March 2014 - phenixbb - phenix-online.org

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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