- phenixbb - phenix-online.org

Call for targets (not-yet-released structures) for CASP13 modelling experiment
by Randy Read 29 Jun '18

29 Jun '18

Posted on behalf of the CASP organizing committee: **** NB: There are only two weeks left to collect new targets for CASP13, so your contributions would be very gratefully received! **** Request for protein structures to test modeling methods - CASP13 CASP community experiments aim to establish and advance the state of the art in protein structure modeling. To this end, CASP collects information on soon-to-be released experimental structures for a three month season every two years. Sequences and other information on these targets is distributed to the protein modeling community, and the resulting models assessed by independent experts in the field. Results are published in special issues of the journal PROTEINS (see all about CASP12 at https://onlinelibrary.wiley.com/toc/10970134/86/S1). About 100 modeling groups from around the world take part. The success of CASP depends completely on the generosity of the experimental community in providing modeling targets. We are now requesting targets for the CASP13 experiment, which will launch at the beginning of May. So, if you have anything suitable, we would be most grateful if you would go to the target entry page: http://www.predictioncenter.org/casp13/targets_submission.cgi The CASP community needs modeling targets over a wide range of difficulty, for modeling with and without the aid of templates. We are particularly interested in membrane proteins, protein complexes, and cryo-EM structures. We are also extending CASP to include more modeling assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, chemical crosslinking, and FRET. For that, protein material is needed (of course this is not expected for most targets, but if its available, it would be much appreciated!). For those of you who have not provided targets to CASP before, the procedure is simple – there is a web page for submitting targets, and an experienced staff to deal with any queries. We don’t need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. More details are available on the web site. Thanks, CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel, Switzerland ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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validating ~100 structures
by CPMAS Chen 27 Jun '18

27 Jun '18

Hi, All, I have about 100 structures needs be validated and optimized. what will be a fast way to do so? Can I somehow put phenix.molprobity in a circle? Thanks! -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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phenix.real_space_refine - Removing rotamer restraints on a per residue basis
by Ashley Pike 26 Jun '18

26 Jun '18

Hi, Is it possible to exclude particular residues from the effects of global restraints in phenix.real_space_refine? In my case rotamer restraints mucks up the sidechain fit to density for certain Phe and Tyr?. Thanks, Ashley

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Software Engineer position to work with Phaser team in Cambridge
by Randy Read 21 Jun '18

21 Jun '18

We've just advertised a position for a Software Engineer to work with us on the development of Phaser. Detailed information on the position and how to apply can be found on the University of Cambridge website (http://www.jobs.cam.ac.uk/job/17918/) and on jobs.ac.uk (http://www.jobs.ac.uk/job/BKS034/software-engineer). The text of the job description is appended, if you'd like to look at that before clicking on one of the links! Best wishes, Randy Read ================= We are looking for a graduate Software Engineer to join the group of Prof Read in the Cambridge Institute for Medical Research (http://www.cimr.cam.ac.uk/), based at the Cambridge Biomedical Campus in Cambridge. The well-established project develops mathematical methods and software for the imaging of biological molecules. The software supports academic and pharmaceutical R&D worldwide. You will be joining a small expert academic team. The successful applicant will have a careful approach to software development. Your software will be required to be reliable, algorithmically fast, and memory efficient. We have a slow development cycle and the code you write will be in use for the foreseeable future. Your individual contribution will be recognised with authorship of peer-reviewed articles; publications from our group have a track record of being highly cited. The project is funded by the National Institute of Health (USA) and the successful applicant will have the opportunity to join bi-annual collaborative meetings that cycle among Lawrence Berkeley National Laboratory (Berkeley, California), Duke University (Durham, North Carolina) and the New Mexico Consortium (Santa Fe, New Mexico). We also have an active collaboration with IBMB- CSIC (Barcelona, Spain). Software is open source (https://git.uis.cam.ac.uk/x/cimr-phaser/phaser.git/summary). We use the C++0x/C++11 standard to maintain cross-platform compilation and compatibility. You will have access to the University of Cambridge's computing resources, and a laptop will be provided. Qualifications and Experience: University degree that includes computer science and/or mathematics, experience with C++ and the Linux OS. Skills in Python scripting, GPU programming and threading would be desirable. Knowledge of biology to A level standard or equivalent would be an advantage. This appointment is full-time (37 hours/week Monday to Friday) but we welcome applications from individuals who wish to be considered for part-time working or other flexible working arrangements. Royalty payments from software will extend beyond the lifetime of the contract. University of Cambridge employment benefits include USS pension, and reduced staff fees for University of Cambridge graduate courses (see http://www.jobs.cam.ac.uk/offer/ for a full list). For more information on the research group see https://www.cimr.cam.ac.uk/research/principal-investigators/principal-inves…, and details of the Phaser project can be found at http://www.phaser.cimr.cam.ac.uk/. Fixed-term: The funds for this post are available untill 30th April 2022. ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Postdoctoral position in membrane protein structure and function at the NIH
by Anirban Banerjee 20 Jun '18

20 Jun '18

There is an open postdoctoral position for a membrane protein structure-function project in my lab at the NIH. We are currently focusing on integral membrane enzymes (Science. 2018, doi: 10.1126/science.aao6326) and transporters of transition metal ions (J Biol Chem. 2018, doi: 10.1074/jbc.M117.817478). Here is the formal announcement - EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA Position Description: The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography and cryo EM with biophysical and biochemical methods such as reconstitution based assays, high resolution light microscopy and small molecule screening to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). We also have an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). Qualifications: The candidates should hold a Ph. D. degree, be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or mammalian expression system for protein purification will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. To Apply: Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. The NIH is dedicated to building a diverse community in its training and employment programs.

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Chair of the Department of Molecular Microbiology and Immunology at Univ. of Missouri
by Tanner, John J. 18 Jun '18

18 Jun '18

The Department of Molecular Microbiology and Immunology at the University of Missouri is searching for a new Chair. Please see the links below for information about the department and the position. I would be happy to discuss this opportunity offline with interested people. https://medicine.missouri.edu/departments/molecular-microbiology-immunology https://medicine.missouri.edu/sites/default/files/MMI_Chair_Advertisement-A… John J. Tanner Professor of Biochemistry and Chemistry Interim Chair of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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Table 1 successor in 3D?
by Gerard Bricogne 13 Jun '18

13 Jun '18

Dear phenixbb subscribers, I sent the message below to the CCP4BB and phenixbb at the same time last Friday. It went straight through to the CCP4BB subscribers but was caught by the phenixbb Mailman because its size exceeded 40K. Nigel, as moderator of this list, did his best to rescue it, but all his attempts failed. He therefore asked me to resubmit it, now that he has increased the upper size limit. Apologies to those of you who are also CCP4BB subscribers, who will already have received this message and the follow-up discussion it has given rise to. With best wishes, Gerard. ----- Forwarded message from Gerard Bricogne <gb10> ----- Date: Fri, 1 Jun 2018 17:30:48 +0100 From: Gerard Bricogne <gb10> Subject: Table 1 successor in 3D? To: CCP4BB(a)JISCMAIL.AC.UK, phenixbb(a)phenix-online.org Dear all, Bernhard Rupp has just published a "Perspective" article in Structure, accessible in electronic form at https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 in which part of his general argument revolves around an example (given as Figure 1) that he produced by means of the STARANISO server at http://staraniso.globalphasing.org/ . The complete results of his submission to the server have been saved and may be accessed at http://staraniso.globalphasing.org/Gallery/Perspective01.html and it is to these results that I would like to add some annotations and comments. To help with this, I invite the reader to connect to this URL, type "+" a couple of times to make the dots bigger, and press/toggle "h" whenever detailed information on the display, or selection of some elements, or the thresholds used for colour coding the displays, needs to be consulted. The main comment is that the WebGL interactive 3D display does give information that makes visible characteristics that could hardly be inferred from the very condensed information given in Table 1, and the annotations will be in the form of a walk through the main elements of this display. For instance the left-most graphical object (a static view of which is attached as "Redundancy.png") shows the 3D distribution of the redundancy (or multiplicity) of measurements. The view chosen for the attached picture shows a strong non-uniformity in this redundancy, with the region dominated by cyan/magenta/white having about twice the redundancy (in the 6/7/8 range) of that which prevails in the region dominated by green/yellow (in the 3/5 range). Clear concentric gashes in both regions, with decreased redundancy, show the effects of the inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline. The blue spherical cap along the a* axis corresponds to HKLs for which no measurement is available: it is clearly created by the detector being too far from the crystal. The second (central) graphical object, of which a view is given in Figure 1 of Bernhard's article and another in the attached picture "Local_I_over_sigI.png") shows vividly the blue cap of measurements that were missed but would probably have been significant (had they been measured) cutting into the green region, where the local average of I/sig(I) ranges between 16 and 29! If the detector had been placed closer, significant data extending to perhaps 3.0A resolution would arguably have been measured from this sample. The right-most graphical object (of which a static view is attached as "Debye-Waller.png") depicts the distribution of the anisotropic Debye-Waller factor (an anisotropic generalisation of the Wilson B) of the dataset, giving yet another visual hint that good data were truncated by the edges of a detector placed too far. Apologies for such a long "STARANISO 101" tutorial but Bernhard's invitation to lift our eyes from the terse numbers in Table 1 towards 3D illustrations of data quality criteria was irresistible ;-) . His viewpoint also agrees with one of the main purposes of our STARANISO developments (beyond the analysis and remediation of anisotropy, about which one can - and probably will - argue endlessly) namely contribute to facilitating a more direct and vivid perception by users of the quality of their data (or lack of it) and to nurturing evidence-based motivation to make whatever extra effort it takes to improve that quality. In this case, the undeniable evidence of non-uniformity of redundancy and of a detector placed too far would give immediate practical guidance towards doing a better experiment, while statistics in Table 1 for the same dataset would probably not ... . Thank you Bernhard! With best wishes, Gerard, for and on behalf of the STARANISO developers ----- End forwarded message -----

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Coupling ligand occupancy with helix displacement
by John Michael Bruning 12 Jun '18

12 Jun '18

Hi, I have a very flexible covalent adduct that adopts three alternative conformations (A,B,C) in my structure . Conformations A and C are solvent exposed, while conformation B is buried. The buried conformation B displaces a regulatory helix (resseq 589:598) by a few angstrom, while the solvent exposed conformations do not displace this helix. I can't seem to write a occupancy .params file that fulfills: 1.) occ. of ligand conformation B = occ. of displaced helix conformation # coupling of ligand binding with helix displacement 2.) occ. non-displaced helix conformation = (1 - occ. displaced helix conformation) 3.) sum occ. ligand conformations A+B+C = 1 # assuming protein was initially labeled 100% It seems like #7 from http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 is my situation, but I can't quite seem to modify this for my case. For example, something like: constrained_group { selection = chain A and resname CPE and altid B or chain A and resseq 589:598 and altid B} Captures the concerted conformation aspect (1) (occupancy for ligand conformation B = occupancy for displaced helix) and the sum occupancy of the displaced and non-displaced helix = 1 (2), but the sum of the the alternative conformations A+B+C > 1.0 (w/ A+C = 1.0) (3) Incidentally, my resolution is 2.4 Ang. Thanks for any help! Cheers, John Cheers, John *********************************** John Bruning, Post-Doctoral Scholar Stanford University, Glenn Lab CCSR Building, #3110 ***********************************

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CSHL X-ray Methods in Structural Biology Course Oct 15-30th 2018: Application deadline June 15th
by Paul Adams 05 Jun '18

05 Jun '18

Dear Colleagues, The June 15th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 15 through October 30 2018, is rapidly approaching. This is a unique opportunity to become expert in the use of X-ray crystallography to solve challenging macromolecular structures. The official course announcement can be found here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=18 please pass this on to people who might be interested and who would benefit, including your students and postdocs. This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography, and consists of extensive lectures and practical sessions from experts in the field. The instructor team is: Alex McPherson, Bill Furey, Jim Pflugrath, Tassos Perrakis, and myself. We are assisted by world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation (see the course link above for more details). The goal of the course is for researchers who have had some exposure to X-ray crystallography to become experts. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. We expect participants to crystallize one or more proteins and determine their structures in a two week period. Students may also work on their own projects, but not exclusively. They will become very well-versed in the theory of X-ray diffraction and crystal structure determination, while also having lots of fun. Both synchrotron data collection and in-house diffraction data collection will be used to solve structures. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar and laboratory settings. Please check the above web link for more details. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. The course is supported with funds provided by the National Institute of General Medical Sciences, for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. If anyone has any questions, please send me an e-mail, we will be happy to answer all queries. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Fwd: phenixbb post from [email protected]
by Nigel Moriarty 05 Jun '18

05 Jun '18

Folks There was a post from Gerard Bricogne that was lost (as far as I can see) in the internals of MailMan because of a 40Kb size limit and other reasons unknown. It was posted to the CCP4BB so you may have already seen it. Please find it below. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov Subject: Table 1 successor in 3D? Dear all, Bernhard Rupp has just published a "Perspective" article in Structure, accessible in electronic form at https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 in which part of his general argument revolves around an example (given as Figure 1) that he produced by means of the STARANISO server at http://staraniso.globalphasing.org/ . The complete results of his submission to the server have been saved and may be accessed at http://staraniso.globalphasing.org/Gallery/Perspective01.html and it is to these results that I would like to add some annotations and comments. To help with this, I invite the reader to connect to this URL, type "+" a couple of times to make the dots bigger, and press/toggle "h" whenever detailed information on the display, or selection of some elements, or the thresholds used for colour coding the displays, needs to be consulted. The main comment is that the WebGL interactive 3D display does give information that makes visible characteristics that could hardly be inferred from the very condensed information given in Table 1, and the annotations will be in the form of a walk through the main elements of this display. For instance the left-most graphical object (a static view of which is attached as "Redundancy.png") shows the 3D distribution of the redundancy (or multiplicity) of measurements. The view chosen for the attached picture shows a strong non-uniformity in this redundancy, with the region dominated by cyan/magenta/white having about twice the redundancy (in the 6/7/8 range) of that which prevails in the region dominated by green/yellow (in the 3/5 range). Clear concentric gashes in both regions, with decreased redundancy, show the effects of the inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline. The blue spherical cap along the a* axis corresponds to HKLs for which no measurement is available: it is clearly created by the detector being too far from the crystal. The second (central) graphical object, of which a view is given in Figure 1 of Bernhard's article and another in the attached picture "Local_I_over_sigI.png") shows vividly the blue cap of measurements that were missed but would probably have been significant (had they been measured) cutting into the green region, where the local average of I/sig(I) ranges between 16 and 29! If the detector had been placed closer, significant data extending to perhaps 3.0A resolution would arguably have been measured from this sample. The right-most graphical object (of which a static view is attached as "Debye-Waller.png") depicts the distribution of the anisotropic Debye-Waller factor (an anisotropic generalisation of the Wilson B) of the dataset, giving yet another visual hint that good data were truncated by the edges of a detector placed too far. Apologies for such a long "STARANISO 101" tutorial but Bernhard's invitation to lift our eyes from the terse numbers in Table 1 towards 3D illustrations of data quality criteria was irresistible ;-) . His viewpoint also agrees with one of the main purposes of our STARANISO developments (beyond the analysis and remediation of anisotropy, about which one can - and probably will - argue endlessly) namely contribute to facilitating a more direct and vivid perception by users of the quality of their data (or lack of it) and to nurturing evidence-based motivation to make whatever extra effort it takes to improve that quality. In this case, the undeniable evidence of non-uniformity of redundancy and of a detector placed too far would give immediate practical guidance towards doing a better experiment, while statistics in Table 1 for the same dataset would probably not ... . Thank you Bernhard! With best wishes, Gerard, for and on behalf of the STARANISO developers

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d99 beyond Nyquist?
by Ricardo Righetto 03 Jun '18

03 Jun '18

Hi, I've seen the d99 criterion in phenix.mtriage reporting a resolution value beyond Nyquist (=2.0 A), or very close to Nyquist in another case. For these particular maps, which are from the same dataset processed with two different single-particle analysis packages (internal benchmarking), half-map FSC-based methods (including blocres) report resolutions in the range of 3.0-3.5 A which are consistent with the features I can see. How can I interpret this? I understand that d99 starts omitting Fourier samples from the corners of the reciprocal box, but does it make sense to report a value beyond Nyquist? I tried supplying unfiltered, masked and unmasked versions of the maps with barely any variation in the d99 results. Thanks in advance for helping figuring this out! Best wishes, -- Ricardo Diogo Righetto

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 02 Jun '18

02 Jun '18

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2018 issue is 22 June 2018. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Table 1 successor in 3D?
by Gerard Bricogne 02 Jun '18

02 Jun '18

Dear all, Bernhard Rupp has just published a "Perspective" article in Structure, accessible in electronic form at https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 in which part of his general argument revolves around an example (given as Figure 1) that he produced by means of the STARANISO server at http://staraniso.globalphasing.org/ . The complete results of his submission to the server have been saved and may be accessed at http://staraniso.globalphasing.org/Gallery/Perspective01.html and it is to these results that I would like to add some annotations and comments. To help with this, I invite the reader to connect to this URL, type "+" a couple of times to make the dots bigger, and press/toggle "h" whenever detailed information on the display, or selection of some elements, or the thresholds used for colour coding the displays, needs to be consulted. The main comment is that the WebGL interactive 3D display does give information that makes visible characteristics that could hardly be inferred from the very condensed information given in Table 1, and the annotations will be in the form of a walk through the main elements of this display. For instance the left-most graphical object (a static view of which is attached as "Redundancy.png") shows the 3D distribution of the redundancy (or multiplicity) of measurements. The view chosen for the attached picture shows a strong non-uniformity in this redundancy, with the region dominated by cyan/magenta/white having about twice the redundancy (in the 6/7/8 range) of that which prevails in the region dominated by green/yellow (in the 3/5 range). Clear concentric gashes in both regions, with decreased redundancy, show the effects of the inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline. The blue spherical cap along the a* axis corresponds to HKLs for which no measurement is available: it is clearly created by the detector being too far from the crystal. The second (central) graphical object, of which a view is given in Figure 1 of Bernhard's article and another in the attached picture "Local_I_over_sigI.png") shows vividly the blue cap of measurements that were missed but would probably have been significant (had they been measured) cutting into the green region, where the local average of I/sig(I) ranges between 16 and 29! If the detector had been placed closer, significant data extending to perhaps 3.0A resolution would arguably have been measured from this sample. The right-most graphical object (of which a static view is attached as "Debye-Waller.png") depicts the distribution of the anisotropic Debye-Waller factor (an anisotropic generalisation of the Wilson B) of the dataset, giving yet another visual hint that good data were truncated by the edges of a detector placed too far. Apologies for such a long "STARANISO 101" tutorial but Bernhard's invitation to lift our eyes from the terse numbers in Table 1 towards 3D illustrations of data quality criteria was irresistible ;-) . His viewpoint also agrees with one of the main purposes of our STARANISO developments (beyond the analysis and remediation of anisotropy, about which one can - and probably will - argue endlessly) namely contribute to facilitating a more direct and vivid perception by users of the quality of their data (or lack of it) and to nurturing evidence-based motivation to make whatever extra effort it takes to improve that quality. In this case, the undeniable evidence of non-uniformity of redundancy and of a detector placed too far would give immediate practical guidance towards doing a better experiment, while statistics in Table 1 for the same dataset would probably not ... . Thank you Bernhard! With best wishes, Gerard, for and on behalf of the STARANISO developers

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Anisotropy with TLS
by Eugene Osipov 31 May '18

31 May '18

Hi, everyone, Can someone shed a light on B-factor refinement in PHENIX.refine. I am refining the structure with 2.5 A resolution, with individual B-factors and automatically defined TLS groups. Despite isotropic refinement of B-factors I still see ANISOU entries for atoms. I figured out that these ANISOU lines appear only after TLS refinement. So the question is how these ANISOU values are calculated? -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osipov(a)gmail.com

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Berkeley Server Downtown (5/29 - 5/31)
by Billy Poon 31 May '18

31 May '18

Dear all, On Tuesday, May 29, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available by 10:00 am Pacific on Thursday (5/31) at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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postdoc crystallographer job offer; International Institute in Warsaw, 15th Jun
by Błażej Bagiński 30 May '18

30 May '18

Dear All, Bujnicki Lab (Laboratory if Bioinformatics and Protein Engineering, located in the International Institute of Molecular and Cell Biology in Warsaw) is looking for an experienced (post-doc level) crystallographer/structural biologist, with an interest in combining various experimental and computational methods for structure determination of RNAs and RNA-protein complexes. Our group is involved in theoretical and experimental research on nucleic acids and proteins. The current focus is on RNA sequence-structure-function relationships (in particular 3D modeling), RNA-protein complexes, and enzymes acting on RNA. The Institute have in-house crystallographic and computing facilities and is located in the Ochota campus, surrounded by Polish Academy of Science's institutes and University of Warsaw's departments of biology/chemistry/physics/medicine/mathematics interests. Please find the full job offer in the attachment, as well as in the link below. The deadline is on 15th of June 2018. http://genesilico.pl/employment/#5 The webpage of our group can be found here; http://genesilico.pl/ as well as more information about the Institute: https://www.iimcb.gov.pl/en/ For more information and questions, please contact this address: Bujnicki, Janusz: iamb(a)genesilico.pl Kind regards, Błażej Bagiński

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d99 resolution measure availability?
by Oliver Clarke 28 May '18

28 May '18

Hi, I think the “d99” criterion described in this preprint (https://www.biorxiv.org/content/early/2018/03/14/279844) looks like a really interesting FSC-independent way to measure res in real space, and I’d like to give it a go on my maps (particularly those where I am suspicious of the FSC-based res based on map appearance, or where I suspect overfitting). Is it available in any phenix package at present? The scripts site mentioned in the preprint (http://phenix-online.org/phenix_data/afonine/cryoem_validation/) is currently rather sparsely populated. (Also, I wonder whether a directional version of the d99 criterion might be useful to estimate anisotropic res in the case of a preferred orientation, analogous to the 3D-FSC approach of Yong-Zi Tan and Dmitry Lyumkis?) Cheers Oli

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rosetta refinement
by Sebastiano Pasqualato 24 May '18

24 May '18

Hi all, it seems that rosetta refinement uses test_flag_value=1 as default. Is there a way to change this? Couldn’t find it in the gui… Thanks s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

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Phenix comes with dials?
by Murpholino Peligro 18 May '18

18 May '18

[murph@localhost ~]$ dials.version DIALS 1.9.3-gb491019a-release Installed in: /home/murph/Bins/dials_stuff/dials-v1-9-3/modules/dials [murph@localhost ~]$ dials.version_1.13-2998 DIALS 1.8.0-gf5b6132-release Installed in: /home/murph/Bins/phenix_stuff/phenix-1.13-2998/modules/dials Why I never saw this on the documentation?

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Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK
by David Barford 15 May '18

15 May '18

Dear colleagues, Please see below an advert for the position of Protein Crystallography Facility Manager at the MRC Laboratory of Molecular Biology. Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laboratory of Molecular Biology (LMB) seeks to appoint a Protein Crystallography Facility Manager. The LMB is one of the birthplaces of structural biology and remains at the forefront of methods development as protein crystallography is a critical technique for understanding the mechanisms of macromolecular complexes, one of the major goals of the LMB. The post-holder will provide support to researchers from all Divisions of the LMB in the collection of X-ray diffraction data using both synchrotrons and in-house X-ray facilities, will maintain and develop the in-house facilities, will provide expert advice and support during subsequent structure determinations, and will act as the coordinator for LMB's synchrotron access. It is expected that there will be the opportunity for collaboration on structural projects with research groups at the LMB. The successful applicant will have several years of post-doctoral experience in the field of protein crystallography including data collection at synchrotrons and all aspects of structure determination. Excellent communication and inter-personal skills are required because the post will involve interacting with a diverse range of scientists with different levels of expertise. Closing date for applications: 11th June 2018 For further details and information on how to apply please visit: https://mrc.tal.net/vx/appcentre-ext/candidate/post/1707/en-GB <https://mrc.tal.net/vx/appcentre-ext/candidate/post/1707/en-GB> Informal enquires should be addressed to Dr. David Barford. E.mail: dbarford(a)mrc-lmb.cam.ac.uk <mailto:[email protected]> Dr. Jan Löwe. E.mail: jyl(a)mrc-lmb.cam.ac.uk <mailto:[email protected]> _______________________________ Dr. David Barford Structural Studies Division MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH, UK. e.mail: dbarford(a)mrc-lmb.cam.ac.uk Tel. +44 (0)1223 267075

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Released: Phenix/DivCon Plugin - DivCon Discovery Suite v7.5.0
by Lance Westerhoff 10 May '18

10 May '18

Hello All- Some of you may have already seen this release, but I wanted to pass it along to the community as well. Today, we release version 7.5.0 of our flagship product: the DivCon Discovery Suite. This release includes fundamental improvements and a complete re-write of several key technologies leading to improved usability and a 14+ fold speedup to our Phenix/DivCon and XModeScore Crystallographic module for protomer/tautomer determination, fragment binding mode determination, and automated QM/MM X-ray refinement (including MOE-independent versions of each of those users who do not have MOE available). This version also includes a completely new tool for crystallographic "water picking" using 3DRISM. For a detailed breakdown of the new features (along with links to tutorials and other documentation), please see the following link: http://www.quantumbioinc.com/news/show/DivCon-7.5.0 As with prior releases, the software available for free for true non-profit/academic research. And of course it is available for industry use for a reasonable license fee. The list of available licenses (for electronic signature) is available here: http://www.quantumbioinc.com/products/software_licensing Thank you for your time and have a great rest of your spring! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909 This message and any attachments are solely for the intended recipient and should be considered confidential. If you are not the intended recipient, please immediately and permanently delete.

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European Crystallography Meeting Oviedo; Neutron Macromolecular Crystallography Satellite Meeting
by John R Helliwell 09 May '18

09 May '18

Dear Colleagues, We draw your attention to the following meeting in Oviedo, Spain in August:- https://ecm31.ecanews.org/en/neutron-macromolecular-crystallography.php Best wishes, John and Matthew Emeritus Professor John R Helliwell DSc; Dr Matthew Blakeley, Institut Laue Langevin.

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Phenix.rosetta build Ubuntu 16.04
by Joseph Brock 08 May '18

08 May '18

Dear phenix community, I am trying to get phenix to run with rosetta on my Ubuntu 16.04 station. I am running the latest official phenix version (phenix-1.13-2998) and and compiled rosetta 3.7 (2016.32.58837) using scons as described: https://www.phenix-online.org/documentation/reference/rosetta_install.html https://www.rosettacommons.org/docs/latest/build_documentation/Build-Docume… Then ran rosetta.build_phenix_interface. All went without error but running rosetta.run_tests then gave the segmentation fault below. Defining variables as suggested did not help. I found a similar question in the phenixbb archives but no resolution: http://www.phenix-online.org/pipermail/phenixbb/2013-October/020274.html Any suggestions on how to move forward greatly appreciated! Cheers, Joseph. _________________________________________________________________________________________________________ Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Traceback (most recent call last): File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module> run(sys.argv[1:], create_dir=True) File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Joseph S. Brock | PhD Researcher Drew Lab Department of Biochemistry and Biophysics Stockholm University

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phenix server down?
by Murpholino Peligro 03 May '18

03 May '18

Is the phenix server down? I cannot access the following links http://www.phenix-online.org/documentation https://www.phenix-online.org/download/phenix/release/ :(

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Introducing ISOLDE
by Tristan Croll 01 May '18

01 May '18

Dear members of the structural biology community, It is with great pleasure that I announce the release of version 1.0b1 of ISOLDE, a new, free for academic/nonprofit use, environment for interactive rebuilding of macromolecular models against low-medium resolution experimental crystallographic or cryo-EM maps. A paper describing ISOLDE is online at http://scripts.iucr.org/cgi-bin/paper?S2059798318002425, and you can also get an overview from my demonstration video at https://www.youtube.com/watch?v=limaUsNAVL8. In brief, though, ISOLDE is designed to help overcome the substantial challenge involved in building high-quality models into “difficult” maps (e.g. those with worse than 3Å resolution) by re imagining the task as one akin to interacting with a real, “living” molecule. At its heart is the use of interactive molecular dynamics: all atoms feel van der Waals and electrostatic interactions with their neighbours as you interact with them, avoiding clashes and constantly settling towards their nearest low-energy state. In addition to this, ISOLDE helps interpret what you're looking at by performing real-time rotamer, Ramachandran and peptide plane validation, flagging up potential problems directly on the model to give you instant feedback on the results of your actions. Specific features: - support for protein, nucleic acid, water and some small molecules/ions (with substantially expanded support to come in later versions) - start an interactive simulation covering anything from a few residues to your entire model (depending on your hardware) at the click of a button - “always-on” validation updates every time coordinates change (results are shown directly as markup on the model itself, and also accessible via more traditional tables/plots) - Interactively apply peptide plane or cis/trans flips and add/remove position, distance, rotamer and secondary structure restraints via a simple graphical interface - Smoothly shift any continuous stretch of backbone forward/backward along the chain to easily recover from register shift errors - Save a checkpoint in a running simulation and return to it with a button click, allowing you to experiment with tricky regions without fear - Real-time visualisation of crystal symmetry contacts: when the master atoms move, they move. - One-button masking of maps to cover any arbitrary atom selection – particularly useful for diagnosing large-scale problems. - Extensive GUI and API documentation, available by clicking the “Help” button in the ISOLDE GUI window. ISOLDE is built as a plugin to UCSF ChimeraX (http://preview.cgl.ucsf.edu/chimerax/download.html) and is currently available for modern Linux distros and MacOS, and can be installed from within ChimeraX via its ToolShed (Tools/More Tools...). It should run on any Linux version that supports ChimeraX itself. NOTE: due to some recent changes in the ChimeraX API, the current build will only work with the ChimeraX 0.6 release (not the version 0.7 daily builds). In terms of hardware, ISOLDE is designed based on the understanding that not everybody has access to high-performance computing facilities, so its minimum requirements are as modest as possible. The most important requirement is a GPU capable of OpenCL 1.2 or CUDA processing. My “go-to” machine for performance testing is a 2016-model gaming laptop equipped with a Nvidia GTX 1070 GPU – this achieves ~20 coordinate updates and >30 graphics updates per second with live validation on the included 229-residue demo model, indistinguishable from (or slightly faster than) my Xeon workstation. At the other end of the scale, it runs at usable speeds on my MacBook Air for simulations of a few dozen residues, sufficient for many tasks. I hope you find it useful, and enjoy using it as much as I've enjoyed making it. The MolProbity score to beat on the demo model is 1.02 (after refinement in your favourite package – ID is in the PDB header so you can download reflections from the wwPDB), and bonus points if you can identify the mystery ligand (I can't). If you recognise it as your model I apologise – I picked it out at random, I swear! Best regards, Tristan

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DNA pucker
by Dyda 01 May '18

01 May '18

Hi, Is it possible and if so how to change the pucker restraint for a particular DNA nucleotide from C2'-endo to C3'-endo in phenix.refine? I have a problem with a terminal nucleotide that is in an active site and the current C2'-endo doesn't seem consistent with the 2Fo-Fc map. Thanks for your help. [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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Abstract deadline is TOMORROW for Diffraction Methods in Structural Biology GRS
by Pearce, N.M. (Nick) 27 Apr '18

27 Apr '18

Dear BB, Tomorrow is the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be considered for oral presentations. This year’s title is Crystallography 2.0: Restructuring the Field Around a New Wave of Experiments We want to have as many young scientists (Post-docs, PhD candidates & Master’s students) at the GRS (and associated GRC) as possible. For Jessica and myself, the 2016 Diffraction Methods GRS & GRC was the best conference we’ve attended during our PhDs, since it allowed us to present our research directly to our peers in a relaxed setting; it also gave many of us the opportunity to gain first-hand experience as session chairs -- an opportunity that is difficult to find as a young scientist. On top of this, the intimate nature and relatively small size of Gordon conferences helped us to build more long-lasting international connections than at any other conference we have attended. Of course, the GRS can only be truly successful if a wide variety of viewpoints are represented — so please consider attending. We would greatly appreciate it if you could also forward this invitation to any young scientists for whom you think this conference might be valuable. You can apply for the seminar (GRS) here: https://www.grc.org/diffraction-methods-in-structural-biology-grs-conferenc…. On this page you can also find a link to the associated Gordon Research Conference (GRC). We hope to see you in July, Nicholas Pearce & Jessica Besaw Chair & Co-Chair, Gordon Research Seminar in Diffraction Methods, 2018

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11th CCP4/APS Crystallographic School in the US
by Qingping Xu 27 Apr '18

27 Apr '18

Just a friendly reminder that the deadline for applying the upcoming CCP4 school at APS is next Wednesday (5/2/2018), please apply or finish your application (if you have already applied) if you wish to participate in the school. Please let us know if you have any questions/concerns. Qingping Xu GMCA/APS Argonne National Laboratory =========== Dear Colleagues, We are pleased to announce the *11th annual CCP4 crystallographic school *“From data collection to structure refinement and beyond” will be held on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php. *Dates*: June 18 through 25, 2018 *Location*: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: *data collection workshop* and *crystallographic computing workshop*. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is *Wednesday May 2nd, 2018*. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php *Registration fees*: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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BCA/CCP4 Summer School in Protein Crystallography at Diamond
by Airlie McCoy 23 Apr '18

23 Apr '18

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Monday 27th August to Saturday 1st September 2018. Note that applications close 18TH MAY 2018 The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines. Up to 10 places for those with BBSRC studentships will be fully funded. We recognise that the social programme plays a role in enabling students to make links that may be maintained throughout a research career. There will be a conference dinner, and a number of other events, including a trip to Oxford. For more information see http://www.diamond.ac.uk/Home/Events/2018/BCA-Summer-School.html Application form: https://extranet2.diamond.ac.uk/ISV/BCA/ApplicationForm.aspx

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Abstract deadline is 28th April for Diffraction Methods in Structural Biology GRS
by Pearce, N.M. (Nick) 23 Apr '18

23 Apr '18

Dear BB, There are five more days until the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be considered for oral presentations. This year’s title is Crystallography 2.0: Restructuring the Field Around a New Wave of Experiments We want to have as many young scientists (Post-docs, PhD candidates & Master’s students) at the GRS (and associated GRC) as possible. For Jessica and myself, the 2016 Diffraction Methods GRS & GRC was the best conference we’ve attended during our PhDs, since it allowed us to present our research directly to our peers in a relaxed setting; it also gave many of us the opportunity to gain first-hand experience as session chairs -- an opportunity that is difficult to find as a young scientist. On top of this, the intimate nature and relatively small size of Gordon conferences helped us to build more long-lasting international connections than at any other conference we have attended. Of course, the GRS can only be truly successful if a wide variety of viewpoints are represented — so please consider attending. We would greatly appreciate it if you could also forward this invitation to any young scientists for whom you think this conference might be valuable. You can apply for the seminar (GRS) here: https://www.grc.org/diffraction-methods-in-structural-biology-grs-conferenc…. On this page you can also find a link to the associated Gordon Research Conference (GRC). We hope to see you in July, Nicholas Pearce & Jessica Besaw Chair & Co-Chair, Gordon Research Seminar in Diffraction Methods, 2018

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mtriage error
by Sara Weaver 21 Apr '18

21 Apr '18

Hi all, I'm trying to process some cryoEM data that goes to 2.9 angstroms in phenix. I can't seem to run mtriage on several different builds. Any ideas? I've put the errors below. I've tried making my input map a .mrc, or a .ccp4 and get the same errors. Thanks! Sara [sjweaver@brmaster job099]$ /hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/bin/phenix.mtriage map_file_name=run_class001.mrc ------------------------------------------------------------------------------- phenix.mtriage: Given map file and optionally model and half-map files compute map statistics. How to run: phenix.mtriage model_file_name=m.pdb map_file_name=m.map half_map_file_name_1=m1.map half_map_file_name_2=m2.map Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2= Feedback: PAfonine(a)lbl.gov phenixbb(a)phenix-online.org ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Input model: ************ No model specified. ------------------------------------------------------------------------------- Box (unit cell) info: ********************* Unit cell: (255.948, 255.948, 255.948, 90, 90, 90) Space group: P 1 (No. 1) Traceback (most recent call last): File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 277, in <module> run(args=sys.argv[1:]) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 190, in run task_obj.run() File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/mmtbx/maps/mtriage.py", line 174, in run self._shift_origin() File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/mmtbx/maps/mtriage.py", line 204, in _shift_origin crystal_symmetry = self.crystal_symmetry) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/cctbx/maptbx/__init__.py", line 112, in shift_origin_if_needed assert [sites_cart, crystal_symmetry].count(None) in [0, 2] AssertionError [sjweaver@brmaster job099]$ /hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/bin/phenix.mtriage map_file_name=run_class001.mrc ------------------------------------------------------------------------------- phenix.mtriage: Given map file and optionally model and half-map files compute map statistics. How to run: phenix.mtriage model_file_name=m.pdb map_file_name=m.map half_map_file_name_1=m1.map half_map_file_name_2=m2.map Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2= Feedback: PAfonine(a)lbl.gov phenixbb(a)phenix-online.org ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Input model: ************ No model specified. ------------------------------------------------------------------------------- Box (unit cell) info: ********************* Unit cell: (255.948, 255.948, 255.948, 90, 90, 90) Space group: P 1 (No. 1) Traceback (most recent call last): File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 287, in <module> run(args=sys.argv[1:]) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 195, in run task_obj.run() File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py", line 204, in run self.call(func=self._compute_d_model_b0, prefix="Compute d_model_b0") File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py", line 185, in call func() File "/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py", line 295, in _compute_d_model_b0 map_data = self.box.map_data, AttributeError: 'NoneType' object has no attribute 'map_data' [sjweaver@brmaster job099]$ /hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/bin/phenix.mtriage map_file_name=run_class001.mrc ------------------------------------------------------------------------------- phenix.mtriage: Given map file and optionally model and half-map files compute map statistics. How to run: phenix.mtriage model_file_name=m.pdb map_file_name=m.map half_map_file_name_1=m1.map half_map_file_name_2=m2.map Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2= Feedback: PAfonine(a)lbl.gov phenixbb(a)phenix-online.org ------------------------------------------------------------------------------- Traceback (most recent call last): File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 274, in <module> run(args=sys.argv[1:]) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 158, in run params = inputs.params) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/modules/cctbx_project/mmtbx/maps/mtriage.py", line 130, in __init__ box = self.params.use_box) File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/modules/cctbx_project/iotbx/map_and_model.py", line 115, in __init__ crystal_symmetry = self._model.crystal_symmetry()) AttributeError: 'NoneType' object has no attribute 'crystal_symmetry' ariel:20180417_lookingatRefinej348_focused sjweaver$ /Applications/phenix-dev-3112/build/bin/phenix.mtriage map_file_name=run_ct8_class001.mrc ------------------------------------------------------------------------------- phenix.mtriage: Given map file and optionally model and half-map files compute map statistics. How to run: phenix.mtriage model_file_name=m.pdb map_file_name=m.map half_map_file_name_1=m1.map half_map_file_name_2=m2.map Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2= Feedback: PAfonine(a)lbl.gov phenixbb(a)phenix-online.org ------------------------------------------------------------------------------- Traceback (most recent call last): File "/Applications/phenix-dev-3112/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 339, in <module> run(args=sys.argv[1:]) File "/Applications/phenix-dev-3112/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 204, in run inputs.model.setup_scattering_dictionaries( AttributeError: 'NoneType' object has no attribute 'setup_scattering_dictionaries' -- Sara J. Weaver *Doctoral Candidate, Jensen Lab* *California Institute of Technology*

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Protein structures sought for CASP13
by Paul Adams 20 Apr '18

20 Apr '18

Posted on behalf of the CASP organizing Committee: Critical Assessment of Techniques for Protein Structure Prediction (CASP) community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. About 100 modeling groups from around the world participate. Results of CASP experiments are published in special issues of the journal PROTEINS (e.g., CASP12: https://onlinelibrary.wiley.com/toc/10970134/86/S1). The success of CASP depends on the generosity of the structure determination community. We are now requesting targets for CASP13 experiment, which will launch at the beginning of May. The CASP community needs modeling targets over a wide range of difficulty, for modeling with and without the aid of templates. X-ray, NMR and cryo-EM structures are welcome. We are particularly interested in membrane proteins, protein complexes, and cryo-EM structures. We are also extending CASP to include more modeling assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, SANS, crosslinking, and FRET. For that, protein material is needed (of course this is not expected for most targets, but if available, it would be much appreciated!). So, if you have anything suitable, we encourage you to mark your PDB deposition as a "CASP target" in the PDB's submission system. Alternatively, you can suggest your protein to CASP directly through the CASP13 target entry page: http://www.predictioncenter.org/casp13/targets_submission.cgi. For those of you who have not provided targets to CASP before, the procedure is simple and fast. We don’t need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. More details are available on the web site. CASP target providers are regularly invited to contribute to special issue papers, for example: 2018: Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. (2018). Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 86 (S1), 27-50. doi: 10.1002/prot.25392. PMID: 28960539 2016:  Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. (2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 84 (S1), 34-50. doi: 10.1002/prot.24942. PMID: 26473983   2014: Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. (2014). Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10. Proteins 82 (S2), 26-42. doi: 10.1002/prot.24489. PMID: 24318984 2011: Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. (2011). Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 79 (S10), 6-20. doi: 10.1002/prot.23196. PMID: 22020785 Thanks, CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel, Switzerland Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casp13/index.cgi Submit a target: http://www.predictioncenter.org/casp13/targets_submission.cgi -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Deadline for the EM and the X-ray bundles of iNEXT extended to 24 April (midnight)
by a.perrakis＠nki.nl 19 Apr '18

19 Apr '18

Dear all, The deadline for the EM and the X-ray bundles of iNEXT is now extended until 24 April (midnight, for all timezones …). For more information http://www.inext-eu.org/inext-em-and-x-ray-bundles/ and to submit a proposal https://www.structuralbiology.eu/submit-proposal/?t=inext Best regards, the INEXT team

1 0

Call for not-yet-released structures as candidates for protein structure predictors
by Susan Tsutakawa 18 Apr '18

18 Apr '18

Critical Assessment of Techniques for Protein Structure Prediction (CASP) community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. About 100 modeling groups from around the world participate. Results of CASP experiments are published in special issues of the journal PROTEINS (e.g., CASP12: Proteins Vol 86, Issue S1, March 2018). The thirteenth CASP round is scheduled to start on May 1, 2018. The organizing committee is particularly keen to include many cryo-EM-derived structure targets in this round. The success of CASP depends on the generosity of the structure determination community. Modeling targets are needed over a wide range of difficulty, for modeling both with and without the aid of templates. Targets that can be modeled based on structural templates should ideally have 50% or less sequence identity to the templates. Access to the structure in advance of its release by the PDB or its publication is not needed. With sufficient notification to CASP (a minimum of three weeks before release, more is better) there is no need to delay structure release. If you have recently determined a novel protein structure and will be depositing it to PDB, please suggest it as a target for CASP by visiting www.predictioncenter.org/casp13/targets_submission.cgi. If you have any questions please contact [log in to unmask] CASP target providers are regularly invited to contribute to special issue papers, for example: 2018: Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. (2018). Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 86 (S1), 27-50. doi: 10.1002/prot.25392. PMID: 2896053 2016: Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. (2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 84 (S1), 34-50. doi: 10.1002/prot.24942. PMID: 26473983 2014: Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. (2014). Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10. Proteins 82 (S2), 26-42. doi: 10.1002/prot.24489. PMID: 2431898 2011: Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. (2011). Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 79 (S10), 6-20. doi: 10.1002/prot.23196. PMID: 2202078 Posted on behalf of the CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis USA Torsten Schwede, University of Basel, Switzerland

1 0

R-factor expectations when translational pseudo symmetry is present
by Tanner, John J. 18 Apr '18

18 Apr '18

Dear PhenixBB, We have a crystal form that xtriage flags as having strong translational pseudo symmetry (Patterson peak 57% the height of the origin peak, p-value = 3E-5). The space group is P21212. We can solve the structure with MR and refine to R=0.233 and R-free =0.276 at 2.25 Angstrom resolution. The maps look very good, but do not suggest major additional modeling that could be done to improve the structure and lower the R-factors. I know that one expects the R-factors from refinement to be higher when TPS is present, but my question is how high is too high? Has anyone done a study that shows the expectations for R-factors when TPS is present? Thanks, Jack John J. Tanner Interim Chair, Department of Biochemistry Professor of Biochemistry and Chemistry Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

4 6

Trouble running getting ERRASER to run
by Shintaro Aibara 18 Apr '18

18 Apr '18

*Dear PhenixBB,* *I am trying to get ERRASER to run and am struggling a bit. I was wondering if somebody could point me in the right way. Apologies if this has been asked before - my Google-Fu is inadequate.* *Phenix Version: dev-3092* *Rosetta Version: 2018.09.60072* *I built rosetta using scons as per the instructions online and fired rosetta.build_phenix_interface with no errors. I've identified that the erraser directory lives in main/source/src/apps/public/ERRASER and accordingly set my environmental variables.* *Being fairly clunky around the linux environment, I am probably doing something very silly. Any help would be much appreciated.* *Best wishes,* *Shintaro* *When I try to run erraser from the phenix GUI I am greeted by this error message:* TypeError : __init__() takes at least 3 arguments (1 given) Traceback (most recent call last): File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/App.py", line 784, in OnTimer self.run_manager.update(update_backgrounded=False) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py", line 213, in update process.update() File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py", line 136, in update self._process.update() File "/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/runtime_utils.py", line 306, in update (error, traceback_info) = easy_pickle.load(self.error_file) File "/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/easy_pickle.py", line 80, in load return cPickle.loads(_open(file_name, "rb").read()) TypeError: __init__() takes at least 3 arguments (1 given) *Alternatively if I try to fire phenix.erraser through the command line, I get something like this:* Running ERRASER Rosetta app... ################################### Path to ERRASER: /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER ERROR: Assertion `scorefxn_->get_weight( cart_bonded ) > 0` failed. ERROR:: Exit from: src/protocols/rna/movers/ErraserMinimizerMover.cc line: 238 BACKTRACE: /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2ea) [0x7f3e2b7798fa] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(core::chemical::ResidueType const&, unsigned long const&)+0x92) [0x7f3e34c17062] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(core::kinematics::MoveMap&, core::pose::Pose&, ObjexxFCL::FArray1D<bool>&, std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > const&)+0x20a) [0x7f3e34c1771a] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::apply(core::pose::Pose&)+0x2020) [0x7f3e34c20f70] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xbed) [0x7f3e344cc9bd] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x166) [0x7f3e344cedc6] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x57) [0x7f3e344b4d67] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x40480e] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4037b1] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f3e32bdc830] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4045b9] Traceback (most recent call last): File "/home/saibara/software/phenix/phenix-dev-3092/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module> erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:]) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__ self.run(params,out=out) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py", line 459, in run erraser(option) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 99, in erraser erraser_minimize( minimize_option ) #full_struct_slice_and_minimize( minimize_option ) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 478, in erraser_minimize subprocess_call(command, sys.stdout, sys.stderr) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel) File "/home/saibara/software/phenix/phenix-dev-3092/base/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease -database /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/database/ -s /home/saibara/Phenix/hsmitoribo_drug/rnaonly_erraser_temp/minimize_0.pdb -score:weights stepwise/rna/rna_hires_elec_dens_FCC2012 -score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo true -rna::erraser::rna_prot_erraser false -rna::vary_geometry true -constrain_P true -attempt_pyrimidine_flip false -rna::erraser::skip_minimize false -chemical:enlarge_H_lj false -in:guarantee_no_DNA false -out:file:write_pdb_link_records true -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_mode true -use_2prime_OH_potential false -edensity:mapfile /home/saibara/Phenix/hsmitoribo_drug/cheatmap.ccp4 -edensity:mapreso 3.0 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255

3 4

Final reminder: 11th CCP4/APS Crystallographic School in the US June 18 through 25, 2018
by Qingping Xu 16 Apr '18

16 Apr '18

Dear Colleagues, This is a reminder for the upcoming CCP4/APS school. The deadline for registering is coming up soon, please register if you plan to attend. Thanks. Charles, Garib and Qingping ====original announcement ==== Dear Colleagues, We are pleased to announce the *11th annual CCP4 crystallographic school *“From data collection to structure refinement and beyond” will be held on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php. *Dates*: June 18 through 25, 2018 *Location*: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: *data collection workshop* and *crystallographic computing workshop*. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is *Wednesday May 2nd, 2018*. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php *Registration fees*: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

1 0

Running on Windows 10
by Plínio Salmazo Vieira 15 Apr '18

15 Apr '18

Dear all I'm having issues on running Phenix. It installs smoothly (I downloaded the point-and-click 64-bit version), but when I try to open, the prompt writes very fast and closes by itself. I tried installing and running on administrator mode and on compatibility mode for Windows 7, but still no good. Below are my laptop configuration: Processor: Intel Core it-7500U CPU @ 2.70 GHz 2.90 GHz RAM: 8 GB System: Operational based on 64 bits, processor x64 Please, could anyone help me? Any guesses? If you need any more information, let me know. Best Regards, Plínio. -- Dr. Plínio Salmazo Vieira Laboratório Nacional de Ciência e Tecnologia do Bioetanol Centro Nacional de Pesquisa em Energia e Materiais Campinas - São Paulo

2 1

Polder comment
by Patrick Loll 14 Apr '18

14 Apr '18

What does it mean when a Polder map calculation finishes with the comment "The polder map is more likely to show bulk-solvent or noise instead of the ligand” ? Thx, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pjl28(a)drexel.edu

3 2

Unflagging accidental "Mark as Failed" in GUI
by Shane Caldwell 14 Apr '18

14 Apr '18

Hi phenixbb, I have a mostly inconsequential and hopefully simple problem to solve, but I can't find info about it online. I accidentally flagged a good run as "failed" in the Phenix GUI, and I can't figure out how to remove that tag. It's possible I'm overlooking something extremely obvious and if so apologies for the spam. How can I reset this marker? Shane Shane Caldwell shane.caldwell17(a)gmail.com

2 2

AsCA 2018/CRYSTAL 32: Registration Open!
by Christopher Squire 11 Apr '18

11 Apr '18

? [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] Dear Colleagues, Registration for the AsCA 2018/CRYSTAL 32 Conference (2 - 5 December 2018 at the University of Auckland, New Zealand) is now open! Please follow this link to register http://asca2018.org/registration/ Workshop registration is not yet open, however please use the voting function here<http://asca2018.org/workshops/> to advise which of the four potential workshops would be of most interest to you. Finally, a reminder that submissions are now open. Please visit the Call for Abstracts<http://asca2018.org/call-for-abstracts/> page for more information and to submit an abstract. Should you have any queries regarding the AsCA 2018/CRYSTAL 32 Conference, please do not hesitate to contact us using the email address listed below. Kind regards, Event Services University of Auckland Email: asca2018(a)auckland.ac.nz<mailto:[email protected]> [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…]

1 0

Phenix video tutorials
by Dorothee Liebschner 11 Apr '18

11 Apr '18

Dear Phenix users, This is an update for the Phenix video tutorials. There are now 25 videos, explaining Phenix tools for X-ray crystallography and cryo-EM. New videos include topics such as model and data validation (Xtriage, Molprobity), phasing (Phaser, AutoSol) and tools for cryo-EM. A categorized overview is on the phenix homepage: https://www.phenix-online.org/documentation/reference/tutorial_channel.html You can also browse the videos directly on the Phenix Tutorial YouTube channel: https://www.youtube.com/c/phenixtutorials (To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button, which is next to the "subscribe" button.) Feedback about the videos is very welcome. Write an email to tutorials(a)phenix-online.org or use the comment section on YouTube. If you want to see a tutorial about a certain (Phenix-related) topic, don't hesitate to tell us. Best wishes, The Phenix team

1 0

9th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 10 Apr '18

10 Apr '18

Second announcement 9th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 11 - June 15, 2018 Travel and accommodation expenses are supported for selected participants. No registration fee. Detailed information can be found on the workshop web page: https://conference.sns.gov/biologyneutrons18/ Application deadline: April 30, 2018 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. Flora Meilleur, Ph. D Neutron Scattering Scientist, Neutron Sciences Directorate Oak Ridge National Laboratory Associate Professor, Molecular and Structural Biochemistry North Carolina State University

1 0

FW: Announcement of European Crystallographic Computing Forum 2018 in Mieres, Spain
by Tom Terwilliger 09 Apr '18

09 Apr '18

Registration for the European Crystallographic Computing Forum is open: https://www.mrc-lmb.cam.ac.uk/harry/ecacomsig/mieres.html A poster for print can be downloaded here: https://we.tl/CyPFzYvorG Spread the word! The Forum will be held in Mieres, Spain, 18th - 22nd August 2018 (preceding the ECM). We invite both beginners (from graduate level) and experienced software developers from all crystallographic disciplines. Participants can bring their own software development project to work on it in teams, interspersed with tutorials and lectures. There will be opportunity to exchange and connect with other crystallographic software developers. The registration fee (360 €) includes: accommodation (4 nights), full board and refreshments and transfer to the ECM. We offer childcare and family rooms. Bursaries are available. We hope to see you there! The Organisers Andrea Thorn, Harry Powell, Laura Roces Fernandez We would like to thank our kind sponsors! - CCP4 - Dectris - Rigaku - Bruker -

1 0

TaBr SAD Autosol and Phaser
by Ian S 09 Apr '18

09 Apr '18

Hi Phenixbb, I trying to phase a structure soaked in TaBr and am running into some technical problems. My anomalous signal goes out to about 4.5 and I have a 1.9A native data set. SIR hasn't worked so far. Autosol SAD has given me several convincing solutions when searching for Tantalum (not TX), finding 11 sites (not clustered) at 6 angstroms: FOM =0.478, map=0.1.3, and corr of 0.82 and a final score of 37+-15.71. By only playing around with the sites I can get an overall score of 73 +- 4.58, map skew to 0.5, and a RMS density to 0.79, thought the R-factor increases to .43 and the FOM . Perhaps not suprisingly at this resolution, the map is uninterpretable (maybe some helices) so I'm trying to improve the phases by model building and by using Phaser and giving it TX sites. If I put the Ta sites in Phaser with the same dataset as Autosol, I get a FOM of .342. If I use the TX label it drops to 0.143. What is happening here? I know that typically TaBr has one or two major sites (my protein isnt massive, only about 1200 aa predicted in the ASU) , so I use only the top two major sites and have the same problem. Does this indicate that the Ta sites Autosol found are not in fact the sites I'm looking for? Or maybe that there really are 10 TaBr sites all with low occupancy? Any suggestions would be appreciated. Thank you. Best, Ian

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linking only one conformer to a thiol
by Krzysztof Bzymek 07 Apr '18

07 Apr '18

Hi, I'm trying to refine a structure with a disulfide bond between a cysteine and a thiol-containing peptide. There are two conformations for the thiopeptide, in one of them the thiol is facing away from SG of the cysteine (~7 A away). I defined the link as: refinement.pdb_interpretation { apply_cif_link { data_link = DRG-CYS residue_selection_1 = chain A and resname DRG and resid 10 residue_selection_2 = chain B and resname CYS and resid 20 } } I also tried: refinement.pdb_interpretation { apply_cif_link { data_link = DRG-CYS residue_selection_1 = chain A and resname DRG and resid 10 and altloc A residue_selection_2 = chain B and resname CYS and resid 20 } } After refinement (with a corresponding data_link.eff file defining the bonds and angles), the thiol of the other conformer that was facing away from the cysteine moves out of the electron density and now faces the cysteine (still about ~5.7 A away). Is there a way to define a link between only one conformer and have the other refine independently? I did try refinement without the above link definition (relying on the proximity of the two cysteines and automatic linking in phenix) but some of the bond and dihedral angles showed higher deviation from ideal values expected for disulfide bonds. Thanks, Chris

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23rd Annual SCSB Symposium, April 28th, Galveston Texas
by Mark A. White 05 Apr '18

05 Apr '18

You and your colleagues are cordially invited to join us for the 23rd Annual Structural Biology Symposium to be held at Levin Hall on the University of Texas Medical Branch Campus on beautiful Galveston Island on Saturday, April 28, 2018. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. This year’s speakers include: Grant Jensen, Ph.D., California Institute of Technology “Progress and Challenges in Electron Cryotomography” Ayyalusamy Ramamoorthy, Ph.D., University of Michigan “Membrane-Assisted Dynamic Protein-Protein Interactions by NMR" Andrew Routh, Ph.D., University of Texas Medical Branch “Parallel ClickSeq and Nanopore Deep-Sequencing Characterizes the Emergence and Evolution of Defective Viral Genomes” Joan-Emma Shea, Ph.D., University of California Santa Barbara “Binding and Assembly of Intrinsically Disordered Peptide” Yizhi Tao, Ph.D., Rice University “The Tail of a Nematode Virus” Adam Zlotnick, Ph.D., Indiana University “Multiple Mechanisms for Assembly-Directed HBV Antivirals” To register or for more information, visit http://scsb.utmb.edu/symposium -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.658A University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 mailto://[email protected] http://xray.utmb.edu QQ: "For a man to conquer himself is the first and noblest of all victories." - Plato

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Rfree and a low resolution data set
by Toon Van Thillo 05 Apr '18

05 Apr '18

Hi all, Currently I am refining a data set which showed anisotropic diffraction. Aimless suggested cutoffs at 2.3, 2.6 and 3.6 angstrom for the h,k and l axis. I chose a general 3.6 cutoff to obtain satisfactory statistics for Rmeas, I/sd(I) and CC1/2. At this resolution the data set consists of approximately 2800 reflections. Generally 5% of the set is set aside as the Rfree test set and I found that a minimum of 500 reflections in total is used to produce a reliable Rfree. However, 5% only amounts to 140 reflections in this case. I am hesitant to include more reflections as I would have to go up to 20% of the reflections to obtain more than 500 reflections for the test set. In a discussion on the CCP4 message boards some time ago it was suggested to do multiple refinements with different test sets: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1411&L=ccp4bb&F=&S=&P=125… In the thread it was also discussed that a least squares approach is prefered when using a small test set. However, when using a LS target, the resulting Rfree is very high (10% higher than when using the automatic option) and phenix.refine? produces awful geometry (24% ramachandran outliers, 105 clashcore...). It seems that the refinement is performed without restraints? Optimize X-ray/stereochemistry weight does not result in improved stereochemistry. My question is if the LS approach is still relevant and if so, is there an explanation (and solution) for the bad statistics? Kind regards, Toon Van Thillo

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A new capability on the STARANISO server: "PDBpeep"
by Gerard Bricogne 29 Mar '18

29 Mar '18

Dear all, Ever since the WebGL viewer became available on the STARANISO server, we have found ourselves using it with increasing frequency to take a quick look (a "peep") at the diffraction data deposited with various PDB entries - for example, to try and identify a root cause for some sub-optimal refinement results, or, quite often, just out of sheer curiosity! This involved a totally straightforward procedure whereby the diffraction data file associated with a given PDB entry was downloaded from the PDB and subsequently uploaded to the STARANISO server. Gradually, however, this operation became so popular among some of us that we thought it would be useful to implement this simple procedure as an autonomous capability - and thus was born "PDBpeep" ! You can access this new feature by connecting to http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi and enter a PDB code into the box. As indicated on that page, this provides only a cursory look at the overall quality of each dataset, and any further analysis or output can only be obtained by submitting the datafile to the STARANISO server. Better results would clearly be obtainable if the raw images for these datasets had been deposited and could be reprocessed, with the untruncated output of that processing then being submitted to the STARANISO server (reprocessing the images with autoPROC would combine those two steps into a single one). Most of the deposited datasets have been isotropically truncated, and their 3D view in WebGL often suggests that this truncation was too drastic. A number of entries will show infelicities - such as cusps and/or missing angular ranges, or even stripes caused by gaps between the modules of pixel detectors if the beam centre is at a position symmetric relative to those gaps - all marked up in blue. Our purpose in sharing this capability with the community is to bring a further contribution to the process of making everyone more "data quality aware" and keen to scrutinise more closely the protocols by which they collect diffraction data, or have such data collected on their behalf. We will be grateful to receive feedback about PDBpeep, just as we have been about the STARANISO server itself. With best wishes, The STARANISO developers.

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MR Rosetta fails
by Aaron Oakley 29 Mar '18

29 Mar '18

Salvete! I am trying (unsuccessfully) to run MR Rosetta. Im using a MacBookPro running OS X 10.13.3. The job terminates with Sorry: mr_rosetta failed... Sorry routine failed Please see log file for full error message The relevant log file rebuild.log terminates with protocols.jd2.JobDistributor: [ WARNING ] The following options have been set, but have not yet been used: -in:file:extended_pose 1 I get the same error with phenix-1.13-2998 and phenix-dev-3092. I'm using rosetta_bin_mac_2018.09.60072_bundle. Advice accepted with thanks. a++ Aaron Oakley Associate Professor School of Chemistry | Science, Medicine and Health University of Wollongong NSW 2522 Australia T +61 2 4221 4347 | F +61 2 4221 4287

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