March 2014 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 21 Sep '15

21 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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BCA/CCP4 Summer School in Protein Crystallography at Diamond
by Airlie McCoy 24 Apr '14

24 Apr '14

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 26th August to Sunday 31st August 2014. Applications close 1st May 2014. References are due by 8th May 2014. The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines. For more information on eligibility, cost, and applications see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School.html Application form: http://extranet2.diamond.ac.uk/ISV/EventWidget/BCA/ApplicationsForm.aspx

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error estimates on coordinates
by Benoît Masquida 27 Mar '14

27 Mar '14

Hello, Can someone shed light on the way coordinates errors are obtained in REMARK 3 using maximum of likelihood as compared to Luzzati or sigmaa? What article can be cited in this respect? Thanks in advance. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

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phenix.pdbtools model_statics=true
by Maehigashi, Tatsuya 26 Mar '14

26 Mar '14

Hi all, What would be the best way to define the "selection" to show average B factors using phenix.pdbtools from command line? I've tried several ways using something like... phenix.pdbtools XXXXX.pdb stop_for_unknown=false model_statistics=true selections="chain QA or chain RA" However, the output always contain the standard/default "ADP statistics" table only (not for the selection I specified). Yes, I'm aware of the GUI option (under other tools) and it works great. However, I'm trying to compute average b for 9 coordinates under 4 separate categories (protein, RNA, ligands... and such), and I think it'll be a lot easier from the command line (using some quick script, for example). Any input will be appreciated! "T" ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Obtaining just the Wilson B with Xtriage
by Morten Grøftehauge 26 Mar '14

26 Mar '14

Hi guys, Is there a way to just have phenix.xtriage compute and output the Wilson B factor and not do everything else? I want to run it on a lot of files and that would simplify things. Cheers Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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2014 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 25 Mar '14

25 Mar '14

Second announcement Fifth Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 16 - June 20, 2014 Application deadline: April 18, 2014 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 may not be able to offer travel or accommodation support. The number of participants will be limited to 15. There is no registration fees 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 18, 2014. Detailed information can be found on the course web page: http://neutrons.ornl.gov/conf/gcnb2014/ Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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xtriage reindexing suggestions
by Todd Jason Green 24 Mar '14

24 Mar '14

Hello all- I am trying to merge a few partial Se datasets. I am certain that I will have to reindex one or more to make sure that + and - reflections are not jumbled up. Can someone confirm that xtriage take this into account in suggesting to reindex one dataset in relation to a reference dataset? ie. does it use something like maximizing the anomalous signal in suggesting whether or not reindexing is necessary? I think the below suggests as much but I wanted confirmation: Automatic re-indexing For each data set supplied (other than the first data set given), all possible re-indexing matrices are derived as described by Grosse-Kunstleve et al. (2005). Each data set isautomatically re-indexed using the matrix that maximizes the correlation of amplitudes Have a good weekend. -Todd My Example: Reference analyses The following reindexing operators have been found: ------------------------------------------------- | Operator | Correlation | matches (%) | choice | ------------------------------------------------- | -k,h,l | 0.874 | 70.1 | <--- | | h,k,l | 0.032 | 76.7 | | ------------------------------------------------- If the data is reindexed with operator (-k,h,l), the correlation of the intensities to the reference data is maximized. sx205b_anom.sca This can be done for instance with: phenix.reflection_file_converter sx205b_anom.sca --change_of_basis="-k,h,l" <output_options>

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Multiprocessor refine
by Kenneth A. Satyshur 23 Mar '14

23 Mar '14

The FAQ on the web says that phenix.refine uses multiprocessors, yet only phenix.autobuild seems to use MP. Do I need a special version of Phenix? I am using GUI 1.8.4-1496 >How can I use multiple processors to run a job? >Only AutoBuild(http://www.phenix-online.org/documentation/autobuild_gui.htm), LigandFit(http://www.phenix-online.org/documentation/ligandfit_gui.htm), phaser.MRage(http://www.phenix-online.org/documentation/MRage.htm), phenix.refine(http://www.phenix-online.org/documentation/refine_gui.htm), the structure comparison GUI(http://www.phenix-online.org/documentation/structure_comparison.htm), and phenix.find_tls_groups support runtime >configuration of parallel processing. In most cases this is done by adding the "nproc" keyword, for instance: etc RHEL6 x86_64 thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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Fwd: Reminder: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 17 Mar '14

17 Mar '14

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Date: Mon, 17 Mar 2014 21:13:27 +0000 Subject: Reminder: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, This is a reminder for approaching deadline to apply for the CCP4 Crystallographic Summer School to be held in June at the APS, near Chicago. Please see the original announcement below for more details. We hope to see you at APS in June. With best wishes, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) 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 ------------------------------ Dear Colleagues, We are pleased to announce the seventh 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-2014/index.php *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two 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. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on 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 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 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<http://www.ccp4.ac.uk/schools/APS-2013/index.php> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) 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 __._,_.___ Reply via web post<https://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJwdmJpN3JlBF9TAzk3MzU5…> Reply to sender <[email protected]?subject=Re%3A%20Reminder%3A%20CCP4%20crystallographic%20summer%20school%20in%20USA%2C%20at%20APS%2C%20June%2024-July%202> Reply to group <[email protected]?subject=Re%3A%20Reminder%3A%20CCP4%20crystallographic%20summer%20school%20in%20USA%2C%20at%20APS%2C%20June%2024-July%202> Start a New Topic<https://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJldnZiMm5wBF9TAzk3MzU5…> Messages in this topic<https://groups.yahoo.com/group/cnsbb/message/2257;_ylc=X3oDMTM0dDhrM2VpBF9T…>(1) -------------------------------------------------------- List information at http://groups.yahoo.com/group/cnsbb. Posting is only allowed for members of this list. Visit Your Group<https://groups.yahoo.com/group/cnsbb;_ylc=X3oDMTJlazc1ZTluBF9TAzk3MzU5NzE0B…> [image: Yahoo! Groups]<https://groups.yahoo.com/;_ylc=X3oDMTJkZGZ1bzZpBF9TAzk3NDc2NTkwBGdycElkAzMw…> * Privacy <https://info.yahoo.com/privacy/us/yahoo/groups/details.html> * Unsubscribe <cnsbb-unsubscribe(a)yahoogroups.com?subject=Unsubscribe> * Terms of Use <https://info.yahoo.com/legal/us/yahoo/utos/terms/> . __,_._,___

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MRage run
by Jobichen Chacko 17 Mar '14

17 Mar '14

Dear All, I am running a molecular replacement using MRage program for almost 1 week with 4 threads, but yet to finish the run. I am using Phenix Version dev-1549 I am having a pretty big protein (around 100 KDa). I gave data file, sequence file, one model pdb and output from HHpred as input. Is there anyway to to find out when it is going to finish the run, or I can extract any information from the current run, if I manually end the run? Thank you. Jobi

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phasing high(er) resolution anomalous difference maps with low resolution phases
by Todd Jason Green 13 Mar '14

13 Mar '14

Hello all- I am working on a huge protein assembly(monomer is ~3000 amino acids, large cell ~200, ~200, ~520) that has between 200 and 300 Se-met residues in the asymmetric unit(depending on the number of molecules I pick in the a.u.). I believe I have low resolution phasing from another heavy atom with limits to ~ 6.2 angstrom. Density modified FOMs dip below 0.6 at that point. I can see many tubes that have the diameter of model alpha helices. I ran phenix.find_helices_strands with the helices_before_trace=True option and got a series of helices encompassing about 3400 residues. Assuming that the phasing on the low resolution derivative is true, is it better to use phasing from the lower resolution derivative or phasing from the helical models to fish out the Se-Met sites via an anomalous difference Fourier? I assume I'm stuck at 6.2 for the derivative phasing though i guess i could extend phasing from the map a little further. How far is too far? How high of resolution can I phase from the helices (or from the derivative map for that matter) and still get accurate enough phasing to yield reliable difference peaks to find the Se sites. I have a couple Se-met datasets between 3 and 2.5 angstroms. What sigma levels should I expect for the difference peaks? also, what is the best way to pick the highest difference peaks in the anomalous difference fourier? I didn't see a tool in phenix. "find difference peaks and holes" seems like a logical choice but it seems to want to structure. I've just created maps and used the very old and reliable peakmax in ccp4. I have solved structures like this before but with a lot more info on ncs, envelopes, ncs averaging and a much much smaller protein. I remember getting sites and plugging them into resolve with scripts where you could fix them/or not and phase without looking for more sites, no build etc. Can i just enter sites and phase followed by density modification with one of the gui programs. any comments would be appreciated? and thanks in advance. -Todd

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Postdoctoral position available
by Peter Zwart 11 Mar '14

11 Mar '14

Dear All, The Berkeley Center for Structural Biology at Lawrence Berkeley National Lab is looking for a postdoctoral fellow to work on the development of computational methods aimed at improving the overall quality of crystallographic data and its resulting atomic models. The results of this work will be integrated into the Berkeley Center for Structural Biology (BCSB) crystallography beam lines at the Advanced Light Source. Please have a look at the job posting and contact me for more information: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=77796 Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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phenix error
by SD Y 04 Mar '14

04 Mar '14

Hi, Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69". Log file ends as follows: ============================= Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 7 Type Number sf(0) Gaussians Zn2+ 1 27.88 1 S 10 15.96 2 P 2 14.95 2 Mg2+ 3 9.96 1 O 635 7.97 2 N 523 6.97 2 C 1983 5.97 2 sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ======================== Summary of geometry restraints ======================= Number of disulfides: simple=0, symmetry=0 Custom bonds:Sorry------------------------------ Thanks a lotSDY

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project not displayed
by SD Y 03 Mar '14

03 Mar '14

Hi, When I open phenix (1.8.4-1496), I dont see my project. If I import it, it appears. If I close and reopen I disappear again. I have the folders and jobs everything and nothing is lost. Though its not a serious problem, I am wondering if I could get some solution. ThanksSDY

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Rwork/Rfree by resolution shell
by Ursula Schulze-Gahmen 02 Mar '14

02 Mar '14

Where can I found the values for Rwork/Rfree by resolution shell in phenix refinement or analysis. I ran phenix.model_vs_data which provides a list of Rwork by resolution, but no Rfree. Any helpful suggestions? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 642 8766

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fwd: Post-doctoral Fellowship at the University of Texas
by Nathaniel Echols 01 Mar '14

01 Mar '14

---------- Forwarded message ---------- From: "Rudenko, Gabrielle" <garudenk(a)utmb.edu> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Date: Sat, 1 Mar 2014 20:36:00 +0000 Subject: Post-doctoral Fellowship at the University of Texas * Macromolecular Crystallography, Biophysics and Biochemistry* A post-doctoral fellowship position is available at the University of Texas Medical Branch (UTMB) located in the greater Houston area in the research team of Dr. Gabrielle Rudenko. We study molecules that mediate the formation, maintenance and plasticity of synapses, the contact and communication point between neurons. Our proteins of interest organize and regulate protein interaction networks in the synaptic cleft and impact how neurons communicate with each other at synapses. Many of the proteins we study are implicated in neurological disease and serve as potential novel therapeutic targets. We are looking for highly motivated, enthusiastic, hard working individuals who are interested in combining the fields of structural biology and neuroscience. Research projects involve protein over-expression and purification, x-ray crystallography, biochemical and biophysical techniques, proteomics, chemical biology and in collaboration electron microscopy and NMR. Our laboratory is part of the endowed Sealy Center for Structural Biology and Molecular Biophysics and the Department of Pharmacology/Toxicology at UTMB. The Sealy Center provides access to exceptional facilities, training and experimental assistance. *X-ray facilities* include a high-brilliance FR-E Superbright x-ray generator, a Rigaku R-AXIS-IV dual 30cm Imaging Plate detector, a Bruker SMART 2K CCD and a Rigaku BioSAXS-1000 2D-Kratky camera (for solution scattering data). *Biophysics facilities* include equipment for analytical ultracentrifugation, fluorescence, MALDI-TOF mass spectrometry, dynamic light scattering, surface plasmon resonance, titration micro-calorimetry, and high throughput screening with the ThermoFluor HTS apparatus. In addition, the *Electron Microscopy facilities*house three modern JEOL cryo-electron microscopes (a 200 keV JEOL 2200FS cryo-EM with in-column electron energy filter and field emission gun, a 200 keV JEOL 2100 EM, and a 120 keV JEM1400 microscope) and the *NMR facilities*include three NMR spectrometers (Bruker Avance III 800, 750 and 600 MHz with cryoprobes). See http://www.scsb.utmb.edu/resources/ UTMB is part of the Texas Medical Center, the world's largest medical center located in greater Houston. UTMB has research facilities situated on Galveston Island offering a pleasant subtropical climate and miles of relaxing beaches. UTMB is located within commuting distance of Houston, the fourth largest city in the United States and a leader in the arts, education, and health care. *Qualifications:* Applicants should have received a Ph.D. degree in a field relevant to structural biology within in the last three years and have a strong publication record. Applicants with experience in cloning, bacterial/insect cell culture, protein purification and crystallization, and macromolecular structure determination are preferred. However, recent graduates with a strong background in protein over-expression and purification, and an exceptional interest in learning crystallography are also encouraged to apply. Good written and oral communication skills in English are essential as well as the ability and desire to work as part of a highly motivated, collaborative team. To apply please e-mail the following to *rudenkolab.application(a)gmail.com*<rudenkolab.application(a)gmail.com>: CV, contact information for three references (address, phone and e-mail), a list of your experimental expertise and skills relevant to this position and a research statement describing your past research experience and future goals (1-2 pages). Visa sponsorship is available for non-US nationals. For questions, please contact Dr. Gabrielle Rudenko at gabrielle.rudenko(a)utmb.edu For more information please visit http://scsb.utmb.edu/labgroups/rudenko/ The University of Texas is a non-discriminatory, affirmative action employer. Gabrielle Rudenko, PhD Dept of Pharmacology and Toxicology Sealy Center for Structural Biology & Biophysics University of Texas Medical Branch 301 University Boulevard Basic Sciences Building Rm. 5.114B Galveston Texas 77555

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