238 C 6.0 1.9707450903 -0.6979131843 2.5449414024 C 6.0 0.4359449408 -0.0451724719 2.8465226464 C 6.0 3.0118766316 1.4363395032 1.6481146467 C 6.0 -0.0653144611 0.1564048347 4.4949200023 C 6.0 0.6249516515 0.4233319450 -2.8992641137 C 6.0 0.1643384668 2.4470081023 -2.2535061934 C 6.0 -0.9128640701 2.5088690737 -0.8469830060 C 6.0 1.5743374229 0.5462852223 -3.8500329514 C 6.0 -1.2118325877 3.9283584299 -0.4940679455 C 6.0 -0.1968029455 -3.0386081819 -0.8007813286 C 6.0 -1.6882650231 -2.4665688184 -1.2935287464 C 6.0 -2.6276161825 -1.2806785380 -0.2996777905 C 6.0 -0.3391479898 -3.6453123923 0.6022767778 C 6.0 -4.1453203443 -1.5862494692 0.1854244826 H 1.0 3.8553615186 -0.4420315035 1.2332199192 H 1.0 2.2818981212 -1.6647647766 3.1911897462 H 1.0 1.9667722755 1.9810594320 1.6970399031 H 1.0 3.6823942975 1.6618943249 2.5365171626 H 1.0 3.6238703905 1.9113333115 0.7438740891 H 1.0 0.8971167594 0.4695270592 5.1329947121 H 1.0 -0.6645891831 1.2206664940 4.5846682936 H 1.0 -0.6246971002 -0.6219821332 4.8583146656 H 1.0 -0.2487681929 -0.1134304045 -3.2439960069 H 1.0 1.1860397915 3.0186834522 -2.1641816248 H 1.0 -0.3750591440 2.8925729326 -3.2804399647 H 1.0 -1.9371292026 2.0739333624 -1.0806155814 H 1.0 1.9496290579 -0.6216286700 -4.2730835081 H 1.0 2.4497745286 1.0199721671 -3.6228827183 H 1.0 1.0277269687 0.9853088788 -4.8324755816 H 1.0 -1.6488875565 4.5338413808 -1.4704889855 H 1.0 -1.7951603842 3.9656768136 0.3514485986 H 1.0 -0.2983062508 4.5239905524 -0.4318350930 H 1.0 0.1219656972 -3.8775516930 -1.5693737575 H 1.0 -2.2141859609 -2.6816187114 -2.2405875656 H 1.0 0.7133579392 -3.9124935444 1.0380228614 H 1.0 -0.7783653014 -2.9666445248 1.3120392457 H 1.0 -0.9150821609 -4.6238970562 0.5814496583 H 1.0 -4.2320258907 -2.8021018481 0.2370382406 H 1.0 -4.7833967302 -1.1881592471 -0.7055025179 H 1.0 -4.4126745266 -1.1246420328 1.0220077683 ******************** 1 ELECTRON INTEGRALS ******************** ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.1 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 100.00% ------------- GUESS OPTIONS ------------- GUESS =HUCKEL NORB = 0 NORDER= 0 MIX = F PRTMO = F PUNMO = F TOLZ = 1.0E-08 TOLE = 1.0E-05 SYMDEN= F PURIFY= F INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE. HUCKEL GUESS REQUIRES 649929 WORDS. SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S). 94 ORBITALS ARE OCCUPIED ( 30 CORE ORBITALS). 31=A 32=A 33=A 34=A 35=A 36=A 37=A 38=A 39=A 40=A 41=A 42=A 43=A 44=A 45=A 46=A 47=A 48=A 49=A 50=A 51=A 52=A 53=A 54=A 55=A 56=A 57=A 58=A 59=A 60=A 61=A 62=A 63=A 64=A 65=A 66=A 67=A 68=A 69=A 70=A 71=A 72=A 73=A 74=A 75=A 76=A 77=A 78=A 79=A 80=A 81=A 82=A 83=A 84=A 85=A 86=A 87=A 88=A 89=A 90=A 91=A 92=A 93=A 94=A 95=A 96=A 97=A 98=A 99=A 100=A 101=A 102=A 103=A 104=A ...... END OF INITIAL ORBITAL SELECTION ...... CPU 0: STEP CPU TIME= 0.24 TOTAL CPU TIME= 0.3 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.49% ---------------------- AO INTEGRAL TECHNOLOGY ---------------------- S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR). S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE). S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5, ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER). S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY). -------------------- 2 ELECTRON INTEGRALS -------------------- DIRECT SCF METHOD SKIPS INTEGRAL STORAGE ON DISK. DIRECT TRANSFORMATION SKIPS AO INTEGRAL STORAGE ON DISK. ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 0.3 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.84% -------------------------- RHF SCF CALCULATION -------------------------- NUCLEAR ENERGY = 2520.5794603055 MAXIT = 199 NPUNCH= 2 EXTRAP=T DAMP=T SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T DENSITY MATRIX CONV= 2.00E-05 SOSCF WILL OPTIMIZE 16544 ORBITAL ROTATIONS, SOGTOL= 0.250 MEMORY REQUIRED FOR RHF ITERS= 640658 WORDS. DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 SCHWARZ INEQUALITY OVERHEAD: 30854 INTEGRALS, T= 0.00 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD VIR. SHIFT DAMPING INTEGRALS SKIPPED 1 0 0 -2059.2212832191 -2059.2212832191 0.988797951 0.000000000 0.000000000 1.000000000 191835514 22895770 2 1 0 -2042.8253644320 16.3959187871 1.142306775 0.674963723 0.000000000 1.000000000 192284889 22920383 3 2 0 -2053.1297307637 -10.3043663316 0.401569267 0.408533345 0.000000000 54.508125229 192386468 22914751 4 3 0 -2054.8896748699 -1.7599441062 0.681705613 0.974133914 0.000000000 3.406757827 185808214 23658736 ---------------START SECOND ORDER SCF--------------- 5 4 0 -2060.2884381280 -5.3987632581 1.089757171 0.228307597 0.000000000 0.000000000 191024572 23175415 6 5 0 -2062.5678087125 -2.2793705845 0.335341404 0.164617327 0.000000000 0.000000000 191517675 23118064 7 6 0 -2063.0509541215 -0.4831454090 0.503307418 0.129756838 0.000000000 0.000000000 189580417 23389152 I think the coords are the final config. Thanks for your help, Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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phenix.elbow with GAMESS
by Nigel Moriarty 01 Mar '16

01 Mar '16

Fred Does the .gam have a final geometry? You'll need to check because performing a QM geometry minimisation is not straight forward. BTW. A PDB file is the lowest quality input format. It's recommended that you try for a most information rich input such as SMILES or mol2. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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5th International Symposium on Diffraction Structural Biology (ISDSB2016)
by Leighton Coates 01 Mar '16

01 Mar '16

Hi All On behalf of the organizing committee, I am pleased to announce the “5th International Symposium on Diffraction Structural Biology” (ISDSB2016). The Symposium will take place on Sunday, August 7, 2016 through Wednesday, August 10, 2016 in Knoxville, Tennessee, USA. This symposium will report on the latest discoveries in structural biology using X-ray, neutron, and electron diffraction, and complementary techniques such as small-angle scattering, nuclear magnetic resonance spectroscopy, electron microscopy, and advanced computational approaches. Scientific insights at the molecular level allow structure guided drug discovery and protein engineering for improved biocatalysis. This basic research is important for supporting applications in the pharmaceutical industry and for new, sustainable, and environmentally friendly approaches to the production of chemical reagents and biofuels. Session topics include: Bioenergy Drug Design Enzyme Mechanism and Allostery Macromolecular Complexes Membranes and Membrane Proteins New Instruments and Methods Sources and Facilities A list of confirmed, invited speakers can be found on the conference web pages. The Symposium will be accompanied by two optional 1-day workshops on August 6, focused on Neutron Protein Crystallography and on Small-Angle Scattering, respectively. Please visit the conference website for further information: https://conference.sns.gov/event/2/ Thanks Leighton

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Command line version of Reflection_file _editor
by Rahel Woldeyes 01 Mar '16

01 Mar '16

Hi all, I was wondering if anyone has implemented command line compatible version of phenix.reflection_file_editor . Thanks! Rahel

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Command line version of Reflection_file _editor
by Rahel Woldeyes 29 Feb '16

29 Feb '16

Hi all, I was wondering if anyone has implemented command line compatible version of phenix.reflection_file_editor . Thanks!

1 0

Simulated annealing composite omit map
by Appu kumar 29 Feb '16

29 Feb '16

Hello All, I am trying to make the simulated annealing composite omit map for a protein ligand complex at 4.37A resolution. I think, Simulated annealing is harsh and rendering the protein distorting a lot as is evident from the helix turning into the some random structure. In order to avoid this protein distortion in protein backbone, do I need to fix some weight or specific parameter or provide reference structure and put harsh weight ? Any advice or suggestions would be much appreciated. Appu

2 1

Phaser-EP log file
by Nishant Pandey 28 Feb '16

28 Feb '16

Hi,I have a confusion regarding solving iodine SAD-data in Phaser-EP.1. GUI result shows Log-likelihood gain: 115037.70 and FOM: 0.527. But in log file SAD Refinement Table (Sorted) ----------------------------- SET SpaceGroup FOM Log-Likelihood Rfac Composition I # 1 P 21 21 2 0.53 -115038 69.4 23 Why there is negative value of Log-Likelihood in log file? Is Log-Likelihood and Log-likelihood gain is two different things?Has Phaser solved it? When I feed these results to Autobuild, the model was ~80 % complete with Rfree and Rwork of 0.3171 and 0.2754 and Model Map correlation 0.74. Model was further refined in phenix.refine upto Rfree = 0.27. 2. When I am solving same dataset with Autosol and Autobuild, the dimer orientation have changed? Is this 'normal' or one of the solution is wrong and if it then which one should choose to refine further? Thanks in advance.

2 1