- phenixbb - phenix-online.org

Phenix refine - R free does not decrease
by Almudena Ponce Salvatierra 05 Feb '15

05 Feb '15

Dear all, I am refining my structure (data at 3 A), with a model that is complete. However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read "Improved target weight optimization in phenix.refine" (In the computational crystallographic newsletter 2011) and what I understand is that just by marking the boxes "improve xray/stereochemistry weight" and "improve xray/adp weight" it should work... giving me the best possible Rfree. I'm refining individual coordinates, occupancies, b-factors (isotropic for all atoms), TLS, and using secondary structure restraints, automatic ligand linking and experimental phases restraints. Also, I chose this strategy because I have finished building the structure and according to some of the suggestions in "towards automated crystallographic structure refinement with phenix.refine". I am actually quite confused and don't know what to think... is it a matter of the weights? is it only that this is as good as it gets? Any suggestions and comments are welcome. Thanks a lot in advance, Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Strange behaviour of phenix.maps fill_missing_f_obs
by Tristan Croll 05 Feb '15

05 Feb '15

Hi, I'm working on a package that makes scripted calls to phenix.refine to generate a series of ccp4 formatted maps, and have run into an odd problem. Using the attached parameter file I get a series of perfectly normal-looking maps, except in the case of the filled 2mFo-DFc map (test-3_2mFo-DFc_fill.ccp4 - the second-last map generated). This comes out as a series of disconnected blobs (it looks rather like a mFo-DFc map, but it doesn't match the actual mFo-DFc map). When I take the resulting .mtz file and generate the filled map in Coot (with or without omission of Rfree flags), on the other hand, it seems to come out fine. There are no error messages in the log, but I suspect the default method to fill in the missing F_obs may be returning only the missing F_obs? I've attached a small example image. Red wireframe is the 2mFo-DFc unfilled map at 1 sigma; green translucent is the 2mFo-DFc filled map at 1 sigma; yellow is the mFo-DFc map at 2 sigma. The test structure I'm using is nothing special: 3WSY, picked more-or-less at random off the protein data bank. Phenix version is 1.9.1692, installed in Fedora 21. Have I done something wrong that I'm just not seeing, or is there a bug here? Thanks, Tristan

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off-topic: Faculty position at all levels in structural biology at Stony Brook University, New York
by Markus Seeliger 05 Feb '15

05 Feb '15

We are recruiting for the above position. More details and the application can be found at https://academicjobsonline.org/ajo/jobs/5289 Stony Brook University Department of Pharmacological Sciences *Tenure-Track Structural Biology / Imaging Faculty Position in Conjunction with the Interdisciplinary Biomolecular Imaging Cluster Hiring Initiative* The Department of Pharmacological Sciences ( http://www.pharm.stonybrook.edu/faculty_research/overview) at Stony Brook University seeks applications for a tenure-track faculty position at the level of Assistant, Associate, or Full Professor. Candidates must have an M.D. and/or Ph.D., at least two years of postgraduate research experience, and an outstanding record of research accomplishment. This search is intended to recruit investigators with translational research programs that make use of *NMR, Cryo-EM, or positron emission tomography (PET) coupled with radiotracer synthesis approaches* to pursue fundamental questions relevant to health-connected fields such as cancer, neuroscience, metabolism, and infectious disease. Senior candidates should also have a record of success with extramural funding and training of students and/or fellows. Applicants must be eligible for a faculty appointment in accordance with the criteria established by the School of Medicine (Criteria for Appointment, Promotion and Tenure.) The Department has pre-doctoral and MSTP training grants, a broad infrastructure for research investigation, and newly renovated lab space housing structural biologists with expertise in NMR and x-ray crystallography. Additional structural biologists and PET imagers are found in the Departments of Biochemistry, Physiology, Chemistry, and Microbiology. With the on-going NYSUNY 2020 Challenge Grant awarded to the University and the recent and largest gift ever to public higher education in the State of New York, Stony Brook University is embarking on a transformational expansion of the biomedical research enterprise. Diverse opportunities for collaborative research on campus include the Cancer Center, the Laufer Center for Physical and Quantitative Biology, the Center for Structural Biology, the Institute for Chemical Biology and Drug Discovery, and the interactive Computer Science and Applied Mathematics Departments. Imaging biological molecules is key to understanding their function, providing a starting point for rational drug design and protein engineering. Stony Brook University is becoming a leader in biomolecular imaging through its newly-upgraded high-field NMR facilities including Bruker 700MHz and 850 MHz instruments with cryogenic probes, a strong program in computational structural and physical biology, world-class computational resources, facilities for radiotracer synthesis and human imaging, and proximity to the new third-generation synchrotron facility at Brookhaven National Lab (NSLS-II). The Biomolecular Imaging Cluster has already recruited junior faculty with expertise in super-resolution microscopy and x-ray crystallography. Stony Brook University, home to many highly-ranked graduate research programs, is located 60 miles from New York City on Long Island's scenic North Shore. Our 1,100-acre campus has more than 24,000 undergraduate, graduate, and doctoral students and 13,500 faculty and staff. The University is a member of the prestigious Association of American Universities and co-manager of the nearby Brookhaven National Laboratory, a multidisciplinary research laboratory supporting world-class scientific programs utilizing state-of-the-art facilities. Stony Brook University is also located close to the Cold Spring Harbor Laboratory with which it interacts through graduate program training and faculty collaborations. To apply, use Academic Jobs Online ( https://academicjobsonline.org/ajo/jobs/5289) to submit a State employment application, a complete curriculum vitae including publications, and a 3-page proposed research plan of current and future research, and have three letters of recommendation submitted through the AJO site. The cover letter should indicate whether the applicant wishes to be considered for appointment at the Assistant, Associate, or Full Professor level. Applicants at the Associate or Full Professor level should add a summary of past and current research funding and administrative and teaching experiences. Electronic submission through AJO is required. Questions should be addressed to Ms. Lynda Perdomo-Ayala, Department Administrator ( lynda.perdomo-ayala(a)stonybrook.edu). 631-444-3050 For a full position description, visit www.stonybrook.edu/jobs (Ref. F-9387/14/12.) Stony Brook University is an Affirmative Action, Equal Opportunity Educator and Employer.

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generating xplor map of specific size
by Scott Horowitz 03 Feb '15

03 Feb '15

Hi all, Sorry for yet another map question: what I'd like to do is be able to generate xplor maps with an explicitly defined size and shape from the command line using phenix. Just choosing a buffer around a selection will result in slightly different sizes for different PDB files, which I'd like to avoid. In my comparisons, having exactly the same dimensions and centering for maps I'm calculating from multiple slightly different variants would be very helpful. Is there a way to do this? 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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serial MR / refinement
by Eike Schulz 03 Feb '15

03 Feb '15

Dear all, I am looking for a way to automate molecular replacement and refinement runs. >From ligand / fragment screening trials we have many datasets of the same protein with various resolutions (2.8 – 1.2Å). The apo-structure is known and well refined. The cell constants are fairly similar but not in all cases identical, hence I would prefer a MR run prior to the refinement. I am sure this can somehow be realized with some shell-script but maybe there is some more sophisticated way of realising this? I would also be happy for partial solutions to the problem. Best regards Eike

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Young scientist travel awards for Intl Conf. on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology"
by Terwilliger, Thomas Charles 02 Feb '15

02 Feb '15

2-Feb-2015 Dear Colleagues, We are pleased to announce the availability of young scientist travel fellowships to the International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology", which will be held on the campus of the Weizmann Institute of Science in Rehovot, Israel June 7-11, 2015. This conference is intended to foster international collaboration and to provide an overview for the most recent developments in Structural Biology and Structural Genomics and future impacts on biology, medicine and disease. Web site: http://www.weizmann.ac.il/conferences/ICSG2015 Poster: https://www.dropbox.com/s/i1s3hsg7a0chqi2/ICSG2015_Poster.pdf?dl=0 There are two types of young scientist travel support available (deadlines are both March 31, 2015): Young scientist travel support of up to $1,000 US will be made available to graduate students and post-doctoral researchers to attend ICSG2015. A total of 5 International Structural Genomics Organization (ISGO) - NIH Protein Structure Initiative (PSI) Student Travel Fellowships have kindly been provided by the ISGO and the NIH PSI. Fellowships of €500 for students from Instruct countries will be awarded to attend the pre-conference workshop “Technical and Analytical Approaches to the Translation of Deep Sequencing Data into Three-Dimensions” (7-June-2014 09:00-12:00) and to stay on and participate in the full conference. A total of 8 Fellowships have kindly been provided by Instruct (https://www.structuralbiology.eu). To apply for a student travel fellowship please see http://www.weizmann.ac.il/conferences/ICSG2015/young-scientists-travel-supp… . The International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology” conference The scientific topics to be covered in ICSG 2015 (see http://www.weizmann.ac.il/conferences/ICSG2015) include: · Deep sequencing for modeling and refinement of macromolecular structures · Membrane protein structure and function using complementary methods · Technological advances in XFEL, Cryo-EM, NMR, SAXS, MS, MX and macromolecular complexes · Combining low and high resolution data and modeling for structural biology · Synergistic use of 3D structures and deep sequencing to realize personalized medicine · Protein design and deep sequencing · Cancer, antibiotic resistance and drug discovery In order to widen the opportunities for younger researchers, we have organized satellite workshops before ICSG 2015 (during the day on June 7, 2015). These include: · Cryo-EM developments for structural biology [Sponsored by FEI] · Approaches to the translation of deep sequencing data into three-dimensions [Sponsored by Instruct] · PHENIX: Automated determination of molecular structures [Tom Terwilliger & Pavel Afonine] · HKL3000: From X-ray diffraction images to structure determination in minutes [Wladek Minor] · Protein expression and characterization workshop [Tamar Unger & Yoav Peleg] · Proteopedia: A Scientific Wiki Bridging the Rift Between 3D Structure & Function [Jaime Prilusky & Joel L. Sussman] Five oral presentations will be chosen from the posters, and six poster prizes will be awarded, so be sure to submit your abstracts by April 15, 2015! Speakers include: Arie Admon (Haifa) Lucia Banci (Florence) Pamela J. Bjorkman (Pasadena) Samir K. Brahmachari (Delhi) Susan Buchanan (Bethesda) Martin Caffrey (Dublin) Mark Gerstein (New Haven) Wayne Hendrickson (New York) Yvonne Jones (Oxford) Roger Kornberg (Stanford) Luhua Lai (Beijing) Michael Levitt (Stanford) Michal Linial (Jerusalem) Abraham Minsky (Rehovot) John Moult (Rockville) Nathan Nelson (Tel Aviv) Stefan Raunser (Dortmund) Monica Roth (Piscataway) Dinakar M. Salunke (Gurgaon) Eran Segal (Rehovot) Philip Selenko (Berlin) Sachdev Sidhu (Toronto) Rotem Sorek (Rehovot) Jan Steyaert (Brussels) Shamil Sunyaev (Boston) Dan Tawfik (Rehovot) Janet Thornton (Hinxton) The FEBS National Lecturer Gunnar von Heijne (Stockholm) Soichi Wakatsuki (Stanford) Shigeyuki Yokoyama (Yokohama) Ada Yonath (Rehovot) Mingjie Zhang (Hong Kong) We are looking forward to welcoming you to the Weizmann Institute in the June of 2015! Sincerely yours, ICSG 2015 Local Organizing Committee Joel L. Sussman, Gideon Schreiber, Tamar Unger and Israel Silman, Weizmann Institute ICSG 2015 International Organizing Committee Cheryl Arrowsmith, (Structural Genomics Consortium, Toronto) Lucia Banci, (University of Florence, Florence) Jacqui Beckmann, (Swiss Institute of Bioinformatics, Lausanne) Mark Gerstein, (Yale University, New Haven) Yvonne Jones, (University of Oxford, Oxford) ------------------------------------------------------------------------- Prof. Joel L. Sussman www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel> Department of Structural Biology tel: +972 (8) 934 4531 www.weizmann.ac.il/ISPC<http://www.weizmann.ac.il/ISPC> Weizmann Institute of Science fax: +972 (8) 934 6312 www.proteopedia.org<http://www.proteopedia.org> Rehovot 76100 ISRAEL www.weizmann.ac.il/conferences/ICSG2015<http://www.weizmann.ac.il/conferences/ICSG2015> -------------------------------------------------------------------------

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Output file of the Phenix refine
by Smith Liu 01 Feb '15

01 Feb '15

Dear All, Will you please tell me which Phenix refine output file contains the information on my input files, my strategies and my parameters for the refinement? Smith

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Question related to Phenix refinement
by Smith Lee 01 Feb '15

01 Feb '15

Dear All, Which strategy or parameter input can be used to reduce the rotamer outliers? Which strategy or parameter input can be used to reduce the bond outliers? For all the Phenix refine strategies, can you sequence it from rough refinement to fine refinement in order? I am looking forward to getting your reply. Smith

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Rwork and Rfree
by Dialing Pretty 31 Jan '15

31 Jan '15

Dear All, After a Phenix refinement (for crystal 2.5A), my Rwork is about 0.19, and my Rfree is about 0.26. Is the gap between Rwork and Rfree too karge? If too large, why it is too large and how to avoid it? I am looking forward to getting your reply. Dialing

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Re: [phenixbb] making coarse maps
by Terwilliger, Thomas Charles 30 Jan '15

30 Jan '15

Hi Scott, You can use the reflection file converter in the GUI to write out map coefficients with any resolution cutoff that you like. That may be the easiest. Alternatively you can take your refined model and use phenix.maps to calculate a map at any resolution that you like without further refinement. You might also consider just adjusting the sharpening on your map which will have something of the same effect as cutting the resolution. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Scott Horowitz [horowsah(a)umich.edu] Sent: Friday, January 30, 2015 6:09 AM To: PHENIX user mailing list Subject: [phenixbb] making course maps Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? 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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