- phenixbb - phenix-online.org

calculating anomalous differences from a model
by Jonathan Grimes 05 Apr '14

05 Apr '14

Given a refined protein structure, is there an straightforward way to calculate the anomalous differences as a function of resolution, at wavelength X. many thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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determining molprobity version?
by Pete Meyer 01 Apr '14

01 Apr '14

Hi, I may be missing something obvious, but how do I determine which version of molprobity is being used for generating the clash scores reported by phenix.model_vs_data ? Pete

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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 27 Mar '14

27 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 27 Mar '14

27 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 26 Mar '14

26 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 24 Mar '14

24 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 18 Mar '14

18 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 14 Mar '14

14 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 12 Mar '14

12 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 05 Mar '14

05 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 04 Mar '14

04 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 03 Mar '14

03 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 02 Mar '14

02 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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Ligands: a BCSB nano-workshop
by Peter Zwart 01 Mar '14

01 Mar '14

Dear All, On May 2, 2014 the BCSB will be hosting a full day event dedicated to ligands in the life sciences. Access is free, but is limited to 30 participants. The lectures will be streamed allowing remote participation to this event. For onsite and remote attendance, please register to receive further instructions. The registration for on-site participation will be on a first come, first serve basis. The program will cover structural science associated with ligands in the life sciences. Viewpoints from macromolecular crystallography, quantum chemistry, small molecule crystallography and solution scattering will provide the participants with a 360-degree perspective of the role of and technology associated with ligands in structural biology. Please have a look at https://sites.google.com/a/lbl.gov/ligands/home for more information. 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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observed reflections error?
by Joel Tyndall 01 Mar '14

01 Mar '14

Hi all, I have a minor issue with phenix reporting the number of observed reflections in the output pdb file where it appears to be roughly double (120080 ) to what is actually in an mtz file (~65000) from scala. Any suggestions where this number might originate from? Joel _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

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Re: [phenixbb] ERRASER location within rosetta
by Terwilliger, Thomas C 28 Feb '14

28 Feb '14

________________________________ From: Terwilliger, Thomas C Sent: Friday, February 28, 2014 8:42 AM To: Benoît Masquida Cc: Terwilliger, Thomas C Subject: RE: [phenixbb] ERRASER location within rosetta Hi Benoit, I'm sorry for the trouble! The error message, "Sorry, Rosetta version 3.5 or later is needed for ERRASER" is printed if erraser cannot find the file erraser_option.py which should be located in $PHENIX_ROSETTA_PATH/rosetta_tools/ERRASER or $PHENIX_ROSETTA_PATH/tools/ERRASER If you don't have PHENIX_ROSETTA_PATH defined then that would fix it as well. Let me know if this doesn't help! All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Benoît Masquida [b.masquida(a)unistra.fr] Sent: Friday, February 28, 2014 8:27 AM To: PHENIX user mailing list Subject: [phenixbb] ERRASER location within rosetta Hello all, I just built rosetta on my Mac OS 10.8.5 and now try to configure ERRASER within the phenix GUI. I correctly indicated the location of the rosetta build and I specified the same location for ERRASER. However when I start an ERRASER job, an error tells me that "ERRASER works with rosetta3.5 or later version". This is strange because i downloaded one of the latest version of rosetta. I don't know if I gave a wrong locate or if my build is corrupted. Any idea from anyone that could have experienced the same problem? pwd outputs this: /Users/benoit1/share/rosetta_2014wk05_bundle/main, where I find database/ and source/ Thanks. 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<mailto:[email protected]>

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ERRASER location within rosetta
by Benoît Masquida 28 Feb '14

28 Feb '14

Hello all, I just built rosetta on my Mac OS 10.8.5 and now try to configure ERRASER within the phenix GUI. I correctly indicated the location of the rosetta build and I specified the same location for ERRASER. However when I start an ERRASER job, an error tells me that "ERRASER works with rosetta3.5 or later version". This is strange because i downloaded one of the latest version of rosetta. I don't know if I gave a wrong locate or if my build is corrupted. Any idea from anyone that could have experienced the same problem? pwd outputs this: /Users/benoit1/share/rosetta_2014wk05_bundle/main, where I find database/ and source/ Thanks. 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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Challenging Refinement at 5 A Resolution
by Erik Walinda 28 Feb '14

28 Feb '14

Dear community, This is my first adventure in crystallography and it seems a rather challenging one. I obtained at dataset at 5.06 A resolution of a 600 residue protein. 3 domains of the protein are already solved by earlier x-ray crystallographic studies. While trying to grow better diffracting crystals and waiting for the next chance to shoot crystals at the synchrotron, I am trying to fit the already solved domains into the electron density of the low data set. Although I tried phaser using the solved structures, I never got a TFZ higher than ~ 6.4. Interestingly, Balbes constructed a model which does not contain any of the already solved domains, but, when using the Balbes output in Phaser, I obtain a TFZ score of 11 and an LLG of 330. (4 molecules / ASU; P2221) If this solution is correct, then in principle it should be possible to fit the already known domains into the structure (I am dreaming of something like a electron-microscopy-type fitting or the early ribosome structures). Phenix refinement however raises the Rfree, instead of lowering it. From my limited knowledge in the field I figured this may be that a) this kind of refinement doesnt work at this resolution or 2) the MR-solution was not really a solution. So I was very excited, when I found the recent papers about DEN refinement and Phenix-Rosetta. I am trying DEN refinement first, using the already solved structures as a reference. The den_refine program nicely creates 2760 DEN restraints. However, after 1 cycle (about 6 h of CPU time at 30 processors), the Rfree goes up (Initial: 0.49; final: 0.57). Indeed, the grid search seems not to be successful, since in the grid search for gamma/w, all Rfree values are rather similar and the lowest Rfree is 0.54. So I would like to ask the community, if ... 1) I shouldn't trust the phaser TFZ score too much and maybe it is just no solution after all? 2) the DEN parameters of phenix.den_refine can be optimized to allow to refine a super-low resolution structure? (I am using the standard parameters from the example: https://www.phenix-online.org/documentation/den_refine.htm) 3) 1 cycle is simply not enough and I should let the computation run for a few days to see, if the Rfree drops down later in the run? 4) Even though Phaser gave me the solution in P2221, may it be that I am trying to refine it in the wrong spacegroup and that's why I fail? Sincerely, Erik

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Re: [phenixbb] unusually high B-factors for selected -heavier- atoms
by Kay Diederichs 28 Feb '14

28 Feb '14

Jan, could it be radiation damage? - that would affect the heavier atoms first/most ... To prove/disprove, use zero-dose extrapolation and re-refine. Kay Am 27.02.14 20:13, schrieb phenixbb-request(a)phenix-online.org: > Date: Thu, 27 Feb 2014 09:50:31 -0800 > From: Jan <jan.abendroth(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] unusually high B-factors for selected -heavier- > atoms > Message-ID: <D87628CC-A657-4B4C-B14F-C230C0C2EF00(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I am refining a pretty high resolution structure (1.65?, P1) with two tetramers of the protein in the ASU using Phenix dev 1630. > Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very clear. However, several sulphur atoms of the protein, and in particular the phosphorous atoms of its cofactor NAD have inflated B-factors, along with distinct FoFc peaks. For instance B-factors for a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4 > > For some of the residues it is comparable when I refine with or without TLS groups. I used one group per chain of this compact protein, the cofactor is part of each TLS group. Restraints for NAD were generated via eLBOW. When I refine the structure in refmac, using either the standard cif file or the eLBOW generated one, B-factors remain low. > > Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway. > > Thanks, > Jan > > > > -- > 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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unusually high B-factors for selected -heavier- atoms
by Jan 28 Feb '14

28 Feb '14

Hi all, I am refining a pretty high resolution structure (1.65Å, P1) with two tetramers of the protein in the ASU using Phenix dev 1630. Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very clear. However, several sulphur atoms of the protein, and in particular the phosphorous atoms of its cofactor NAD have inflated B-factors, along with distinct FoFc peaks. For instance B-factors for a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4 For some of the residues it is comparable when I refine with or without TLS groups. I used one group per chain of this compact protein, the cofactor is part of each TLS group. Restraints for NAD were generated via eLBOW. When I refine the structure in refmac, using either the standard cif file or the eLBOW generated one, B-factors remain low. Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway. Thanks, Jan -- 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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FAQ high res refinement
by Eike Schulz 28 Feb '14

28 Feb '14

> > Dear all, > > I am currently refining a rather well resolved protein at 0.97Å. However, even > after many cycles of refinement the R-factors are stuck at around Rwork/Rfree > 14.5/16.5. Considering number of aa, Rmerge (3.5%) and resolution this seems > to be too high. I assume 10 25 macrocycles should be enough for effective > weight refinement in phenix, however no improvement of the R-factors. > > A quick run with default settings in competitor software 'R' yields >2% better > R-factors. > > I would appreciate suggestion how to improve my refinement protocol, values > differing from default are listed below. > > Thank you very much in advance > > Eike > > > > > > > refine { > adp { > individual { > isotropic = element H > anisotropic = not element H > } > group_adp_refinement_mode = one_adp_group_per_residue \ > *two_adp_groups_per_residue group_selection > } > } > main { > apply_overall_isotropic_scale_to_adp = False > nqh_flips = False > ordered_solvent = True > place_ions = True > number_of_macro_cycles = 10 > hydrogen_bonds = True > use_convergence_test = True > target = auto *ml mlhl ml_sad ls > random_seed = 3326496 > wavelength = 0.885611 > nproc = 4 > } > hydrogens { > refine = individual *riding Auto > } > tls { > find_automatically = False > one_residue_one_group = False > } > ordered_solvent { > mode = second_half filter_only every_macro_cycle \ > *every_macro_cycle_after_first > h_bond_min_mac = 1 > h_bond_min_sol = 1 > h_bond_max = 6 > refine_occupancies = True > new_solvent = isotropic *anisotropic > b_iso_min = 0 > } > peak_search { > max_number_of_peaks = 1303 > } > target_weights { > optimize_xyz_weight = True > optimize_adp_weight = True > wxc_scale = 0.2 > wxu_scale = 0.2

2 1

Option for renumber the pdb
by Rojan Shrestha 28 Feb '14

28 Feb '14

Hello, I have found the program phenix.pdbtools. Maybe, it can renumber residues of pdb. I have found the options renumber_residues options but I am unable to see the options for starting residues. I have pdb starts from 1 and want to renumber 1 into 250. Can somebody tell me how to put the option for starting residue? Regards, Rojan

5 5

scaling in phenix.fobs_minus_fobs_map
by Michael Thompson 27 Feb '14

27 Feb '14

Hello, I have a very simple question about phenix.fobs_minus_fobs_map, and it's implementation in the GUI. I just want to make sure I am not skipping an important step in generating my isomorphous difference map. I'm trying to create an Fo-Fo map for two data sets at pretty different resolutions, using phases from a model. I truncated the higher-res data so the high resolution limit matches the lower-res data set. Are these 2 mtz files sufficient for input into phenix.fobs_minus_fobs_map, or do I need to use another utility to scale the two data sets together prior to calculating the map coefficients? I suppose another way to ask my question would be, does phenix.fobs_minus_fobs_map perform scaling of the two Fobs arrays before calculating the new map? Thanks for clarifying, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

2 1

problem phenix ensemble
by Firas FADEL 26 Feb '14

26 Feb '14

Hello, I am using phenix ensemble to refine an X-ray structure of a protein (40kDa) at 1.05 A in complex with a ligand. The occupancy of the ligand is 73%. After refining the structure, I found out that the program confused the position of the ligand and put some water molecules. Do you have any suggestion or a command to avoid this problem. If you need details I can send you the mtz and pdb files. Thanks in advance. Firas Fadel Firas FADEL Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC Equipe Alberto PODJARNY, 1 Rue Laurent Fries, 67404 Illkirch-France Email : fadel(a)igbmc.fr<mailto:[email protected]> Tel: + 33 (0) 3 88 65 33 13<tel:%2B%2033%20%280%29%203%2088%2065%2033%2013>

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Announcement: QuantumBio Release of QM-based X-ray Crystallography Plugin v1.0 for Phenix
by Lance Westerhoff 25 Feb '14

25 Feb '14

Hello All- We are pleased to announce the release of our linear scaling, quantum mechanics DivCon Discovery Suite plug-in v1.0 for the Phenix, x-ray crystallography platform. As was detailed in the recent Phenix Newsletter, when this plugin is installed, the conventional refinement functional along with the stereochemical restraints or CIFile for the ligand(s) and for the surrounding active site(s) are replaced with QM data in "real time" during the refinement in order to increase structural accuracy and decrease artificial strain. To see the full press release along with references and links for further information, please take a look at the following website: http://www.quantumbioinc.com/news/show/PhenixAnnouncement To encourage adoption, we have waived the license fee for non-profit, academic use and we have posted our commercial evaluation license as well. These licenses are available at the following link: http://www.quantumbioinc.com/products/software_licensing Certainly, let me know if you have any questions or if you would like to try out the technology on your own structures. -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com

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revisiting "Problem with loop fitting "
by Alejandro Buschiazzo 24 Feb '14

24 Feb '14

Dear phenix community I am attempting to use phenix.fit_loops for the first time and getting an error message: "No suitable gap found matching residues" I found a short exchange exactly about this (Jan 2011), but eventually Tom Terwilliger asked for the files directly to see if he could solve it. I can't seem to find a later summary of the solution. (apparently, the most probable reason was some kind of mismatch between PDB numbering and sequence file...which I shouldn't have... I'm probably missing some silly here - I have been fiddling around with the sequence file in many ways...with no success) many thanks for any help! alejandro -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

2 4

Questions about phenix.mr_rosseta
by Yonglin Hu 24 Feb '14

24 Feb '14

Hello List, I am very new to using Phenix/Rosetta to solve MR. I just finished a job by following the procedures described on phenix-online.org using Phenix GUI. The program reported that no solution was found, but when I went through the RUN_FILE_*.log, I found that despite all the log files ended with the following sentences: Stage to relax: refined_rescored_rosetta_solution No solutions to relax No autobuilt solutions to iterate... Finishing up mr_rosetta... one solution had a Rfree of 0.48 with correct number of molecules in ASU. When I refined that solution using phenix, Rfree went down further, proving to be a correct one. So my question is: why phenix.mr_rosetta did not report this solution as a good one? My second question is regarding model rebuild using phenix/rosetta. No matter I used the GUI or command lines copied from phenix-online like the following: phenix.mr_rosetta \ seq_file=~/MA/Mpa.pir \ data=~/MA/MA.mtz \ search_models=~/MA/refine_6.pdb \ already_placed=True \ fragment_files = ~/MA/MA-3mer \ fragment_files = ~/MA/MA-9mer \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=6 \ space_group="C 1 2 1" \ use_all_plausible_sg=False \ nproc=4 the program always fails. The log files have the following messages: Sorry, a subprocess has failed... ...... Sorry: Failed to run REBUILD...see log file in MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log They pointed to rebuild.log files, but these files don't contain error message and they ended with the following seemingly innocuous lines: protocols.relax.FastRelax: CMD: accept_to_best -3682.86 0.994359 0.994359 0.44 core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 requested but only 401 protein CA atoms found. core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 requested but only 401 protein CA atoms found. protocols.relax.FastRelax: CMD: endrepeat -3682.86 0.994359 0.994359 0.44 protocols::checkpoint: Deleting checkpoints of FastRelax protocols::checkpoint: Deleting checkpoints of FastRelax protocols.jd2.JobDistributor: S_MA_R_0005 reported success in 4573 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 5 jobs considered, 5 jobs attempted in 20716 seconds I would appreciate it if you could tell me what could be the causes of the failures. Thank in advance, Yonglin

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stop_for_unknowns=False in new version ?
by Michaela Renner-Schneck 20 Feb '14

20 Feb '14

Hi, I haven’t been running phenix.refine for a couple of weeks and meanwhile we have updated to the latest version. Now I need to re-run an old job but unfortunately the pdb-interpretation option "stop_for_unknowns=False“ which I needed for this seems to be no longer valid. Is there a way to get this option work again ? thx in advance Michaela

2 1

New position
by Gillette, William (NIH/NCI) [C] 19 Feb '14

19 Feb '14

Dear colleagues, We have an opening for a structural biologist here in Frederick, MD. If not interested, please forward this email to those who might be. Thank you. Best regards, Bill <http://jobs.leidos.com/job/Frederick-Lead-Structural-Biology-603181-%28NCI%…> http://jobs.leidos.com/job/Frederick-Lead-Structural-Biology-603181-%28NCI%… ______________________________________________________ Bill Gillette, Ph.D. (Contractor) Sr. Scientist, Protein Expression Laboratory Cancer Research Technology Program Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research (FNL) P.O. Box B, Frederick, MD 21702 Phone: 301-846-1029 William.Gillette(a)nih.gov<gillettew(a)mail.nih.gov> Notice: This communication may contain privileged or other confidential information. If you are not the intended recipient, or believe that you have received this communication in error, please do not print, copy, retransmit, disseminate or otherwise use the information. Please indicate to the sender that you have received this email in error and delete the copy you received.

1 0

phenix.composite-omit-map and PBScluster
by Mark A Saper 19 Feb '14

19 Feb '14

Hi, This is a technical question for cluster experts. I tried to run phenix.composite-omit-map which can divide the calculations into separate jobs, on a very large cluster controlled by the PBS system. I used this command of which the first 2 lines specify to divide the work up into 16 processes, and each process will use 1 of the CPU's in the cluster. phenix.composite_omit_map nproc=16 background=False technology=pbs \ qsub_command="qsub -V -l procs=1,walltime=00:30:00,mem=2000mb,qos=flux -j oe -M saper(a)umich.edu -q flux -m abe " \ omit_type=anneal map_type=2mFo-Dfc output.file_name=composite_omit_map9.mtz \ reflections3_5percent.mtz Refine_122.pdb This is the end of the log file before it aborted: ----------Calculating individual omit maps---------- |-----------------------------------------------------------------------------| | target_work(ml) = 4.65539 r_work = 0.1750 r_free = 0.2066 | |-----------------------------------------------------------------------------| And this is the error log: Traceback (most recent call last): File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 238, in <module> run(sys.argv[1:]) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 166, in run out=out) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/phenix/phenix/automation/composite_omit_map.py", line 395, in __init__ preserve_exception_message=True) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/easy_mp.py", line 502, in parallel_map display_stderr = not preserve_exception_message, File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/queuing_system_utils/processing/__init__.py", line 405, in PBS raise RuntimeError, "PBS does not support synchronous submission" RuntimeError: PBS does not support synchronous submission I know that PBS doesn't support synchronous submission. Perhaps each job (or map region) requires more than one processor? Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan c/o Biophysics, Chem 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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list policy change: Reply-To header
by Nathaniel Echols 19 Feb '14

19 Feb '14

Hi all-- Since the current practice of directing all replies to the entire phenixbb seems to cause confusion, we've changed this so the reply will be sent to the original sender. Because we rely on the list archives as a form of ongoing "live" documentation, we encourage everyone to use "reply to all" unless you are really certain that you do not want your message to go to the list. (This especially applies to my colleagues: if you don't copy the entire list, the rest of us have no way of knowing if a question has been answered or not.) thanks, Nat

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Re: [phenixbb] Real space refinement
by Pavel Afonine 18 Feb '14

18 Feb '14

Hi Mavis, there are two options. One is convert your EM map into structure factors Fobs and HL coefficients using phenix.map_to_structure_factors command and then use phenix.refine to do reciprocal space refinement. This is somewhat indirect way. The good thing about it is that phenix.refine has a broad range of tools to handle low resolution refinement. Another option is to use phenix.real_space_refine to refine model against the map directly. This is a preferred way but phenix.real_space_refine is new, less mature program and it generally is still under development (though it's functional if you try it now). So if it does not work as you expected or you have any feature requests or any questions or any other feedback - please do not hesitate to let me know, as this may help to improve this tool. All the best, Pavel On 2/17/14, 6:14 AM, Agbandje-Mckenna,Mavis wrote: > Dear Pavel, > > Thank you so much for getting back to me - this is much appreciated. We received a script from Hong Zhou's group who have been using Phenix to refine the model for their 3.3 Angs cryo-EM Aquareovirus structure that we were going to try but this seems a lot more simpler! > > Thanks again. I will let you know how it turns out. > > And thank you for the attached pdf. > > Best wishes > > Mavis > > Mavis Agbandje-McKenna, Ph.D. > Director, Center for Structural Biology > Professor, Dept. of Biochemistry and Molecular Biology > Center for Structural Biology > The McKnight Brain Institute > P.O. Box 100245 Tel.: 1-352-392-5694 > University of Florida Fax.: 1-352-392-3422 > Gainesville, FL 32610-0245 e-mail: mckenna(a)ufl.edu > Website: http://msg.mbi.ufl.edu > ________________________________________ > From: Pavel Afonine [pafonine(a)lbl.gov] > Sent: Monday, February 17, 2014 2:28 AM > To: Agbandje-Mckenna,Mavis; phenixbb(a)phenix-online.org > Cc: Lins, Bridget; Drouin,Lauren M > Subject: Re: Real space refinement > > Hi Mavis, > > you can do it in Phenix. Command line tool for this is: > phenix.real_space_refine. Just give it map and model and see what > happens, like this: > > phenix.real_space_refine model.pdb ccp4_formatted_map.map > > I wrote this program specifically to do various kinds of model > refinement against the map, with the main focus on EM maps. Have a look > at the article that briefly describes it here: > http://www.phenix-online.org/newsletter/CCN_2013_07.pdf > "New tool: phenix.real_space_refine". > The article is from last year but I haven't done much since then so it > pretty much documents the current state of the art. > > Should you have any questions or problems or need any help with this > please let me know off list. > > All the best, > Pavel > > On 2/14/14, 8:45 AM, Agbandje-Mckenna,Mavis wrote: >> Dear Pavel, >> >> I don't believe we have met, but you have received several e-mails from people in my group (including Sujata (Tina) Halder) and also helped them with their use of Phenix - thank you. >> >> I have a question for you regarding real space refinement in Phenix. We have a 3.7 Angs cryo-EM reconstructed structure for a virus capsid and we have been able to build a model for the capsid VP using COOT. I would like to refine this model further against the map using real space refinement. I am trying to find a suitable program that would allow me to do this. I believe Phenix can do it, but I am not sure. Could you give me some direction? >> >> Thanks in advance. >> >> Best wishes >> >> Mavis >> >> Mavis Agbandje-McKenna, Ph.D. >> Director, Center for Structural Biology >> Professor, Dept. of Biochemistry and Molecular Biology >> Center for Structural Biology >> The McKnight Brain Institute >> P.O. Box 100245 Tel.: 1-352-392-5694 >> University of Florida Fax.: 1-352-392-3422 >> Gainesville, FL 32610-0245 e-mail: mckenna(a)ufl.edu >> Website: http://msg.mbi.ufl.edu

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Gordon Conference on Diffraction Methods in Structural Biology
by Anastassis Perrakis 18 Feb '14

18 Feb '14

Dear all, The biannual Gordon Research Conference in Structural Biology, accompanied by the first Gordon Research Seminar, will take place in the last week of July at Bates College, New England, a few hours drive from the IUCr meeting that follows in the first week of August. The theme for the GRC is "Faster, Smaller, Better: Novel Technologies for Diffraction Experiments in Molecular Biology and Drug Discovery" and of the GRS (which precedes the GRC and is targeting young scientists giving them an opportunity to present their own work to their peers prior to the meeting) "Towards Integrative Structural Biology". We have a truly fantastic line of speakers and discussion leaders, including John Kuriyan , Randy Read, Ana Gonzales, Ilme Schlichting , Henry Chapman , John Spence, Graeme Winter , Aina Cohen, Thomas Schneider , Gwyndaf Evans , Bob Fischetti , Flora Meilleur, Janet Newman , John Hunt , Michael Duszenko , Jose Antonio Marquez, Paul Adams , Clemens Vonrhein , Airlie McCoy , Brent Nannenga, Zbyszek Dauter , Tom Terwilliger , Garib Murshudov , Gerard Kleywegt , Paul Emsley, Dmitri Svergun , Peter Zwart , Michael Hammel , Lois Pollack, Elspeth Garman, Lisa Keefe , Gary Gililland , Aydnan Achour and Giovanna Scapin. For more details visit our web site: https://www.grc.org/programs.aspx?year=2014&program=diffrac And here is the largely unavoidable motivational speech for anyone interested to my highly biased personal view: I first went to this meeting in 1998, as a young post-doc, presenting results that later led to the 'ARP/wARP' software: in fact, I had changed my slides (for the younger audience: slides were pieces of photographic film that were typically projected as mirror images of what you really wanted) a month or so before the meeting, as we got our very first models auto-built. I thought it was the most educational and exciting meeting I have ever been to, and in many ways it has shaped my research plan and my career (and my hate for golf). I wish I could also say that I never missed any of the subsequent meetings, but courtesy of the US Visa authorities and the Greek Army, I actually did a miss a couple. However, I still find them as exciting as so many years ago, but for a whole different set of scientific reasons: the diffraction methods landscape is changing rapidly, new machines and concepts make possible experiments that we do not even know what they are going to be! I am honored to be chairing this year's edition, and I hope that I will hear from at least one of you, what I had heard from a few before: "this is the best meeting I have been in my life". Science aside, I am glad there is no golf course nearby the Bates College site where we are holding this meeting for the last decade, I am equally happy for the "Great Outdoors" site where we do the mid-week excursion, and I am looking forwards to the football (sorry: "soccer") and basketball games. The Bates College boasts an excellent auditorium for the talks, a truly outstanding lounge for the poster sessions (that are always accompanied by drinks, an observation that might partially explain the tendency to finish well after midnight in a very positive spirit) and a somewhat confusingly and an unexpectedly good quality restaurant in the very friendly College site. A limited amount of (partial) bursaries to young scientists will be available for this year - when this becomes definitive we will post the news. I should also mention that one session will host eight seminars that will be selected from the poster sessions, giving all particpants the opportunity to present their own research! In the meantime, I am looking forward to welcome you all at the meeting and I hope you will register ... today! Best regards, 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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Re: [phenixbb] Real space refinement
by Pavel Afonine 17 Feb '14

17 Feb '14

Hi Mavis, you can do it in Phenix. Command line tool for this is: phenix.real_space_refine. Just give it map and model and see what happens, like this: phenix.real_space_refine model.pdb ccp4_formatted_map.map I wrote this program specifically to do various kinds of model refinement against the map, with the main focus on EM maps. Have a look at the article that briefly describes it here: http://www.phenix-online.org/newsletter/CCN_2013_07.pdf "New tool: phenix.real_space_refine". The article is from last year but I haven't done much since then so it pretty much documents the current state of the art. Should you have any questions or problems or need any help with this please let me know off list. All the best, Pavel On 2/14/14, 8:45 AM, Agbandje-Mckenna,Mavis wrote: > Dear Pavel, > > I don't believe we have met, but you have received several e-mails from people in my group (including Sujata (Tina) Halder) and also helped them with their use of Phenix - thank you. > > I have a question for you regarding real space refinement in Phenix. We have a 3.7 Angs cryo-EM reconstructed structure for a virus capsid and we have been able to build a model for the capsid VP using COOT. I would like to refine this model further against the map using real space refinement. I am trying to find a suitable program that would allow me to do this. I believe Phenix can do it, but I am not sure. Could you give me some direction? > > Thanks in advance. > > Best wishes > > Mavis > > Mavis Agbandje-McKenna, Ph.D. > Director, Center for Structural Biology > Professor, Dept. of Biochemistry and Molecular Biology > Center for Structural Biology > The McKnight Brain Institute > P.O. Box 100245 Tel.: 1-352-392-5694 > University of Florida Fax.: 1-352-392-3422 > Gainesville, FL 32610-0245 e-mail: mckenna(a)ufl.edu > Website: http://msg.mbi.ufl.edu

1 0

100 Years of Crystallography
by George Phillips 13 Feb '14

13 Feb '14

Rice University symposium to celebrate 100 years of crystallography HOUSTON – (Feb. 10, 2014) – Rice University and the Gulf Coast Consortia will host an all-day public symposium titled “International Year of Crystallography: Structure Matters” Feb. 14 at the BioScience Research Collaborative. Experts in X-ray crystallography – the technique scientists use to determine the structure of matter at very small scales – will discuss the significance of the technology and how it’s used to visualize the structures of proteins, a critical step in the design of drugs to fight disease. Speakers include George Phillips, the Ralph and Dorothy Looney Professor of Biochemistry and Cell Biology at Rice; Yizhi Jane Tao, an associate professor of biochemistry and cell biology at Rice; Choel Kim, an assistant professor at Baylor College of Medicine; John Spence, the Richard Snell Professor of Physics at Arizona State University and director of science for the National Science Foundation (NSF) BioXFEL Science and Technology Center; and Stephen Burley, professor and director of the Center for Integrative Proteomics Research at Rutgers University. The program will begin at 9 a.m. with poster presentations and science exhibits for high school students. Crystallography is being recognized by the United Nations on the 100th anniversary of the awarding of Nobel Prizes to its discoverers, German physicist Max von Laue and the father-son team of William Henry and William Lawrence Bragg. Rice researchers led by Phillips are part of the NSF’s BioXFEL consortium, founded last year and based at the University of Buffalo, to explore the use of strong X-ray lasers to detail the atomic structures of molecules with a resolution approaching the nanoscale. The symposium is free and sponsored by the Gulf Coast Consortium (GCC) for Protein Crystallography, the Wiess School of Natural Sciences, the NSF BioXFEL Science and Technology Center and the Rigaku Corp. Who: Scientists, students and the public. What: “International Year of Crystallography: Structure Matters.” When: Friday, Feb. 14, from 9 a.m. to 5 p.m. Where: Rice’s BioScience Research Collaborative, 6500 Main St. An agenda and registration information are available at the symposium website, http://gcc.rice.edu/2014_Crystallography_Symposium.aspx - See more at: http://news.rice.edu/2014/02/10/rice-symposium-to-celebrate-100-years-of-cr… George N. Phillips, Jr. Ralph and Dorothy Looney Professor Department of Biochemistry and Cell Biology Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 http://www.bioc.rice.edu/

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mmCIF output _atom_site.B_iso_or_equiv
by Dan McNamara 12 Feb '14

12 Feb '14

Hi all, I have a structure with 96 chains in the ASU and mmCIF format is required for using the RCSB PDB software tools with two-letter chain IDs. That's all fine, but when I use the argument "output.write_model_cif_file=True" with my refinement run, the B-factors reported in the .cif output are not consistent with those in the .pdb output from phenix.refine. Trying to deposit the mmCIF output with U=0.00008 flags their returned final .PDB copy as 0.00. Is there functionality for having the isotropic B-factor equivalent recorded for mmCIF format output? I have not found a way to parameterize phenix.pdbtools so that the mmCIF output has the B-factor the PDB is looking for, and all the information desired from the phenix.refine mmCIF output. I can use "convert to isotropic" and output as mmCIF, but then the ANISOU information from TLS refinement is not retained. Best, Dan

2 1

Phenix refine selection within distance
by Andrew Waight 12 Feb '14

12 Feb '14

Hello All, I am trying select a subsection of my molecule only to run TLS refinement on. I want to select all residues within a certain distance from a given chain. I am using the selection editor within the Phenix interface and can't seem to figure out if Phenix provides this functionality in the view/pick selection editor. The Phenix.refine manual describes some "smart" selections, but they don't seem to work in the selection box. I have tried many variations of. within(5, chain 'H') To no avail. Is this possible to do in the selection editor? Thanks for your help. Andrew Waight

2 1

2014 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 12 Feb '14

12 Feb '14

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

1 0

assign multiple ligand conformations
by Wei Shi 12 Feb '14

12 Feb '14

Hi everyone, I am working with protein-ligand complex structure. For the head group in one of the ligands in the structure, two more positions in addition to the current position look possible according to the blue density in Coot. I am thinking of assigning multiple occupancies/positions to this head group. So, I am wondering what I should do to achieve this. Is the following strategy right? 1. Fit the head group to the density at three different positions separately in Coot and save them separately. 2. Find out the atoms that are different among the three ligand positions and combine the same atoms with different positions and change the occupancy of those atoms to something between 0 to 1. 3. Use Phenix. refine to refine. The occupancy refinement should be automatically on, right? Is this the best way to assign multiple occupancies/positions to the head group? Thank you so much! Also, anything to look after refinement which can tell me whether I am assigning the right multiple conformations to the ligand? Thank you so much! Best, Wei

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metal ions in phenix.ensemble_refinement
by Scott Horowitz 11 Feb '14

11 Feb '14

Hi, I'm trying to use phenix.ensemble_refinement, and my structure has several zinc atoms, both coordinated to amino acids and free imidazoles, and sometimes both. It looks as though it's not really understanding that the zincs really should stay more or less in their coordination spots, and are spending some time in kind of weird spots. I couldn't find anything documented that seems like it will help, unless there's some clever way to use the harmonic restraints for this that I haven't figured out. And while I'm at it, I have another potentially related problem: the rfree of my final ensemble (0.27) is substantially higher than my input structure (0.24). And yes, I had been doing my refinement in phenix, with hydrogens added, and I optimized pTLS. If you're curious, this is a 1.9 A structure. Any help and/or suggestions would be greatly appreciated! Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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exporting results, reduce
by jp d 11 Feb '14

11 Feb '14

hi, we have a large complex at low resolution (7A) and just want to see general conformational changes. Occasionally phenix gets stuck at 'Exporting Results' and top shows 'reduce' running and using lots of RAM . so much RAM that it starts using swap. is there a way to bypass or limit the reduce step. thanks jpd

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ACA2014 Albuquerque
by Peter Zwart 11 Feb '14

11 Feb '14

Dear All, This May 24 to 28, the ACA meeting in Albuquerque will be host to an exciting scientific program. There will be workshops covering (Grazing Incidence) Small Angle Scattering, Joined X-ray/Neutron Crystallographic Refinement and the visualization of diffraction data. The Transactions sessions will celebrate the impressive legacy of the first 100 years of Crystallography.The scientific sessions will feature the latest developments in crystallography and scattering methods and is host to host an impressive list of speakers, such as John Helliwell (Patterson Award),Wayne Hendrickson, Axel Brunger, Richard Neutze and Borden Lacy (Etter Early Career award). We are still accepting the submission of abstracts and we encourage you to do so as quickly as possible: (most of) the session leaders have not finalized their session program yet, so there still is an opportunity to get selected to give a talk. Regards Christine Beavers & Peter Zwart

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Running Phenix on a small cluster
by Mads Beich-Frandsen 10 Feb '14

10 Feb '14

Dear all, We have a small cluster running Ubuntu, using the Condor distribution package. –Does anyone have experience in setting up Phenix to run in such an environment? Thanks in advance, /Mads ******************************** Mads Beich-Frandsen, PhD Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain Tel: +34-9340-37188 | Fax: +34-9340-39960 E-mail: mads.beichfrandsen(a)irbbarcelona.org

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RNA sugar pucker
by Benoît Masquida 08 Feb '14

08 Feb '14

Hello everyone, Does someone know how to define the sugar pucker in eLBOW? I am trying to force a C3' endo conformation for GDP. Thanks for your help. 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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Meeting Announcement: Northwest Crystallography Workshop
by Dale Tronrud 08 Feb '14

08 Feb '14

(Pacific) Northwest Crystallography Workshop http://oregonstate.edu/conferences/event/nwcw2014/ June 20-22, 2014 Registration is now open for this year's edition of the Northwest Crystallography Workshop. It is being hosted at Oregon State University in Corvallis in the heart of the Willamette Valley surrounded by wine country, wildlife refuges, and with both the Cascade Mountains and the Pacific Ocean within easy driving distance. It can be easily accessed from either the Portland or Eugene airports. This biennial meeting has been held at various locations in the Pacific Northwest since 1981. It has always proven to be a great venue to meet other researchers in the region who are interested both in using macromolecular crystallography to solve structures and in developing and enhancing methods. The "workshop" part of the name will be taken seriously. We will have talks and posters with priority for speaking slots given to students and post-docs who focus on methodologies or interesting structure determination stories, and/or how structural observations provide insight into function and biology. There will be a reception on Friday evening. On Saturday there will be talks during the day and a banquet followed by a keynote address in the evening. Talks will continue on Sunday morning with the workshop wrapping-up at noon. A light lunch will be served on Saturday and a boxed lunch will be available on Sunday. Register today and get your abstracts submitted anytime between now and the April 30 abstract deadline. We've tried to keep registration costs low and early registration (through April 30) is $75 for students and $100 for others. Reasonably priced on-campus dormitory housing is available and must be arranged at the time of registration. Special rates at two local hotels have been arranged for those who want to book their own lodgings. We look forward to a great meeting and celebration of the International Year of Crystallography. Dale and Andy Dale E. Tronrud and P. Andrew Karplus Department of Biochemistry & Biophysics 2011 ALS Bldg Oregon State University Corvallis, OR 97331 USA

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how to remove hydrogen from pdb
by Afshan Begum 08 Feb '14

08 Feb '14

Dear Experts, Could you kindly tell me how can i remove hydrogen from my coordinate. Actually i refine my structure with phenix along all hydrogen now its almost done but before submitting the molecule into PDB data bank i want to remove hydrogen from the coordinate which i do not know how to do, suggestion would be appreciated Best Regards AFSHAN =========================================== Dr. Afshan Begum

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weight_selection_criteria
by Mark A Saper 07 Feb '14

07 Feb '14

Can anyone explain what the weight_selection_criteria parameters (see below)? How do they interact with other weights. Are they still used if I set optimize_xyz_weight=TRUE? I'm using dev-1616. target_weights optimize_xyz_weight= False optimize_adp_weight= False wxc_scale= 0.5 wxu_scale= 1.0 wc= 1.0 wu= 1.0 fix_wxc= None fix_wxu= None shake_sites= True shake_adp= 10.0 regularize_ncycles= 50 verbose= 1 wnc_scale= 0.5 wnu_scale= 1.0 rmsd_cutoff_for_gradient_filtering= 3.0 force_optimize_weights= False weight_selection_criteria bonds_rmsd= None angles_rmsd= None r_free_minus_r_work= None r_free_range_width= None mean_diff_b_iso_bonded_fraction= None min_diff_b_iso_bonded= None Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan c/o Biophysics, Chem 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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