[ccp4bb] NIGMS Mature Synchrotron Program Evaluation
Dear Colleagues, Apologies for the US-centric posting, but I think this is of interest to many of the bulletin board subscribers who make use of synchrotron facilities in the US. NIH is seeking feedback on the Mature Synchrotron Program: https://grants.nih.gov/grants/guide/notice-files/NOT-GM-24-019.html This program supports synchrotron-based user resources where the technologies are at an advanced level, including Macromolecular Crystallography, Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other synchrotron-based techniques that generate important data, with an emphasis on structural biology. Responses to the RFI will be accepted through 6/17/2024. All comments will be anonymous and should be submitted electronically via a web form at: https://www.research.net/r/P30_RFI As the Director of one of the resources it has been suggested that I help make the community aware of the RFI, so there is the opportunity to provide feedback in a timely manner. Feel free to pass this on to any of your colleagues who may be interested. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility
the Editor in the coming days. >> > >> > >> > >> >Please see the entire letter here. >> > <https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link> >> > >> > <https://urldefense.com/v3/__https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AqTp0-CX$> >> > If you want to endorse this letter, please fill out your name, >> > affiliation, and email in the form. >> > >> > >> > >> >Additionally, a PDF version of the letter can be found here >> > <https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing> >> > >> > <https://urldefense.com/v3/__https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AmjNPgIH$>. >> > >> > >> > >> >Thank you, >> > >> > >> > >> >Stephanie Wankowicz, UCSF >> > >> >Pedro Beltrao, ETH >> >Benjamin Cravatt, Scripps >> >Roland Dunbrack, FCCC >> >Anthony Gitter, UW Madison >> >Kresten Lindorff-Larsen, Copenhagen >> >Sergey Ovchinnikov, MIT >> >Nicholas Polizzi, DFCI/HMS >> >Brian Shoichet, UCSF >> >James Fraser, UCSF >> > >> > >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AoA8pumq$> >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB >> <https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AgFZZaeK$>, >> a mailing list hosted by www.jiscmail.ac.uk >> <https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7An7YNOzL$>, >> terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7ApCXqJeM$> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AoA8pumq$> >> This communication is intended for the addressee only. It is confidential. >> If you have received this communication in error, please notify us >> immediately and destroy the original message. You may not copy or >> disseminate this communication without the permission of the University. >> Only authorised signatories are competent to enter into agreements on behalf >> of the University and recipients are thus advised that the content of this >> message may not be legally binding on the University and may contain the >> personal views and opinions of the author, which are not necessarily the >> views and opinions of The University of the Witwatersrand, Johannesburg. All >> agreements between the University and outsiders are subject to South African >> Law unless the University agrees in writing to the contrary. >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AoA8pumq$> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NE
[ccp4bb] Phenix version 1.21.1 released
The Phenix developers are pleased to announce that version 1.21.1 of Phenix is now available (build 1.21.1-5286). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download Highlights for this bug fix 1.21.1 version of Phenix include: - Added support for joint X-ray/neutron refinement to phenix.refine GUI - Fixed DMSO restraint - Fixed excessive printing when processing PAE matrix file - Added tutorial for low resolution restraints - Bugfix for LigandPipeline - Bugfix for PredictAndBuild - New program - phenix.renumber_fab: renumber FAB chains using Kabat, Chothia or Martin conventions Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Macromolecular Crystallography - CSHL Course October 2024
Dear Colleagues, The Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoqek2kVhNZhYit0f8DSBc_cgi7RCdxoS4dG97E7URwRGgxydv6yzeOikM4jJhfzJKPAxQR8TL1P3PpzwKI35wF5uJDxuDOjhUOE_UtQ06NT-RvmvLS3RLEb=hFMkxRE6JPZrmWip-_ps3iPWJ4kxUQnirsAwFcXgUp_G3Zndm8y1Fw===gQ24lsYHhUPuocw10AKYiW24-hnwg8_VqqlYiavzYUVvlXhfKEo2nQ==> <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoqek2kVhNZhYqApQjM02o9w5ayJZ-cN0k9Vgia00kP95bxw9YTf_vYNwtaCfhJ3Fl_JQPdT9myGfN5RtsoQhVv9cxAZl166xu1fYDFeeRIsv48B2SJ4sYswNuf5cri5g5rT_eN5RPmtZNA0oXUMdTnM23CVeH1hgNw==hFMkxRE6JPZrmWip-_ps3iPWJ4kxUQnirsAwFcXgUp_G3Zndm8y1Fw===gQ24lsYHhUPuocw10AKYiW24-hnwg8_VqqlYiavzYUVvlXhfKEo2nQ==> Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoqek2kVhNZhYqApQjM02o9w5ayJZ-cN0k9Vgia00kP95bxw9YTf_vYNwtaCfhJ3Fl_JQPdT9myGfN5RtsoQhVv9cxAZl166xu1fYDFeeRIsv48B2SJ4sYswNuf5cri5g5rT_eN5RPmtZNA0oXUMdTnM23CVeH1hgNw==hFMkxRE6JPZrmWip-_ps3iPWJ4kxUQnirsAwFcXgUp_G3Zndm8y1Fw===gQ24lsYHhUPuocw10AKYiW24-hnwg8_VqqlYiavzYUVvlXhfKEo2nQ==> October 13 - 29, 2024 Applications Due: July 15 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia Topics Covered Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) For further information and to apply please visit the Macromolecular Crystallography course website. <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoqek2kVhNZhYqApQjM02o9w5ayJZ-cN0k9Vgia00kP95bxw9YTf_vYNwtaCfhJ3Fl_JQPdT9myGfN5RtsoQhVv9cxAZl166xu1fYDFeeRIsv48B2SJ4sYswNuf5cri5g5rT_eN5RPmtZNA0oXUMdTnM23CVeH1hgNw==hFMkxRE6JPZrmWip-_ps3iPWJ4kxUQnirsAwFcXgUp_G3Zndm8y1Fw===gQ24lsYHhUPuocw10AKYiW24-hnwg8_VqqlYiavzYUVvlXhfKEo2nQ==> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Rwork and Rfree the same?
By setting wxc (weight of the X-ray term) to 0.1 there is good chance that the refinement is dominated by the geometry term and the model isn’t really seeing the effect of the X-ray data. I suspect this would result in R-factors that are similar. Why they are so low is less clear, but as others have pointed out 38% completeness is a problem. It would be good to check if that is 38% overall, or just very incomplete in the higher resolution shells. If it is complete at lower resolution you might be able to do something with the dataset, but not using the default parameterization in refinement programs - you’ll need to apply constraints and additional restraints if you can, and look at the weighting (by modifying wxc_scale, not wxc). There is a Phenix mailing list you might want to use as well (I assume you are using phenix.refine): https://phenix-online.org/mailman/listinfo/phenixbb > On Feb 28, 2024, at 8:21 AM, Justin Cruite > wrote: > > Thanks everyone, > > I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å dataset. > The data was processed using autoProc and the staranisano mtz was used for > MR. The completeness is only 38%. It could be that the Rfree and Rwork > reflection sets are small because of this? What is the best way to check the > number of reflections used for Rwork and Rfree? Is this dataset usable at all? > > Thanks! > > Justin > > On Wed, Feb 28, 2024 at 10:21 AM nicfoos <mailto:nicf...@embl.fr>> wrote: >> Hello Justin, >> >> There is something weird in your results. You mention Rwork/Rfree of >> 0.1837. >> This means a pretty good refinement and also is very unusual to be >> obtain for a resolution of 3.37. >> Additionally you should not have Rfree = Rwork. >> I suspect something wrong with you Rfree reflections sets. What size is >> it ? Is your dataset complet ? >> How did you cut the res. ? >> >> I hope this may help you. >> >> Nicolas >> >> >> >> On 2024-02-28 16:10, Justin Cruite wrote: >> > Hi everyone, >> > >> > What does it mean if your Rwork and Rfree are exactly the same? >> > >> > I solved a 3.37 Å structure with Phaser-MR and immediately ran 10 >> > cycles of refinement with wxc = 0.1. Everything else at default. The >> > Rwork and Rfree are both 0.1837. Is this bad? >> > >> > Thank you! >> > >> > Justin >> > >> > - >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Updated links - Phenix version 1.21 released
The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download Highlights for the 1.21 version of Phenix include: - Likelihood-based docking of models into cryo-EM maps. • Full support for structure determination with AlphaFold models. • New joint X-ray and neutron refinement algorithm. • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ. Detailed changes are: - Full support for structure determination with AlphaFold models in Phenix GUI - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences - Phenix AlphaFold server - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation - Cryo-EM tools support ChimeraX visualization - Cryo-EM density modification and anisotropic scaling display local resolution - Tutorials available for automated structure determination with PredictAndBuild - New em_placement and emplace_local tools - likelihood-based docking of models into cryo-EM maps - MOPAC v22 is now distributed with Phenix - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface - Defaults to MOPAC's PM6-D3H4 - Higher level QM available via 3rd-party Orca package - Restraints - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd - Automated tests for programs in the Phenix GUI - ERRASER no longer supported and removed from installation - Remove rebuild_predicted_model (duplicated by predict_and_build) - JSON output added to MolProbity structure validation scripts Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Phenix version 1.21 released
The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.21 version of Phenix include: - Likelihood-based docking of models into cryo-EM maps. • Full support for structure determination with AlphaFold models. • New joint X-ray and neutron refinement algorithm. • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ. Detailed changes are: - Full support for structure determination with AlphaFold models in Phenix GUI - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences - Phenix AlphaFold server - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation - Cryo-EM tools support ChimeraX visualization - Cryo-EM density modification and anisotropic scaling display local resolution - Tutorials available for automated structure determination with PredictAndBuild - New em_placement and emplace_local tools - likelihood-based docking of models into cryo-EM maps - MOPAC v22 is now distributed with Phenix - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface - Defaults to MOPAC's PM6-D3H4 - Higher level QM available via 3rd-party Orca package - Restraints - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd - Automated tests for programs in the Phenix GUI - ERRASER no longer supported and removed from installation - Remove rebuild_predicted_model (duplicated by predict_and_build) - JSON output added to MolProbity structure validation scripts Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] 2023 Cold Spring Harbor Macromolecular Crystallography Course
Dear Colleagues, The July 15th deadline for applications to the CSHL Macromolecular Crystallography Course to be held later this year, October 15th through October 31st 2023, is rapidly approaching. This is a unique opportunity to become expert in the use of crystallography to solve challenging macromolecular structures. The official course announcement can be found here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS=23 please pass this on to anyone who you think might be interested and would benefit, especially 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: Janet Newman, Tom Peat, Jim Pflugrath, Dorothee Liebschner, 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 structural biology to become experts in crystallography. 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 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 will also include the use of computationally predicted structures to aid in solving the crystallographic phase problem. 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. Scholarship support is also provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me an e-mail, we will be happy to answer all queries. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ] [ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] ALS Webinar April 10th
Dear Colleagues, A reminder that we will be hosting a webinar (registration link below) that provides information for the synchrotron structural biology user community about accessing the resources at the Advanced Light Source in Berkeley. This is timely because of the imminent closure of the Advanced Photon Source for a year for their upgrade. Synchrotron capacity for biosciences research will be significantly impacted, and we want to be sure that the community has information about alternative facilities during the APS dark time. http://als-enable.lbl.gov/wordpress/2023/03/14/als-enable-webinar-april-10th-2023/ The webinar will cover capabilities at the beamlines in macromolecular crystallography, small angle X-ray scattering, and X-ray footprinting, as well as information on how to apply for beamtime. While the webinar is of most relevance to the US research community, we welcome participation by anyone who is interested. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] 2022 Cold Spring Harbor Macromolecular Crystallography Course
Dear Colleagues, The July 15th deadline for applications to the CSHL Macromolecular Crystallography Course to be held later this year, October 10 through October 25 2022, is rapidly approaching. This is a unique opportunity to become expert in the use of crystallography to solve challenging macromolecular structures. The official course announcement can be found here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS=22 please pass this on to anyone who you think might be interested and would benefit, especially 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: Janet Newman, Tom Peat, 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 structural biology to become experts in crystallography. 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 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 will also include the use of computationally predicted structures to aid in solving the crystallographic phase problem. 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. Scholarship support is also provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me an e-mail, we will be happy to answer all queries. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ] [ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Phenix version 1.20 released
The Phenix developers are pleased to announce that version 1.20 of Phenix is now available (build 1.20-4459). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.20 version of Phenix include a number of tools to leverage new structure prediction methods: - New tools and methods - Phenix AlphaFold2 notebook: Run AlphaFold on Google Colab from Phenix GUI - phenix.process_predicted_model: Identify useful domains in AlphaFold model - phenix.dock_predicted_model: Dock domains of AlphaFold model into cryo-EM - phenix.rebuild_predicted_model: Rebuild AlphaFold model in cryo-EM map using docked domains - phenix.dock_and_rebuild : Process, dock and rebuild AlphaFold model with cryo-EM map - phenix.model_completion: Connect fragments and fill in gaps based on a map - phenix.rebuild_model: Rebuild a model using a map and keeping connectivity - phenix.replace_with_fragments_from_pdb: Rebuild a model using fragments from PDB - phenix.search_and_morph: SSM search PDB; morph to match target - phenix.fragment_search: Search for a fragment in PDB matching target - phenix.reverse_fragment: Reverse chain direction of a fragment - phenix.superpose_and_morph: SSM or least-squares superpose one model on another; optionally trim and morph to match - phenix.voyager.casp_rel_ellg: Calculate relative eLLG score for predicted model quality - phenix.match_maps: - Bug fix (superposed map was not matching target map) - phenix.real_space_refine: - Symmatry multiprocessing aware individual ADP and occupancy refinement - Multiple changes to improce runtime (for certain refinement strategies) - Make NQH flips symmetry aware - phenix.superpose_pdbs: - Add feature to transform additional models with matrix found with moving model - phenix.dock_in_map: - Allow splitting model into domains based on chain ID from phenix.process_predicted_model - Restraints - GeoStd updated with 12k plus entity restraints files - cis-PRO default updated to EH99 - phenix.fetch_pdb, iotbx.cif_as_mtz: - Bug fix: Multiple datasets with different unit cells in a cif file now preserved as multiple crystals in mtz file. Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ] [ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455
[ccp4bb] Macromolecular Crystallography - CSHL Course
Dear Colleagues, The July 16th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 4 through October 19, 2021 is rapidly approaching. Please see the attached announcement, and the official course web site is here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS=21 please pass this on to folks who might be interested and who would benefit. The course is designed for researchers who are either new to, or who wish to increase their in-depth knowledge of, macromolecular crystallography. We anticipate holding the course in person as long as the pandemic situation continues to improve. Appropriate COVID-19 precautions will be followed to ensure the safety of all participants. Everyone will be required to provide documentary proof of a prior FDA or EMA approved vaccine. This immersive course is an outstanding place to learn both the theoretical and practical aspects of Macromolecular Crystallography because of the extensive lectures from world-renowned teachers, which are combined with hands-on experiments. This 2021 course will be lead by Jim Pflugrath (Rigaku, ret.), Tassos Perrakis (NKI), Paul Adams (LBL), Janet Newman (CSIRO), Tom Peat (CSIRO) and an All-Star cast of lecturers. Attendees can expect to participate in a course that is unparalleled in the world, with experts each devoting several days to teaching the fundamentals, theory and practical considerations of crystallographic structure solution. We expect to have the participants crystallize several proteins and determine their structures all in about two weeks. Students may also work on their own projects, but not exclusively. They will also become well-versed in the theory of X-diffraction and crystal structure determination while having lots of fun, but not much sleep. There will be data collection at state-of-the-art beamlines at NSLS-II. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar room and laboratory settings. Please check the above web link for more details. In particular, please note the information about fellowships, scholarships, and stipends that are available. It is often possible for applicants to receive some level of support to help offset the course fee. This 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. Scholarship support is provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me e-mail, I will be happy to answer any queries. Thanks for spreading the word, Janet, Tom, Tassos, Paul, and Jim > Begin forwarded message: > > From: Cold Spring Harbor Laboratory Meetings & Courses > Subject: Macromolecular Crystallography - CSHL Course > Date: June 24, 2021 at 5:20:20 AM PDT > To: pdad...@lbl.gov > Reply-To: meetm...@cshl.edu > > > > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFcYTJsNKVNY4dm1_PgW5qo-99nzCvbE23iV0E2YZjPvhwkoJmzfNJ2ppgqkDbU8Y0VmMrYTKDSFMfyrK8a16li3ZSccjoNR3cq3IbAflINucALxjm0gJVOQ=f6-XRY5ZwGsmnf8lQOl7zXzDW0qRVcpgqB0oaHmDdl1pE2O99AwCcA===q7ShevqbNThKJM_fcxc76rhMcFKTjc0vPsYuk4J_SaEutikLx0acdg==> > > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFcYTJsNKVNY4eHzXSq4U43Qr4KZxVRbZZjZEneOcWJWRN45Ql8y0KKYUEMC3NmHp-IIUOZZSlg4TcGTnaLm3xETiv9uO2Q45sD9xUugNyAH-EXSEJqXiuwQ4ZHEIhbgNEMOuWNx3cjj-ijP7tkOLUiDLV1GVUInH-I==f6-XRY5ZwGsmnf8lQOl7zXzDW0qRVcpgqB0oaHmDdl1pE2O99AwCcA===q7ShevqbNThKJM_fcxc76rhMcFKTjc0vPsYuk4J_SaEutikLx0acdg==> > Macromolecular Crystallography > <https://r20.rs6.net/tn.jsp?f=001eym31bmCvuxG3gZdQKD4XByq24-SM132UB2keWmTzFcYTJsNKVNY4eHzXSq4U43Qr4KZxVRbZZjZEneOcWJWRN45Ql8y0KKYUEMC3NmHp-IIUOZZSlg4TcGTnaLm3xETiv9uO2Q45sD9xUugNyAH-EXSEJqXiuwQ4ZHEIhbgNEMOuWNx3cjj-ijP7tkOLUiDLV1GVUInH-I==f6-XRY5ZwGsmnf8lQOl7zXzDW0qRVcpgqB0oaHmDdl1pE2O99AwCcA===q7ShevqbNThKJM_fcxc76rhMcFKTjc0vPsYuk4J_SaEutikLx0acdg==> > October 4 - 19, 2021 > Application & Materials Deadline: July 16 > We anticipate that the vaccine situation may sufficiently improve to allow us > to offer this course safely in-person. > > All participants will be required to provide documentary proof of a prior FDA > or EMA approved vaccine. > Instructors > Janet Newman, CSIRO, Australia (likely remote) > James Pflugrath, Rigaku Americas Corporation (ret.), Texas > Anastassis Perrakis, Netherlands Cancer Institute > Paul Adams, Lawrence Berkeley National Laboratory > Co-Instructor: > Tom Peat, CSIRO, Australia(likely remote) > X-ray crystallography has been the cornerstone of structural biology for half > a century, and remains t
[ccp4bb] Cryo-EM Facility Manager - Berkeley California
Dear Colleagues, I would like to draw your attention to a job opening here in Berkeley California, for a Cryo-EM Facility Manager: https://lbl.referrals.selectminds.com/jobs/cryo-em-facility-manager-3801 This position requires expertise in biological cryo electron microscopy (cryo-EM). The successful candidate will be responsible for maintaining the in-house transmission electron microscopes (TEMs) and accessory equipment in excellent working order as well as training new users, scheduling access, and assisting with the collection of high-quality data. Duties will include providing complex technical support for sophisticated biotech-laboratory equipment including maintenance, calibration, repair and troubleshooting of instrumentation, control systems, experimental apparatuses, computers, and peripheral equipment as well as coordinating and scheduling vendor related maintenance and repairs. This is a full time, 3 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Diversity, equity, and inclusion are core values at Berkeley Lab. Our excellence can only be fully realized by faculty, students, and staff who share our commitment to these values. Successful candidates for our faculty positions will demonstrate evidence of a commitment to advancing equity and inclusion. Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers. Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Please register - Phenix Workshop - April 14
Dear Colleagues, The Phenix developers will be holding another online *Phenix User Workshop on the 14th of April at 4-9pm PDT.* These times will work best for researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/X18KrWR6GvRUKYJ49>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. *AGENDA:* *14 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session The recorded workshops are here <https://www.youtube.com/c/PhenixTutorials/playlists> for these and previous ones. Cheers, The Phenix Developer Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL ( http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL ( http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute ( http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source ( http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area ( http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley ( http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ] [ 1-510-486-5455 ] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Please register - Phenix Workshops - April 7 & 14
Dear Colleagues, The Phenix developers will be holding an online *Phenix User Workshop on the 7th and 14th of April at 4-9pm PDT.* These times will work best for researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/X18KrWR6GvRUKYJ49>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. *AGENDA:* *7 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Paul Adams - Phenix Overview - 4.30pm - Tom Terwilliger - Map Improvement - 5.45pm - Tom Terwilliger - Model Building - 7.00pm - Question/Answer session *14 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session Cheers, The Phenix Developer Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL ( http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL ( http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute ( http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source ( http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area ( http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley ( http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ] [ 1-510-486-5455 ] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Phenix version 1.19.1 released
The Phenix developers are pleased to announce that version 1.19.1 of Phenix is now available (build 1.19.1-4122). This fixes bugs in the 1.19 release. If you have previously downloaded 1.19 we recommend upgrading to 1.19.1. Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.19.1 version of Phenix: - phenix.real_space_refine - Fix bug in restoring previous jobs - Clarify NCS options Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] The weekly nonsense
I think this stems from Brian being way too prolific. As I understand it, he used a correlation metric in a paper about T4 lysozyme in 1975, this is what they call the Matthews Correlation Coefficient in machine learning. I suspect our machine learning colleagues are less familiar with the Matthews Coefficient that we all know and love. So, confusing for everyone. Why they mistook the excellent work of Kantardjieff and Rupp in 2003 with a paper of Brian's from 1975 is less clear. > On Jan 22, 2021, at 3:03 PM, Bernhard Rupp wrote: > > Dear CCP4 Fellows, > > for the subscribers of my immensely popular show “The weekly nonsense” I > recommend > https://arxiv.org/pdf/2101.06308.pdf <https://arxiv.org/pdf/2101.06308.pdf> > particularly reference [27] and its contextual environs. > > Am I alone suspecting that this is some AI generated auto-paper-mill product? > > Cheers, BR > > -- > Bernhard Rupp > The Amt > http://www.hofkristallamt.org/ <http://www.hofkristallamt.org/> > b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> > +1 925 209 7429 > +43 676 571 0536 > -- > Many plausible ideas vanish > at the presence of thought > -- > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul <http://cci.lbl.gov/paul> ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Phenix version 1.19 released
The Phenix developers are pleased to announce that version 1.19 of Phenix is now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that this recent publication should now be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Highlights for the 1.19 version of Phenix: - phenix.real_space_refine: - Improved rotamer fitting (use multiprocessing, in case of NCS constraints work on one copy only and propagate changes to all related copies, various performance improvements and bug fixes) - Improved map/restraints weight calculation - Morphing can now use multiprocessing (nproc) - phenix.map_to_model and phenix.trace_and_build - Improved high-resolution model-building including detection of insertions and deletions - New methods - phenix.local_resolution: calculates a local resolution map - phenix.local_aniso_sharpen: optimizes a map taking into account local resolution-dependence and anisotropy of the map and its errors - New scripting tools - High-level scriptable Python tools are now available for map and model analyses and manipulation as well as for model-building - Restraints - Adjusting the "positions" of atom names in (pseudo-)symmetric amino acid side chains is now the default - Improved restraints for ARG allows more flexibility of the CD atom - Bug fixes - Chains with modified amino or nucleic acids can be aligned - Fixed handling of modified amino/nucleic acids in sequence alignment For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
or >> everything together (just in case I have already prepared my subscription to >> Netflix). >> >> https://www.nature.com/articles/d41586-020-03348-4 >> <https://www.nature.com/articles/d41586-020-03348-4> >> >> Well, I suppose that we still have the structures of complexes (at the >> moment). I am wondering how the labs will have access to this technology in >> the future (would it be for free coming from the company DeepMind - >> Google?). It seems that they have already published some code. Well, >> exciting times. >> >> Cheers, >> >> Isabel >> >> >> Isabel Garcia-Saez PhD >> Institut de Biologie Structurale >> Viral Infection and Cancer Group (VIC)-Cell Division Team >> 71, Avenue des Martyrs >> CS 10090 >> 38044 Grenoble Cedex 9 >> France >> Tel.: 00 33 (0) 457 42 86 15 >> e-mail: isabel.gar...@ibs.fr <mailto:isabel.gar...@ibs.fr> >> FAX: 00 33 (0) 476 50 18 90 >> http://www.ibs.fr/ <http://www.ibs.fr/> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul <http://cci.lbl.gov/paul> ORCID: -0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Phenix User Workshop, 17th and 18th of November
Dear Colleagues, The Phenix developers will be holding an online *Phenix User Workshop on the 17th and 18th of November at 8am-12pm PDT.* These times will work best for researchers in North and South America, Europe and Africa. We plan to hold a future workshop at a time better suited to researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/Q8P6ZC9fYqTkS7qD7>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. Cheers, The Phenix Developer Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL ( http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL ( http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute ( http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source ( http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area ( http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley ( http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ] [ 1-510-486-5455 ] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Sad News
Dear Bob, Many thanks for posting this memory of Ward. It was such a sad shock to learn of his passing. Like many of the newsgroup readers I remember Ward as an outstanding colleague and program manager. It was my pleasure to talk with him regularly as my point of contact for Phenix and ALS-ENABLE funding. I will miss our calls and his sage advice and generous spirit. He will be greatly missed by many of us. Paul > On Jul 18, 2020, at 4:36 AM, Sweet, Robert > <27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk> wrote: > > I'm writing to acknowledge the passing of Ward Smith during the weekend of 5 > July. Ward got his PhD with Martha Ludwig at U. of Michigan, and then came to > UCLA in 1977 to join Dave Eisenberg’s group as a postdoc. During the course > of things, he met Cheryl Janson, a Paul Boyer postdoc, and they were married > in 1980. During his time at UCLA Ward became expert in operation of the > Xuong/Hamlin/Nielsen multi-wire system at UCSD and tutored the UCLA users in > its use. In 1985 Ward and Cheryl left UCLA and went to Monsanto in St. Louis, > where Ward worked as a structural biologist. In 1987 they went to Agouron > Pharmaceuticals in San Diego. And then in 1995 went cross-country to > SmithKline Beecham (which became Glaxo SmithKline, merging with > GlaxoWellcome). > > Ward was very involved with getting IMCA set up as a functional facility for > pharmaceuticals at Argonne as SmithKline's representative. This experience > gave him significant credibility in synchrotron macromolecular > crystallography, and in 2003 he joined the GM/CA-CAT beamlines at the APS to > help Bob Fischetti and others construct that excellent facility. During this > time Cheryl worked at Shamrock Structures. > > Ward moved to the NIH headquarters in 2007. There he took some responsibility > for the Protein Structure Initiative, also playing an important role in > supporting NIH synchrotron facilities. In 2010 he became the branch chief for > the Structural Genomics and Proteomics Technology Branch in the Division of > Cell Biology and Biophysics. He remained in that position through 2017. At > the 2018 NIGMS re-organization Ward went to the Biophysics, Biomedical > Technology, and Computational Biosciences division as the branch chief for > the Biomedical Technology Branch. > > Ward helped oversee the big NIH-funded, $45 M construction of three major > beamlines at NSLS-II, a project called ABBIX that ran 2011-2017. In 2017 he > became program director for NIH support of structural biology beamlines at > NSLS-II and other DOE synchrotrons. > > Many knew Ward for his always calm, reasoned demeanor; he was unflappable, > resilient, and friendly. He was well read and devoted to his family. > > > Robert M. Sweet E-Dress: sw...@bnl.gov > Scientific Advisor, CBMS: The Center for BioMolecular >Structure at NSLS-II > Photon Sciences and Biology Dept > Brookhaven Nat'l Lab. > Upton, NY 11973 U.S.A. > Phones: 631 344 3401 (Office) >631 338 7302 (Mobile) > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-b
[ccp4bb] Phenix version 1.18 released
The Phenix developers are pleased to announce that version 1.18 of Phenix is now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that this recent publication should now be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Highlights for the 1.18.2 version of Phenix: 1.18.2 Changes - Fix weighting for iron sulfur clusters 1.18.1 Changes - General bug fixes 1.18 Changes - Amber - Automatic creation of Amber files in phenix.refine GUI - Added AmberPrep GUI - Restraints - Engh & Huber restraints (2001) for cis-peptides now implemented - Restraints added for FeS - Metal coordination library is default to Zn+2 and FeS clusters - Rama-Z: New global Ramachandran score for identifying protein structures with unlikely stereochemistry in CLI (phenix.rama_z, mmtbx.rama_z) and GUI (validation reports). - Density modification for cryo-EM - Includes model-based density modification with automatic model generation - Optimized defaults and additional documentation - Real-space refinement - Hydrogen atoms no longer included in map target function, which improves fit. - Add NQH flip option (enabled by default) - Other - New tool for ordered solvent picking in cryo-EM maps (phenix.douse) - New map and model superposition tool (phenix.match_maps) - New FindProgram to find any Phenix program with a text search - Project details now has a button for opening the README file for tutorials For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Advanced Light Source open for COVID-19 related research
Dear Colleagues, A quick note to alert researchers to the status of the Advanced Light Source in Berkeley (https://als.lbl.gov): The ALS is now operating in a limited capacity supporting COVID-19 related research. A number of MX beamlines from the ALS-ENABLE program are now taking proposals from the general user community working on COVID-19 via the ALS RAPIDD program (https://als.lbl.gov/rapidd/); choose ALS-ENABLE as the beamline and your proposal will receive prompt review with fast turnaround for beamtime. We are evaluating the possibility of expanding access to include to other techniques such as soft X-ray tomography, and BioSAXS in the near future. Please feel free to contact me with any questions. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix Postdoc Position - Berkeley, California
tion Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix Postdoc Position - Berkeley, California
tion Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix version 1.17 released
The Phenix developers are pleased to announce that version 1.17 of Phenix is now available (build 1.17.1-3660). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that there is a new publication that describes recent Phenix developments for structure determination with X-rays, neutrons and electrons: https://doi.org/10.1107/S2059798319011471 Highlights for the 1.17 version of Phenix: 1.17.1 Changes - Fix bug on Windows where xtriage results would fail to display - Other bug fixes 1.17 Changes - Improved handling of SHELX data in phenix.reflection_file_converter - eLBOW can output files for Amber and supports the Orca QM package - dials.image_viewer is used for viewing diffraction images - Updated map smoothing - Fix inconsistency in clashscore values in phenix.validation_cryoem when hydrogens are in the model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Nikki Humphreys [ nhumphr...@lbl.gov ][ 1-510-486-4610 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Berkeley Server Outage (Starting October 26th)
Dear Colleagues, yet again, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down this weekend and will return later the following week. 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. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Berkeley Server Outage (Starting October evening 8th)
Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this week meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down today and will return later in the week. 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. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Berkeley Web Services Downtime
Dear Colleagues, as a result of electrical work at LBNL the following servers will be unavailable over the weekend: - 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/) We expect that the servers will be available some time on Monday July 15th. 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. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab (https://als.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Low resolution structure determination workshop at ECM32
Dear Colleagues, I’d like to draw your attention to a workshop that we’ll be hosting at the 32nd European Crystallographic Meeting in Vienna: Low resolution structure determination and refinement of biological macromolecules by crystallography and cryo-EM Organizers: Paul Adams, Dorothee Liebschner (Lawrence Berkeley Laboratory, Berkeley, USA) Date: 18th August 2019 Time: 9 a.m. – 5 p.m. More details: https://www.ecm2019.org/satellites/ Meeting and satellite registration: https://www.ecm2019.org/submission-registration/registration/online-registration/ 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Electron microscopy software tools workshop at ACA
Dear Colleagues, I’d like to draw your attention to a workshop that we’ll be hosting at the American Crystallographic Associate meeting in Covington: Introduction to PHENIX for Electron Cryo-Microscopists Organizers: Paul Adams (Lawrence Berkeley Laboratory, Berkeley, USA) Date: Saturday, July 20, 2019 Time: 9 a.m. – 5 p.m. More details: https://www.aca2019mtg.com/workshops Meeting registration: https://www.aca2019mtg.com/registration 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix version 1.15 released
The Phenix developers are pleased to announce that version 1.15 of Phenix is now available (build 1.15.2-3472). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for this version: New and improved tools - New algorithm for phenix.map_to_model is faster and builds longer chains - phenix.trace_and_build can build protein into maps at resolutions as low as 4.5 A - phenix.fix_insertions_deletions can build models in places where the map is poor - phenix.refine_ca_model for optimizing C-alpha only models - phenix.comparama for generating Kleywegt-like plots that show how residues moved in the Ramachandran plots before and after refinement - eLBOW can find unique instances of a ligand from the PDB and optionally create Polder OMIT maps - Updated structural library for phenix.structure_search - Updated ligand library for phenix.ligand_identification - Improved reporting of cis-peptides for residues with altloc atoms - Output of mmCIF format files by default by major tools: phenix.refine, phenix.real_space_refine, phenix.pdbtools - Bugfixes in Phaser-2.8.3 Other improvements - Updated mmCIF support (stuct_conn loop, ligand restraints, sequence) - phenix.refine, phenix.real_space_refine, and phenix.pdbtools will also output models in mmCIF format by default - Dependencies are now based on conda packages, which will be more compatible with new operating systems and will improve consistency across all platforms (macOS, linux, Windows) - Bug fixes For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoc Position - Berkeley
Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 85784 Division: Molecular Biophysics & Integrated Bioimaging (Joint BioEnergy Institute) Date Opened: 11/1/2018 Summary: A postdoctoral position is immediately available to study the structure and function of macromolecular complexes and enzymes using biochemical, X-ray crystallographic and electron cryo-microscopy (cryo-EM) methods. The biological systems to be studied are: - Glycosyl transferases responsible for the synthesis of hemicelluloses in plants - Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production - Enzymes involved in lignin biosynthesis, degradation and valorization - Secondary metabolite and natural product enzymes This position will be part of the Structural Biology group of the Technology Division at the Joint BioEnergy Institute (JBEI) in Emeryville, California. To learn more about JBEI visit: http://www.jbei.org/ Duties: The successful candidate will have experience characterizing enzymes using biochemical techniques, and using crystallographic methods. Familiarity with cryo-EM methods would be helpful, but not essential. Robotic hardware for performing crystallization trials and imaging results are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. For appropriate systems cryo-EM data will be obtained using in-house microscopes, the Bay Area Center for Cryo-EM, and other national user facilities. Qualifications: a Ph.D. in biochemistry, molecular biology, structural biology, chemistry or a related field. Demonstrated experience of scientific research using biochemistry techniques including enzymatic assays, and crystallographic methods. Experience with macromolecular crystallization techniques. Experience with cloning methods and protein purification methods would be helpful. Strong problem solving skills. Solid interpersonal skills and the ability to work in a team environment are critical. This is a full time, 2 years, postdoctoral appointment with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. You must have less than 3 years paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree. Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 85784 or visit: https://lbl.referrals.selectminds.com/jobs/crystallography-postdoctoral-scholar-1279 -- 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix version 1.14 released
The Phenix developers are pleased to announce that version 1.14 of Phenix is now available (build 1.14-3260). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for this version: - Reorganization, updates and addition of cryo-EM tools: - phenix.mtriage - assess map and model quality - phenix.auto_sharpen - map sharpening - phenix.map_symmetry - identify symmetry in maps - phenix.map_box - cut out unique parts of maps - phenix.combine_focused_maps - combine different maps - phenix.dock_in_map - automatically place an atomic model into a map - phenix.map_to_model - automatically build atomic model from a map - phenix.sequence_from_map - identify sequence from a map - phenix.real_space_refine - improved refinement of models - phenix.validation_cryoem - separate tool for comprehensive validation of models and maps - phenix.cablam_idealization - Tool to automatically fix Cablam outliers - eLBOW - better support for metals and metal clusters - added plugin for QM package Orca - Phaser-2.8.2 - bugfixes - Phassade substructure search when starting from seed substructure - fix crash in MR_ATOM - problems with cumulative intensity distribution for extremely weak data - improve computation and presentation of data information content - Performance improvements - NCS search - Generation of secondary structure restraints - Clashscore calculation - AmberPrep is more robust - Restraints for ARG improved - New Phenix video tutorials - GUI - New section in main window for cryo-EM tools - Separate validation GUI for cryo-EM structures - Added phenix.map_symmetry - Added phenix.dock_in_map - Added phenix.map_to_structure_factors - Added phenix.combine_focused_maps - Added phenix.sequence_from_map - phenix.ligand_identification: - Added an option to generate ligand library based on sequence and structural homologs of the input pdb model. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] tCNS and space group determination
ry > along with a twin operator that parallels the pseudosymmetry. If that's > true, it's hard to be sure of the symmetry. For instance, if the structure > really is monoclinic, can you be sure you chose the correct axis to be the > 2-fold? > > I am not sure. However, I tried two possible axis to be the 2-fold and none > of them gave me reasonable maps after MR and refinement. > > > Since you have a good model that gives clear MR solutions even in P21, you > can probably process the data in P1 and solve it with 8 copies in the unit > cell. Then you can look at the symmetry of the MR solution (e.g. in Zanuda) > and see whether it obeys any higher symmetry than P1. > > I processed data in P1. After MR (with 8 copies in the ASU), it resulted in > TFZ=11.6 and LLG=1434. But the map is still bad and high Rwork and Rfree. > According to Zanuda, the data should be P21: > ^ >| >> 4 | P 1 21 1 | 68.6868 | 0.6289 | 0.5487 | 0.5523 | >- >| 1 | P 1| 69.4151 | 0.6171 | 0.5471 | 0.5559 | >| 4 | P 1 21 1 | 69.3810 |--| 0.5482 | 0.5442 | >| 11 | P 21 21 21 | 52.0271 |--| 0.6107 | 0.6178 | >- >| << 4 | P 1 21 1 | 69.3810 |--| 0.5482 | 0.5442 | >- > I processed in P21 using two different unit cells, and MR resulted in > TFZ=20.8 and LLG=511, and TFZ=56 and LLG=2867. However, again, no good maps > and statistics. > > Best regards > > Marcelo Liberato > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > -- 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] R-flag choose
I’ll also add for completeness, that (in Phenix at least) by default a total of 2000 reflections will be selected at most - meaning if you have a lot of reflections the total percentage selected will be substantially less than 10% or even 5%. > On Jul 10, 2018, at 7:44 AM, Pavel Afonine wrote: > > It's important to remember that free-R reflections are not only used to > calculate Rfree, but also are used in calculation of m and D scales in > 2mFo-DFc and mFo-DFc maps, as well as in likelihood-based refinement targets. > The fact is that you need to have a sufficient amount of free-R reflections > in each relatively thin resolution bin. Some authors estimate this number as > at lest 50 reflections per bin. In Phenix binning is defined such that each > sufficiently thin bin gets no less than 150 reflections. Bernhard pointed out > about "precision or significance of Rfee". Also, I would add that too few > free-R reflections can affect refinement progress (not only robustness of > Rfree value) (I've done relevant tests to convince myself more than a decade > ago)! Thus I favor having 10% just to be on a safer side. > > Pavel > > > On Tue, Jul 10, 2018 at 1:02 AM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote: > Dear all > > I am confusing the choose of free R-flags recently. Rfactor means calculatted > from reflection not used in refinement,so what's big the difference between > different percentage of R-flags,like it's about 5% in ccp4 -refmac, while it > is 10% in phenix-refinement,what's the difference between them and how they > affect the Rwork and Rfree values when do refinement. Thanks a lot ! > > best regards > > shijun > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Python3 and MTZ
Dear Kay, I’m even more biased that Graeme of course, but I agree completely with what he says. You can write code that is compatible with both 2.7 and 3 and easily make use of the libraries available. Cctbx, and Phenix, are moving to python 3 compatibility in the not so distant future. Cheers, Paul > On Jun 6, 2018, at 4:22 PM, graeme.win...@diamond.ac.uk > wrote: > > Dear Kay, > > > While I am obviously biased, I have to say that using cctbx (even if it is > "old" Python) has a lot to be said for it - there are a lot of tools in there > which are useful once you have read the reflection data & want to do > crystallography. > > > Re: Python 3: within xia2, DIALS and other cctbx-derived projects we have > moved to writing Python which is compatible with 2.7.x and 3.x language > standards - by and large it is not a hardship and means you can write code > today which will continue to be useful. There is a wider push to migrate > cctbx to 2.7.x and 3.x compatibility however it is a large code base and it's > a fair amount of work. There's more to it than just adding brackets after > print though :-) > > > Best wishes Graeme > > > From: CCP4 bulletin board on behalf of Kay Diederichs > > Sent: 06 June 2018 19:47:07 > To: ccp4bb > Subject: Re: [ccp4bb] Python3 and MTZ > > Dear Nicolas, > > my (our) motivation is purely that when learning Python today, and developing > something from scratch, Python3 appears like the better choice (compared to > version 2) - provided that basic crystallographic libraries can be used. > > Just a note (for those whose operating system provides only one of the two > Python flavours): RHEL7 has Python2 as system library, but Python3 can be > installed in parallel (using "Software Collections"). The user makes a choice > by setting the PATH variable. > > best, > > Kay > > On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS wrote: > >> Dear Kay, >> >> depending of the motivation to develop in python3 (could be due to an OS >> using python3 by default or you really prefer to work with python3). If >> it's due to the OS, a possible strategy is to use virtualenv >> (https://virtualenv.pypa.io/en/stable/) which let you use python2 even >> if python3 is the default version for the OS. It exist probably other >> method to have a contain installation of python2 with all the library needs. >> >> I used this strategy (virtualenv) to install ccp4 (with the installer >> which needed python2) on a manjaro linux (Arch based) running python3 >> and that works very well. >> >> Nicolas >> >> Nicolas Foos >> PhD >> Structural Biology Group >> European Synchrotron Radiation Facility (E.S.R.F) >> 71, avenue des Martyrs >> CS 40220 >> 38043 GRENOBLE Cedex 9 >> +33 (0)6 76 88 14 87 >> +33 (0)4 76 88 45 19 >> >> On 06/06/2018 14:25, Kay Diederichs wrote: >>> Dear all, >>> >>> I haven't tried to read MTZ files from Python until now, but for a new >>> project in my lab I'd like to do that - and with Python3. >>> >>> Googling around, it seems that iotbx from cctbx is not (yet) >>> Python3-compatible. >>> >>> So, what are my options? >>> >>> thanks, >>> >>> Kay >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not use, > copy, retain, distribute or disclose the information in or attached to the > e-mail. > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company
[ccp4bb] CSHL X-ray Methods in Structural Biology Course Oct 15-30th 2018: Application deadline June 15th
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=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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix version 1.13 released
The Phenix developers are pleased to announce that version 1.13 of Phenix is now available (build 1.13-2998). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights for this version: - phenix.map_to_model - better symmetry support and improved runtime efficiency - phenix.structure_search - structural library and internal support for mmCIF - phenix.ligand_identification - limit ligand size for search - Phaser 2.8.1 - various bug fixes - Structure Comparison - more/improved validation information (ligands, waters, cis/trans peptides, HIS protonation) - GUI - automatic validation after phenix.real_space_refine; visual improvements in validation - Improved handling of model mmCIF input/output - New Phenix video tutorials - Internal bug fixes and performance improvements - NEW FEATURES - Phenix.map_to_model: - Allows cases where symmetry that is neither point-group nor helical is present - Allows splitting runs into many small independent steps - Set defaults for quick=True to run somewhat more quickly - GUI - Validation information added to phenix.real_space_refine results - phenix.real_space_refine GUI accepts input for reference models - Polygon stand-alone GUI deprecated; rolled into Comprehensive Validation GUI - Old Polygon jobs cannot be restored - Validation GUI - Stoplight colors (green/orange/red) added to validation summary - In rotamer outlier table, uncalculated chi angles now display blank instead of None - Validation table columns adjusted to reduce whitespace - Updated dependencies - Python 2.7.13 -> 2.7.14 - Boost 1.56 -> Boost 1.63 - Numpy 1.8.1 -> 1.8.2 - phenix.structure_search: - Updated to November 2017 RCSB non-redundant library (representatives of 100% sequence-identity clusters.) - Changed to mmcif-based coordinate handling internally. - phenix.ligand_identification: - Added search limit on ligand sizes (Non-H atoms) - Run LigandFit algorithm internally as default. - Phaser-2.8.1 - bugfixes - anisotropy correction of map coefficients after MR - detection of duplicate solutions - correct cell for PDB after refinement of cell for input data - packing places molecules near origin in compact arrangement - Structure Comparison - Updated to include favoured, allowed and outliers for validations tabs such as rotamers - Add featurs such as ligands information & locations; water locations; cis/trans peptides; and histidine protonation - General increase of robustness and flexibility - Greater flexibility for model/data input including directory tree travesal and user defined scripts - Restraints - Added better SF4 restraints - Added mechanism to improve SF4 linking - Various performance enhancements - Better handling of model mmCIF input/output - New Phenix video tutorials: - Cryo-EM tools in Phenix - overview - How to run MolProbity - step by step (web interface and Phenix GUI) - MolProbity: All atom contacts tutorial For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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 33R
[ccp4bb] Phenix version 1.12 released
- phenix.auto_sharpen - phenix.map_to_model - phenix.ncs_average (under "Other Tools") - phenix.sculpt_ensemble (alpha) - Updated interfaces - Comprehensive Validation shows real-space correlations from phenix.map_model_cc when map files are used - Structure Comparison - Validation - improved speed of clashscore validation - bug fix to handling of cis-peptides in ramalyze - contours for ramalyze, rotalyze, and cablam now accessible at https://github.com/rlabduke/reference_data - validation GUI now shows altloc identifirs for most outliers - improved internal code accessibility of validation statistics - Phaser-2.8.0 - refinement of cell for data (electron micrcoscopy) - more analysis using eLLG for component addition - more analysis using eLLG for polyalanine residues for target eLLG given rms - more analysis using eLLG for single atoms more ordered than average - more analysis using eLLG for chains/gyre-and-gimble * Phassade: Fast Fourier Transform Anomalous Substructure Determination - SOLU TRIAL records RF-LLG for trial orientation - gyre and translation function report RF recorded for trial orientations - 'scons --ccp4' command line flag for ccp4 build (generates ccp4-style headers) * improved tNCS detection and analysis * gyre and gimble improved for output and python scripting * NMA outputs all perturbed files in MODEL delimited pdb file '.nma.pdb' * sceds outputs domains to chain delimited file '.nma.pdb' - sceds domain pdb file have TER separated domains - NMA option to output separate pdb files for each perturbation (XYZOUT NMA ALL OFF) - sceds option to output separate pdb files for each domain (XYZOUT NMA ALL OFF) - NMA has option to turn off output of input coordinates (NMA ORIG ON) - pdb chain identifies can be left unchanged from input (XYZOUT CHAIN COPY) (for Eleanor) - bugfixes -- allow peaks and purge percent to override one another if not default -- rms estimation developer options not being set correctly -- throw out of memory error if Patterson map allocation fails For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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 80, Room 247 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
Re: [ccp4bb] Bond length and angle outlier fixing
To add to Pavel’s comments, it is also possible to do the automated model building in Phenix: http://www.phenix-online.org/documentation/reference/map_to_model.html As Pavel said: there is Phenix mailing list for Phenix-specific questions > On May 17, 2017, at 10:24 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > Hi, all. > > I have collected cryoEM data and want to use Coot and CCP4 program to build > model and to refine it. > > 1. What is the steps to do this? > 2. How do I convert cryoEM map file to MTZ file? > 3. Can I also use Phenix for this purpose? > > Thanks to all for your help in advance. -- 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 80, Room 247 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
Re: [ccp4bb] Phenix version 1.11.1 released
Hi Tim, you are correct as it is scattering by the nucleus. Support for ions means that users can use an “ion name”, e.g. Ca+2 for an atom and the appropriate scattering factors will be used. The neutron scattering table previously didn’t include the ionic names. Cheers, Paul > On Nov 2, 2016, at 2:41 PM, Tim Gruene <tim.gru...@psi.ch> wrote: > > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Paul, > > I am surprised by the mentioning of support for ions in the neutron > scattering > tables. > > Would you have a reference? I always though neutron scattering was > independent > of the electronic state of an atom. > > Best, > Tim > > On Wednesday, November 02, 2016 12:04:55 PM Paul Adams wrote: >> The Phenix developers are pleased to announce that version 1.11.1 of Phenix >> is now available (build 1.11.1-2575). Binary installers for Linux, Mac OSX, >> and Windows platforms are available at the download site: >> >> http://phenix-online.org/download/ >> >> Highlights for this version: >> >> New tools for omit maps without bulk solvent in omitted region, automated >> sharpening of cryo-EM and crystallographic maps, and segmentation of maps. >> Improved NCS search. New automated model-building tools for low-resolution >> maps - especially cryo-EM, tools for matching chains (both residues and >> direction), multiple improvements to phenix.real_space_refine and addition >> of new GUI. Improved model geometry restraints, many improvements to >> Phaser, improved validation incorporating new MolProbity features, >> simplified Rosetta installation, improved support for Amber, updated >> dependencies, Unicode support in GUI, new unified interface for atom >> selections. >> >> - General >> - Improved geometry restraints: >>- Conformation-Dependent Library for omega added (omega_cdl=True) >> - Installation >>- Rosetta installation centralised for phenix.rosetta_refine, >> phenix.mr_rosetta and ERRASER >> - Improved NCS search procedure with simplified parameters. Provides >>status of user-supplied NCS groups during validation >> (refused/modified/ok) - Updated dependencies >>- biopython 1.64 -> 1.66 >>- sphinx 1.2.2 -> 1.4.4 >>- ipython 2.1.0 -> 3.2.1 >>- pip 6.0.7 -> 8.0.2 >> - Neutron scattering tables: support ions >> >> - Amber refinement >> - Alpha release dev-2203 >> >> - GUI >> - New interfaces >>- phenix.map_comparison >>- phenix.polder >>- phenix.structure_search >>- phenix.real_space_refine >> - New selection editor >>- Unified interface for selecting atoms >> - Secondary structure annotations >> - NCS groups >> - TLS groups >> - Refinement strategy options >> - Unicode support >>- Non-ASCII characters are supported for most fields (e.g. file paths >> and job titles) >>- Using non-ASCII characters in projects/jobs will prevent earlier >> versions that do not have Unicode support from opening the project list >> correctly - Migrated validation after phenix.refine to use regular >> MolProbity for consistency (older versions of Phenix will not open new >> jobs) >> - phenix.real_space_correlation can now accept map files >> - phenix.molprobity can now accept map files >> - Updated dependencies for Linux >>- libpng 1.2.52 -> 1.5.26 >>- freetype 2.4.2 -> 2.6.3 >>- gettext 0.18.2 -> 0.19.7 >>- glib 2.12.11 -> 2.46.2 >>- expat 1.95.8 -> 2.1.0 >>- fontconfig 2.3.95 -> 2.11.1 >>- render 0.8 -> 0.11.1 >>- xrender 0.8.3 -> 0.9.7 >>- xft 2.1.2 -> 2.3.2 >>- pixman 0.19.2 -> 0.34.0 >>- cairo 1.8.10 -> 1.14.4 >>- pango 1.16.1 -> 1.38.1 >>- atk 1.9.1 -> 2.18.0 >>- libtiff 3.6.1 -> 4.0.6 >>- gtk+ 2.10.11 -> 2.24.29 >>- matplotlib 1.3.1 -> 1.5.1 >> >> - Maps >> - phenix.polder calculates omit maps which exclude the bulk solvent around >> the omitted region. This way, weak densities possibly obscured by bulk >> solvent may become visible. >> - phenix.model_map: Given PDB file calculate model map and output as CCP4 >>formatted binary map file. >> - phenix.mask: Given PDB file calculate bulk-solvent mask and output as >> CCP4 formatted binary map file. >> - phenix.auto_sharpen: Optimizes resolution dependence of a map to improve >> clarity >> - phenix.segment_and_split_map: Carri
[ccp4bb] Phenix version 1.11.1 released
read TNCS/anisotropy binary files to avoid refinement, when running through scripts - write tNCS and anisotropy parameters to binary files (non-python interface) - default reading of I (or failing that, F) from mtz file (LABIN optional) - trace for ensembles from maps = hexgrid of 1000+/-100 points - trace for ensembles from coordinates above 1000 Calpha = hexgrid of 1000+/-100 points - trace for ensembles from coordinates twixt 1000 atoms and 1000 Calpha = Calpha atoms - trace for ensembles from coordinates under 1000 atoms = all atoms - packing by pairwise percent only, other packing modes obsoleted - packing test during FTF run by default with 50% pairwise packing cutoff - automatic tNCS NMOL determination in presence of commensurate modulation - added MODE GIMBLE, which splits ensembles by chain for rigid body refinement - support for unicode - solution coordinates placed nearest to input coordinates if possible - phenix.reduce - Updated reduce_wwPDB_het_dict as of Aug 12, 2016 - New script for updating het dict - Reduce no longer rotates methionine methyls by default. -DOROTMET flag reinstates old behavior - phenix.ramalyze - Improved handling of residue connectivity - Summary statistics provided for altloc A specifically where multiple altlocs present For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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 80, Room 247 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Berkeley Server Downtime
Dear Colleagues, the CCI group in Berkeley is moving to a new building this week. As a result several structural biology web services will be offline for a short while. These include: - 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/) The servers will be shutdown at 9am Pacific time on Wednesday 10th. Services should resume by the morning of Friday 12th at the latest. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Building 80, Room 247 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 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Postdoc Position - Berkeley, California
Lawrence Berkeley Laboratory Postdoctoral Fellow Job ID: 80929 Division: Physical Biosciences Date Opened: 5/8/2015 Summary: A postdoctoral position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: Development and implementation of computational algorithms for structure determination using crystallography. Including methods for the assessment of crystallographic data quality, improved methods for minimization of target functions, algorithms for the automated parameterization of structure refinement, new target functions for the refinement of structures, and enhanced structure deposition tools. Qualifications: Ph.D., or equivalent experience, in computational crystallography, computational biology, bioinformatics, computational chemistry or a related field. Demonstrated experience with computational methods development. Publications in macromolecular crystallography or related field. Familiarity with software development tools such as C++, C and scripting languages such as Python. Good programming and mathematical skills. Solid interpersonal skills and the ability to work in a team environment are important. Ability to communicate with a broad range of researchers. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years, and 57 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 80929 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=enjob=80929 -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix - Research Scientist Position
Lawrence Berkeley Laboratory Career-track Research Scientist Job ID: 80447 Division: Physical Biosciences Date Opened: 1/14/2015 https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=enjob=80447 Summary: A research scientist position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: This position will develop and maintain a powerful graphical user interface for the PHENIX system, and develop code within the Computational Crystallography Toolbox (cctbx). This position will include the development of new methods for crystallographic structure determination and completion in the context of the PHENIX program. This position also has a significant responsibility for the maintenance of PHENIX automated compilation tools, web-based interfaces for software downloads and coordinating releases of Phenix to the user community. The incumbent will work under the general direction of the Principal Investigator (PI; Paul Adams) for this project. Duties will also include testing, documentation writing, and extensive interaction with users and other developers. Qualifications: Demonstrated expertise with computational methods for protein crystallography. First-author publications in the area of macromolecular crystallography. Familiarity with software development: C++ and the Python scripting language. Advanced knowledge of Python-based or similar graphical user interface development tools. Solid interpersonal skills and the ability to work in a team environment are critical. A Ph.D. in computational crystallography, biophysics, chemistry, computer science, or related field is strongly preferred. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Berkeley Lab addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status. Learn more at http://www.lbl.gov. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Building 80, Room 247 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 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.9 released
/Phenix refinement of protein X-ray crystal structures for difficult cases at low resolution - reference: DiMaio et al. (2013) Nature Methods - phenix.molprobity (new command): - Unified validation tool for command-line users; similar to existing comprehensive validation in the Phenix GUI - optional output of script for viewing results in Coot, or kinemage file - phenix.composite_omit_map (new command): - Default method uses very fast iterative de-biasing procedure - Can also generate either a simple or composite omit map with refinement and optional simulated annealing - Will generate multiple map types at once - parallelizable on multi-core systems or managed clusters - phenix.sceds (new command, formerly phaser.splitter): - implements normal mode-based domain finding method - reference: McCoy et al. (2013) Acta Cryst D69 - phenix.real_space_refine (new command): - tool to refine a model against a map (especially EM maps) - phenix.fem (new command): - Compute feature-enhanced map (FEM) - this protocol modifies a 2mFo-DFc sigmaA-weighted map such that the resulting map has strengthened weak signal, if present, and a reduced amount of noise and model bias. - combines randomization and averaging, treatment of missing reflections, residual composite omit map, and histogram equalization - resulting maps are more interpretable and have less bias compared to the starting 2mFo-DFc map - very fast procedure, no refinement required - phenix.map_to_structure_factors (new command): - convert map into structure factors (also intended for EM) - phenix.angle (new command): - compute angle between two axes or two atom selections - phenix.model_model_distances (new command): - Given two PDB files compute distances per atom, residue, chain, model and overall. It is assumed (and asserted in the code!) that the amount and order of atoms in both files are identical. - phenix.fab_elbow_angle (new command): - Calculating Fragment Antigen-Binding (Fab) elbow angle - phenix.f000 (new command): - Given PDB file estimate F(0,0,0); includes atomic model and bulk-solvent Ligands: - phenix.ligand_identification: - Now you can use ligand cif files (in addition to .pdb files) to build your own custom ligand library. Just specify Ligand directory (GUI) or use keyword ligand_dir (command line) to tell the program to use .pdb or .cif files in your own ligand directory. - Bug fix to properly handle mtz labels when using difference maps. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Building 80, Room 247 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 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.8.4 released
- phenix.guided_ligand_replacement: - Guided Ligand Replacement (GLR) can now search for a protein-ligand complex suitable for the guided fitting using web services on the PDB website or in a local directory. - GLR ligand input has been reworked to allow the use of the three-letter code relying on eLBOW to generate the restraints. - REEL: - simplification and improvement of molecule building - support for cis/trans E/Z enantiomers - view .geo files Miscellaneous: == - PDBTools: - simple dynamics option moved to new command, phenix.dynamics - remove_alt_confs and truncate_to_poly_ala options made compatible with other model modifications - HySS: - converted to use standard Phenix parameter syntax - Many new optional features: - Parallel pre-scoring of 2-site solutions - Parallel completion and scoring - Comparison with a fixed solution - Resolution cutoff for Phaser rescoring - Top-scoring solution written even if no matches found - All solutions written - Skip direct methods completion - LLG completion sigma cutoff - Scoring of input sites - Randomization of input sites For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Building 80, Room 247 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 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
Re: [ccp4bb] mmCIF as working format?
Tim, I'm sure your email was tongue-in-check, but it's provocative nevertheless. I suspect that Nat's point was that scientific software developers (who are predominantly scientists of course) are helpful people who want to see their field of research be successful. If it is possible to spend an hour writing a tool that helps several thousand researchers to do their work that's probably a valuable use of time. An enlightened funding agency might even see the value! Sometimes it's a challenge to figure out exactly what would be of most help, hence Nat's plea for input. I don't know about other software development efforts, but we're very happy to get ideas and suggestions from researchers - just don't assume that we can implement them all (by tomorrow)! Cheers, Paul On Aug 8, 2013, at 12:17 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 08/07/2013 11:54 PM, Nat Echols wrote: PLEASE tell the developers what you need to get your job done; we can't read minds. -Nat Dear Nat, I have a student working for me until the end of the month. I asked her to calculate the mean ratio of U(H)/U(X) where X is the atom the corresponding hydrogen is bound to. I would like her to group together as follows: 1) all N-H and O-H within that protein 2) all Calpha-Halpha 3) all remaining C-H bonds 4) all O-H from the H2O and H3O in the structure. I am not sure whom to address this request to, so please forward it to the developer. If the could would actually work on a shelxl res-file it would be brilliant. I shall not ask George for this software because as a scientist he has much more important and much more general problems to work on than this. At the moment the person is doing it by hand which might take a day. So if you could return the code by tomorrow that would be nice. Out of the tens of thousands of crystallographers coming up with funny ideas (because, yes, you cannot read minds) you might receive such requests several times a day. And you seriously think this is the way we should go? Bless your funding agencies. Cheers, Tim P.S.: I found this discussing about mmCIF quite interesting, and since I was reminded that mmCIF is still kind of line oriented, I am pretty relieved. I just don't think that a 'universal' API exists - the student I am talking about does not know any programming language at all, and the next student might require an API in scheme, ruby, java, C#++-3.141, fortran-123, ... - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSA0YIUxlJ7aRr7hoRApyzAJ94tzJVf81vOggf7KO9SEwoidUz2QCcCkwQ 9IB2FlSTW7oiMP21vUP7QsY= =dGz8 -END PGP SIGNATURE- -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Building 80, Room 247 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 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Postdoc Position - Berkeley
Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 76029 Division: Physical Biosciences (Joint BioEnergy Institute) Date Opened: 6/5/2013 Summary: A postdoctoral position is available at the Joint BioEnergy Institute in Emeryville to work on proteins involved in plant cell wall synthesis. To learn more about JBEI visit: http://www.jbei.org/ Duties: Implementation of methods for the cloning, protein expression, and purification for glycosyl transferases, typically using the Gateway system for gene manipulation. Transformation of host organisms for protein expression, followed by assay of protein expression, and scale up of expression and sample processing (such as deglycosylation). Purification of proteins for biochemical and structural studies. Expression in multiple systems, including E. coli, yeast and insect cells. Qualifications: a Ph.D. in biochemistry, molecular biology, structural biology, or a related field. Demonstrated experience with protein expression, especially in systems other than E. coli. First-author publications demonstrating prior results in the area of protein expression. Experience with cloning methods and protein purification methods. Strong problem solving skills. Solid interpersonal skills and the ability to work in a team environment are critical. Experience with the practical aspects of structure solution by X-ray crystallography would be helpful but not essential. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years, and 57 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 76029 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=enjob=76029 -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Postdoc Position - Berkeley
Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 75785 Division: Physical Biosciences Date Opened: 4/9/2013 Summary: A postdoctoral position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: Development and implementation of computational algorithms for structure determination using crystallography. Including methods for the assessment of crystallographic data quality, improved methods for minimization of target functions, algorithms for the automated parameterization of structure refinement, new target functions for the refinement of structures, and enhanced structure deposition tools. Qualifications: Ph.D. in computational crystallography or a related field. Demonstrated experience with computational methods development. Publications in macromolecular crystallography or closely related field. Familiarity with software development tools such as C++, C and scripting languages such as Python. Strong programming and mathematical skills. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years, and 57 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 75785 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=enjob=75785 -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.8.2 released
): - combined assessment of model and data quality, as outlined in Karplus Diederichs (2012) Science 336:1030-3. - summary also output by phenix.model_vs_data if additional unmerged_data keyword is specified - phenix.maximum_entropy_map (new command): - tool to compute maximum entropy map from map coefficients. The program reads input Fourier map coefficients and modifies corresponding synthesis using Maximum-Entropy Method (MEM). The MEM modified map is everywhere positive, smooth and is of higher resolution. The method uses is a modification of Gull Daniell (1978) algorithm. - phenix.sort_hetatms (new command): - rearranges heteroatoms (ligands, waters, etc.) in a model so they are paired with the nearest macromolecule chain, similar to the PDB's processing of models - phenix.pdb_editor (new command): - graphical editor for PDB files, based on tree view of model hierarchy - perform common operations such as chain renaming, renumbering, manipulation of atomic properties, add/remove atoms Ligands: - phenix.ready_set: - methyl rotations now automatic when adding explicit hydrogens (also in phenix.reduce) - more options adding deuteriums to a model have been introduced Miscellaneous: == - phenix.xtriage: - include merging statistics if unmerged intensities are used as input - phenix.maps: - added wavelength parameter and support for anomalous residual and Phaser LLG map coefficients For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.8.1 released
The Phenix developers are pleased to announce that version 1.8.1 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: - New GUIs: phenix.find_alt_orig_sym_mate General: - Multiple bug fixes - New commands: phenix.erraser, phenix.merging_statistics - Added geometry restraints for over 400 non-standard amino acid entries Refinement: === - Overall B-cart now applied to individual atomic B-factors (restores pre-1.8 behavior) - Improvements to torsion NCS rotamer correction - Real-space refinement (including rotamer fitting) for twinned data New command: - phenix.erraser: - New method from Fang-Chieh Chou and Rhiju Das (Stanford) combining Rosetta nucleic acid rebuilding with phenix.refine (requires separate installation of Rosetta 3.4 or more recent) Molecular Replacement: == - Phaser updated to version 2.5.2: - Scattering from HETATM records that represent modified amino acids (e.g. MSE/SeMet) included so that maps no longer show holes for these HETATM records in the model; occupancies will not be reset. - Packing test was incorrectly applied to reoriented molecules where there was PTNCS Experimental Phasing and Model Building: - AutoSol: - Scale of derivative in SIR (for RIP phasing) can be set with keyword derscale - AutoBuild: - Unassigned chains are now given the segid of UNK and are normally given chain ID=U Ligands: - eLBOW: - New option, --multiple-planes, to generate planes around double bonds - Saturated rings now have dihedral restraints to maintain chair conformation - REEL: - View relationships between ligands using PubChem fingerprint and tanimoto score. Miscellaneous: == - phenix.real_space_correlation: - Simplified command-line behavior - phenix.merging_statistics (new command): - Calculate statistics for unmerged data in a variety of formats, including I/sigmaI, R-merge, R-meas, R-pim, CC1/2 - References: Diederichs K Karplus PA (1997) Nature Structural Biology 4:269-275 Weiss MS (2001) J Appl Cryst 34:130-135. - phenix.kinemage: - Improvements to handling of alternate conformations. - phenix.combine_models: - Combine two models, taking the best parts of each to create a new model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.8 released
The Phenix developers are pleased to announce that version 1.8 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: - New GUIs: phenix.multi_crystal_average, phenix.morph_model, phenix.table_one, phenix.find_peaks_holes - Improved layout for AutoBuild and reflection file editor GUIs - Editor for custom bond/angle/plane restraints in phenix.refine - Project groups: manage defaults for similar projects General: - New very fast bulk-solvent and overall anisotropic scaling procedure - Experimental Windows installer (32-bit only) - Improved support for anomalous difference arrays (F SIGF DANO SIGDANO ISYM) - New commands: phenix.den_refine, phenix.find_peaks_holes - Overall Molprobity score now calculated in phenix.model_vs_data and the validation/refinement GUIs Refinement: === - Change in default NCS restraints behavior: - use torsion-angle parameterization - restraints on NCS-related B-factors turned off - Automatic matching of chains to reference model; allows multiple chains to be restrained to a single reference chain - Support for multiple reference model files - New method for filling of missing Fobs using simple density modification Molecular Replacement: == - phaser (version 2.5): - TNCS support enabled by default for both MR and SAD Experimental Phasing and Model Building: - AutoSol: - TNCS support for SAD phasing Miscellaneous: == - phenix.pdbtools: - ability to set atomic charge field (used for X-ray scattering factors and VDW radii in nonbonded restraints) - phenix.find_peaks_holes (new command): - standalone map peak search program: highlight difference map features - includes analysis of anomalous maps, flag suspicious water molecules - phenix.maps: - simplified execution on command line: phenix.maps model.pdb data.mtz - generates default map coefficients (2mFo-DFc, mFo-DFc, anomalous if available) and 2mFo-DFc CCP4-format map. - phenix.fetch_pdb: - added --maps option: generates 2mFo-DFc and mFo-DFc map coefficients - phenix.get_cc_mtz_pdb: - added atom_selection keyword: compute CC for a subset of atoms - phenix.real_space_correlation: - simplified execution on command line: phenix.real_space_correlation model.pdb data.mtz - calculates CC of model to 2mFo-DFc map - added atom_selection keyword: compute CC for a single selection (instead of per-atom or per-residue statistics) For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Trueblood Award Nominations
Dear Colleagues, on behalf of the selection committee I'd like to draw your attention to the the Trueblood award: http://www.amercrystalassn.org/content/pages/main-award-descriptions This will next be awarded in 2013, however nominations are sought now so that the winner can be announcement this Summer. The award will be presented at the 2013 ACA meeting. Please follow this link to obtain the nomination form: http://www.amercrystalassn.org/documents/ACAnomNEW.pdf Note that the deadline for nominations is May 1st, which should be sent to mar...@hwi.buffalo.edu. Here is a summary of the award: Kenneth N. Trueblood Award To recognize exceptional achievement in computational or chemical crystallography. The award is established in memory of Professor Kenneth N. Trueblood, UCLA 1949-1998, who was a major force in the early use of computers and the development of crystallographic computer programs. He applied these programs to the examination of chemical and molecular details of many structures at the frontiers of research. His contribution to the famous work on vitamin B12 is one example. Professor Trueblood was a leader in the development of techniques for analysis of anisotropic motion and was also a superb teacher and a lucid author. Established in 2001, the award will be given every three years and consist of an honorarium of $1,500 and up to $1,500 in travel expenses to accept the award. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
Re: [ccp4bb] REFMAC5 residues with bad geometry
Hi James, my understanding is that phenix.refine allows any number of alternate conformers. There may have been a limit of 4 some time in the past, but no longer. So your idea could be tested. Cheers, Paul On Mar 27, 2012, at 12:33 PM, James Holton wrote: Try this: 1) take your favorite PDB file and set all the B factors to ~80 (reduces series-termination errors) 2) use sfall/fft in CCP4 to calculate structure factors to 4A resolution 3) use sftools to add a SIGF column (0.1 will do) to make refmac5 happy 4) refine the perfect model against these fake data for ~5 cycles (with solvent no) 5) load this up in coot and contour at 1 sigma 6) repeat the refinement with a PDB file containing only main chain. 7) repeat the refinement after putting all the side chains in their most likely (Ponder-Richards) rotamers. Ask yourself these questions: 1) can you see the side chains? 2) can you see the waters? 3) what are the R factors from these refinements? Answers: 1) no, 2) no, 3) ~3% for perfect, ~50% for main chain, and ~36% for likely rotamer Now ask yourself: even though there is no density for side chains and waters, is there really no evidence that they exist? The point I am trying to make here is that you EXPECT side chains to poke out of density at low resolution, even under ideal conditions (perfect phases). For example, the C-deltas of Leu will breach the 1-sigma contour at around 2.8A resolution and worse. You can see this in my old movie: http://bl831.als.lbl.gov/~jamesh/movies/index.html#reso When it comes to building, yes, once an atom dips below the 1-sigma contour it gets harder and harder to know exactly where it is, but it does have to be somewhere. Somewhere nearby. Formally, there is prior knowledge of bond lengths, etc. at play. And if you know that there is one copy of a given atom in every unit cell of the crystal, then occupancy 1 is inappropriate. Much better to use B = 999, which models the atom as a Gaussian with the electrons spread over an area about 3.5 A wide. This is roughly the range your average side chain atom has available to it, given that it is attached to the main chain by covalent bonds. Of course, a more Bayesian model for the I don't know what the rotamer is situation would be to build in ALL possible rotamers, with occupancies equal to their Ponder-Richards probabilities. Some improvement to this initial guess would no doubt be made by using constrained occupancy refinement of rigid-body side chains. Unfortunately, this is impossible with any refinement program I know about, since refmac, phenix.refine, etc. don't support more than 3 or 4 alternate conformers. Building in all possible conformers and using the occupancy as a p-value would also help solve the problem of the careless and/or uneducated over-interpreting PDB files. Which is the right one? Good question! I think its time we started dispelling the myth of the single-conformer protein anyway. -James Holton MAD Scientist On 3/26/2012 7:40 AM, Ed Pozharski wrote: On Mon, 2012-03-26 at 10:17 -0400, Gregory Bowman wrote: But what about the issue of resolution? As was previously pointed out, at say 3.2 Å resolution, many side chains will fail to fit, but it doesn't seem appropriate to trim them all down. Why is it inappropriate to trim them down? Sometimes at low resolution all one can be confident about is the backbone trace. Just to be clear, I am talking about atoms whose positions are not supported by electron density, i.e. where difference map in the absence of the side chain is featureless. I assume that is the likely situation when one would set occupancy to zero. Cheers, Ed. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.7.3 released
). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Job Opportunity - Head of the Berkeley Center for Structural Biology
The Physical Biosciences Division at Lawrence Berkeley National Laboratory is seeking candidates for the Head of the Berkeley Center for Structural Biology. This position provides scientific, technical and operational oversight of the BCSB at the Advanced Light Source (ALS), a third generation synchrotron facility. The BCSB is a user resource for structural biology experiments and consists of 5 beamlines at 2 sectors of the ALS, with a staff of 16. This Staff Scientist position will provide leadership and direction to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation, and on projects involving the structure determination of biological molecules using X-ray crystallography. This position focuses on the field of crystallography, and involves interactions and collaborations with researchers from multiple scientific disciplines including chemistry, crystallography, biochemistry, biology, physics and computational sciences. For full details please visit the job application link at: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=enjob=73970 Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more about the Lab at http://www.lbl.gov. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.7.2 released
The Phenix developers are pleased to announce that version 1.7.2 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: - phenix.data_viewer added under Reflection Tools - New GUIs: HySS, phenix.cut_out_density, phenix.reciprocal_space_arrays General: - New commands: phenix.cut_out_density, phenix.data_viewer, phenix.morph_model - Default map output format changed to CCP4 - Native support for CIF-format reflection files (e.g. from PDB) in many commands and GUI Refinement: === - New Xray/restraints weight optimization. Keywords optimize_wxc and optimize_wxu replaced with optimize_xyz_weight and optimize_adp_weight, respectively. - Grid searches parallelized: use 'nproc' parameter to set number of CPUs to use - this affects bulk solvent mask optimization, and XYZ and ADP weight optimization (in addition to TLS identification) - can reduce runtime by 75% or more depending on settings (see manual for details) - Modified non-bonded parameters resulting in improved geometry, especially at low resolution - Rigid-body refinement mode defaults to grouping by chain - Printout of validation statistics during coordinate refinement - Bug fix in phase-combined map calculation results in significantly improved maps - Bug fix in X-ray/ADP restraints weight calculation results in smaller B-factors deviations for bonded atoms - Experimental feature (still in testing): - Torsion-space NCS (ncs.type=torsion), automatic parameterization, similar to reference model restraints - Uses top-out potential to allow deviations between NCS related atoms New commands: = - phenix.cut_out_density: - carve out a region from map coefficients (MTZ file) - density may be specified as a sphere, a box, or masked around a PDB file - phenix.data_viewer: - visualization of reciprocal-space reflection data - 3D OpenGL view of all data, or 2D view of planes (pseudo-precession photograph) - phenix.morph_model: - Use after molecular replacement to improve model for rebuilding - Morphs model to match a prime-and-switch map Molecular Replacement: == - Phaser (and AutoMR wizard): - significant speedup of fast rotation function Miscellaneous: == - phenix.reel: - better integration with main GUI, especially eLBOW - phenix.fobs_minus_fobs_map: - option to disable strict unit cell isomorphism check - phenix.ramalyze: - optional output of PNG images of Ramachandran plots; add --plot to command line arguments - phenix.fetch_pdb: - new flags: --all fetches PDB, CIF, and FASTA files simultaneously --mtz runs phenix.cif_as_mtz on downloaded CIF file For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 Head, Berkeley Center for Structural Biology Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.7.1 released
Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ klmo...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Phenix version 1.7 released
The Phenix developers are pleased to announce that version 1.7 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical Interface --- - Simplified AutoMR interface for single-component searches. - Multi-criterion validation kinemage display in KiNG. - Validation of RNA, isotropic ADPs, occupancies. - Improved project management interface, which will automatically import old projects to the new format when upgrading from a previous version of Phenix. - Integrated help browser on Mac with contextual help buttons embedded in program windows. - phenix.find_tls_groups available as part of the phenix.refine GUI. - Improved and expanded documentation for wizard and Phaser GUIs. Structure refinement - A new fast real space refinement protocol, which can substantially improve poor starting models. - A fast method for automated identification of TLS groups (phenix.find_tls_groups). - Reference model, Ramachandran, and secondary structure restraints to improve refinement at low resolution. - Automated secondary structure restraint generation for non-Watson-Crick base pairs (using the Saenger classification). - Automatic support for D-peptides when using standard PDB residue names. Molecular Replacement - - A new command, phenix.mr_rosetta, which integrates molecular replacement, automated model building and Rosetta model rebuilding for difficult structures. - A new fast search method in Phaser for efficiently locating multiple copies of the same molecule - A new program (mr_model_preparation) for preparing models for molecular replacement, which automatically downloads related molecules based on a sequence alignment and runs sculptor. - Improvements to ensemble generation (phenix.ensembler), with an option to use secondary structure matching (using code from Eugene Krissinel). Ligand fitting -- - New tool for automated ligand fitting using previous structures of related protein/ligand complexes (phenix.guided_ligand_replacement). - Bug fixes and other improvements to phenix.elbow. Analysis - Multi-criterion kinemages can now handle custom restraints (from a .cif file). - RNA model validation is now available on the command line (phenix.rna_validate). - Updates to phenix.model_vs_data, which now generates Sigma-A plots and more detailed ADP statistics. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ klmo...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] Computational Crystallography Newsletter Issue 2
Dear Colleagues, I am pleased to announce the publication of the second issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to Nigel Moriarty at nwmoria...@lbl.gov Articles - Fuzzy space group symbols: H3 and H32 - Visualizing the raw diffraction pattern with LABELIT - Electron density illustrations - Maximum likelihood refinement for twinned structures - TLS for dummies Short communications - Multi-criterion kinemage graphics in PHENIX - phenix.ensembler: a tool for multiple superposition - phenix.mr_rosetta: a new tool for difficult molecular replacement problems Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ klmo...@lbl.gov ][ 1-510-495-2506 ] --
Re: [ccp4bb] (non-crystallographic content ALERT)
While I have as keen an interest in Russian history as the next person, I personally feel that this thread has travelled far enough from CCP4 and crystallography to warrant moving any further discussion in this vein to another forum. On Aug 25, 2010, at 3:57 PM, Ed Pozharski wrote: I don't see what George's attempt to point out that pure-phenix questions should be asked in phenix bb (and the point itself may be subject to different opinions) has to do with renaming Moscow streets and subway stations (unless you thought that the proposition to rename ccp4bb is serious). You do realize that most of the renamed streets existed prior to 1917 and were renamed by Bolsheviks at some point to honor the ideology and group of people who committed the most massive atrocity in the history of humankind? The comprehensive list of renamed streets can be found here http://onlinelibrary.wiley.com/doi/10./j.1467-9434.2005.00371.x/abstract and except for occasional writer with anti-monarchy leanings or anarchist we are talking about representatives of the first class mass murder machine. I sincerely hope you are not allergic to changing Dzerzhinsky square back to Lubyanka (which name people used anyway). Cheers, Ed. On Wed, 2010-08-25 at 14:38 -0700, Pavel Afonine wrote: Hey Garib, LOL... no of course, I was just saying that I'm a bit allergic to re-naming well established things, and some other people may be too -:) Why don't we rename you Mr. Refmac -:) ? Pavel. On 8/25/10 2:25 PM, Garib Murshudov wrote: Are you suggesting ccp4 is collapsing and people are coming back to the original source? Garib On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse / -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Marian Harris [ mshar...@lbl.gov ] [ 1-510-486-6886 ] --
[ccp4bb] Phenix version 1.6.4 released
The Phenix developers are pleased to announce that version 1.6.4 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6.4) are: - GUI: - new interfaces for eLBOW, CIF to MTZ conversion, phenix.find_ncs, phenix.superpose_maps - new structure comparison tool (evaluation of multiple related structures) - supports execution of jobs on the Sun Grid Engine queueing system - maps for PyMOL now output in (smaller, faster) CCP4 format - display of sequence and secondary structure in wizards and validation - new wide-format windows for wizards and phenix.refine - many bug fixes - Automated model building: - phenix.autosol now much faster and improved model-building after density modification - phenix.phase_and_build (carries out an iterative process of building a model as rapidly as possible and uses this model in density modification to improve the map. Up to 10x faster compared to AutoBuild, but model quality is nearly as good) - phenix.build_one_model (quickly build a single model from a map and sequence file, or extend an existing model) - phenix.assign_sequence (carry out an improved sequence assignment of a model that you have already built. Uses the new loop libraries available in phenix.fit_loops) - phenix.apply_ncs (apply NCS operators to a single copy of a protein to create all the NCS‐related copies) - phenix.find_ncs (now supports identification of NCS operators from a density map) - phenix.fit_loops (two main algorithms now available - fit short gaps using a loop library derived from high‐resolution structures in the PDB, or build loops directly by iterative extension with tripeptides - phenix.refine: - reference model restraints (restraint dihedral angles to a higher resolution reference model) - alternate ideal angles for torsion definitions (preserves side chain rotameric states) - automatic flipping of incorrect N/Q/H rotamers - custom planarity restraints - hydrogen-bond restraints for Watson-Crick base pairs - reflections with Fobs=0 used in refinement - automatic optimization of mask parameters - map parameters now consistent with phenix.maps - new custom_nonbonded_symmetry_exclusions atom selection parameter to fine tune non-bonded interactions across symmetry axes - Phasing: - Option for Phaser likelihood scoring of substructure solutions in HySS - SOLVE converted to C++; FORTRAN compiler no longer required for Phenix compilation - Other: - KiNG kinemage viewer incorporated into Phenix - Real space refinement option in ligand fitting - B-factor sharpening option for maps For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Marian Harris [ mshar...@lbl.gov ] [ 1-510-486-6886 ] --
[ccp4bb] Computational Crystallography Newsletter - Issue 1
Dear Colleagues, I am pleased to announce the publication of the first issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ It features articles, meeting announcements and reports, information on research and other items of interest to crystallographers and users of crystallographic software. The target audience is structural biologists including both students and experts. Although this first issue has many Phenix and cctbx related articles we would like this to be a resource for the entire community and expect to see a broad range of topics covered in future issues. Anyone interested in publishing articles or other items in the newsletter is encouraged to contact the editor at any time. Submission of text by email using the word-processing templates available online is requested. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Marian Harris [ mshar...@lbl.gov ] [ 1-510-486-6886 ] --
[ccp4bb] Phenix version 1.6.1 released
The Phenix developers are pleased to announce that version 1.6.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6.1) are: - Fast automated rotamer fixing in phenix.refine - Use of atomic charge in calculation of scattering factors - New Graphical User Interfaces for phenix.superpose_pdbs, phenix.get_cc_mtz_mtz, phenix.get_cc_mtz_pdb, and phenix.fmodel - Consolidated validation tool in GUI - New map calculation tool, phenix.maps (also used in GUI) - Rapid loading of structures in GUI selection editor - Improved geometry restraints to maintain amino acid rotameric states - Alpha version of secondary structure restraints - Automated secondary structure analysis with KSDSSP (code from UCSF CGL) For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ pajime...@lbl.gov ] [ 1-510-486-7963 ] --
[ccp4bb] Technology Specialist Position, Lawrence Berkeley National Laboratory
We are seeking a structural biologist technology specialist to research, document, and communicate new technologies to the scientific community. This project is part of the NIH-funded Protein Structure Initiative (PSI) Knowledgebase. The position requires interactions with other groups in the Knowledgebase, members of the Protein Data Bank, researchers at NIH-funded PSI centers, scientific journals, and the broader biological research community. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities are promoting new PSI- developed technologies to the broader scientific community, and maintaining and further developing a web portal describing these technologies. The successful candidate will need to be able to produce attractive online content, and have good scientific writing /proof reading skills. There is also a large community outreach element to the role, including presentations at meetings, the answering of questions via email, and the possibility of establishing an online forum. Additional tasks may include setting up a SVN software repository, and other online tools which will be of assistance to the structural biology community. Qualifications: B.S., M.S., Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using either computation or instrumentation. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Excellent spoken and written English skills are essential. Familiarity with scripting languages such as Python. Experience with maintaining web sites. To apply: visit http://cjo.lbl.gov/ and search for the keyword PSI or the job number 24114. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ pajime...@lbl.gov ] [ 1-510-486-7963 ] --
[ccp4bb] Phenix version 1.6 released
The Phenix developers are pleased to announce that version 1.6 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6) are: - New Graphical User Interfaces for AutoMR, and Phaser (in MR and SAD modes) - Improved reflection file editor GUI and command line tool - Updated map calculation GUI - C++ version of Resolve - Refinement of residues spanning symmetry axes in phenix.refine - New RNA sugar pucker geometry restraints in phenix.refine - Torsion angle dynamics refinement updates - Optional real space refinement of ligands in LigandFit wizard For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ pajime...@lbl.gov ] [ 1-510-486-7963 ] --
[ccp4bb] Phenix version 1.5 Released
The Phenix developers are pleased to announce that version 1.5 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.5-2) are: - A new Graphical User Interface (accessed by typing phenix at the command line) - Two-way communication with Coot - The latest version of Phaser (2.2) - A development version of torsion angle dynamics available in phenix.refine - Real space refinement in phenix.refine - New GUIs for Autosol, AutoBuild and LigandFit wizards - A number of MolProbity and other validation tools now available - Fast loop building with phenix.fit_loops - Improved ligand geometry generation with phenix.elbow - Inclusion of Nicholas Sauter's LABELIT system for autoindexing and more For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ pajime...@lbl.gov ] [ 1-510-486-7963 ] --
[ccp4bb] Postdoc Crystallographer Position - Berkeley
Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 22539 Division: Physical Biosciences Date Opened: 3/24/2009 Summary: A postdoctoral position is immediately available to study structure and function of macromolecular complexes and enzymes using X-ray crystallographic methods. This position is joint between the Center for Protein Folding Machinery (www.proteinfoldingcenter.org) and the Joint BioEnergy Institute (www.jbei.org). Robotic hardware for performing crystallization trials and imaging results are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. The biological systems to be studied are: - Type-II chaperonins responsible for the refolding of unfolded proteins in archeal and mammalian cells. - Glycosyl transferases responsible for the synthesis of hemicellulose in plants. - Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production. Duties: Using robotic hardware to perform screens for crystallization conditions. Optimization of crystallization conditions. Biophysical characterization of protein samples using standard techniques, such as dynamic light scattering. Characterization of crystals using the Berkeley Center for Structural Biology beamlines at the Advanced Light Source. Collection and analysis of diffraction data, model building and structure refinement. Extensive email and verbal interaction with other researchers. Qualifications: Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using crystallographic methods. Experience with crystallization methods. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Note that this is a one-year appointment with renewal based on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit http://cjo.lbl.gov/ and search for the job number 22539 or visit: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=22539p=1 -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ pajime...@lbl.gov ] [ 1-510-486-7963 ] --
[ccp4bb] Postdoc Crystallographer Position - Berkeley
Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 22539 Division: Physical Biosciences Date Opened: 1/5/2009 Summary: A postdoctoral position is immediately available to study structure and function of macromolecular complexes and enzymes using X-ray crystallographic methods. This position is joint between the Center for Protein Folding Machinery (www.proteinfoldingcenter.org) and the Joint BioEnergy Institute (www.jbei.org). Robotic hardware for performing crystallization trials and imaging results are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. The biological systems to be studied are: - Type-II chaperonins responsible for the refolding of unfolded proteins in archeal and mammalian cells. - Glycosyl transferases responsible for the synthesis of hemicellulose in plants. - Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production. Duties: Using robotic hardware to perform screens for crystallization conditions. Optimization of crystallization conditions. Biophysical characterization of protein samples using standard techniques, such as dynamic light scattering. Characterization of crystals using the Berkeley Center for Structural Biology beamlines at the Advanced Light Source. Collection and analysis of diffraction data, model building and structure refinement. Extensive email and verbal interaction with other researchers. Qualifications: Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using crystallographic methods. Experience with crystallization methods. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Note that this is a one-year appointment with renewal based on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit http://cjo.lbl.gov/ and search for the job number 22539 or visit: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=22539p=1 -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Kristine Sawyer [ kksaw...@lbl.gov ][ 1-510-486-4151 ] --
[ccp4bb] PHENIX 1.3 Available
= PHENIX 1.3 Release = The PHENIX developers are pleased to announce that the 1.3 general release version of PHENIX is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ This version of PHENIX includes tools for: - Assessing data quality (phenix.xtriage) - Includes the detection of twinning, tNCS, and missed symmetries - Automated structure solution (phenix.autosol) - Combines automated substructure solution (phenix.hyss) with phasing (Phaser/SOLVE), substructure completion, phase improvement (RESOLVE) and fast initial model building (RESOLVE) - Automated molecular replacement (phenix.automr) - Maximum likelihood molecular replacement with Phaser - Automated protein and DNA/RNA model building/rebuilding (phenix.autobuild) - Combines automated model building (RESOLVE), phase improvement (RESOLVE) and structure refinement (phenix.refine) - Automated ligand fitting (phenix.ligandfit) - Fitting a known ligand or screening against a library of the 200 most common ligands - Structure refinement (phenix.refine) - Maximum likelihood targets, simulated annealing, TLS, constrained occupancy refinement, f'/f'' refinement, water picking, anisotropic B-factor refinement, twinned refinement, automatic treatment of alternate conformations, and joint refinement against X-ray and neutron data - Generation of ligand coordinates and restraints (phenix.elbow/ phenix.reel) - Input formats include SMILES and PDB - Restraints can be manipulated with the phenix.reel GUI Full documentation is available here: http://www.phenix-online.org/documentation/ There is a PHENIX bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: [EMAIL PROTECTED] and [EMAIL PROTECTED] Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium. The development of PHENIX is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. = PHENIX 1.3 Release = -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
Re: [ccp4bb] PHENIX question
Phenix uses its own internal python so nothing to worry about there.
The cause of the problem Alex is seeing stems from the way Mac OSX
deals with sockets. We have a fix for this and will be releasing a
new Phenix version imminently. Why the problem should appear after an
update through fink is not clear.
On Jul 26, 2008, at 5:18 AM, William G. Scott wrote:
Alex:
try moving /sw out of the way or not sourcing the /sw/bin/init.(c)
sh script when you start a new shell and see if that makes a
difference. My guess is phenix is using the wrong python (i.e., one
in /sw). Fink won't touch anything outside of /sw (apart from your
shell's environment, if you run the initialization script).
If that solves the problem, just ensure phenix sees /usr/bin/python
first.
Having said that, I use phenix every day, update fink every day,
and have /sw/bin and the head of my path and have not experienced
any problems...
Bill
PS: There is a phenix bb.
On Jul 26, 2008, at 4:50 AM, [EMAIL PROTECTED] wrote:
Dear Phenix Programmers/Users,
after running a 'fink selfupdate' on OS X 10.5.2 (Xquartz 2.2.3) I
am no
longer able to use my Phenix Suite (Ver 1.3 of 26-05-2008) . It
crashes
everytime with obscure (at least to me) error messages (see below).
Does anyone have a clue as to how to proceed and maybe fix it?
Thanks very much in advance!
Alex Berndt
MRC-LMB
[EMAIL PROTECTED]
Python(78825,0xb0185000) malloc: *** mmap(size=4083712) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
set meta data failed
Traceback (most recent call last):
File /usr/local/phenix-1.3-rc2/phenix/wxGUI/wxtask.py, line
522, in
OnGoButton
try: self.parent.OnGo()
File /usr/local/phenix-1.3-rc2/phenix/wxGUI/Dialogs.py, line
470, in OnGo
gp.RunStrategy()
File /usr/local/phenix-1.3-rc2/phenix/wxGUI/BMPTaskCanvas.py, line
1170, in RunStrategy
self.RunRemotely()
File /usr/local/phenix-1.3-rc2/phenix/wxGUI/BMPTaskCanvas.py, line
1293, in RunRemotely
prefs = PDSServerClient.GetPreferences()
File /usr/local/phenix-1.3-rc2/phenix/phenix/server/
PhenixClient.py,
line 201, in GetPreferences
return self._remote_call('GetPreferences',arg,kw)
File /usr/local/phenix-1.3-rc2/phenix/phenix/server/
PhenixClient.py,
line 449, in _remote_call
cPickle.dump(all,self.send,1)
File
/usr/local/phenix-1.3-rc2/build/mac-intel-osx/base/
Python.framework/Versions/2.5/lib/python2.5/socket.py,
line 262, in write
self.flush()
File
/usr/local/phenix-1.3-rc2/build/mac-intel-osx/base/
Python.framework/Versions/2.5/lib/python2.5/socket.py,
line 249, in flush
self._sock.sendall(buffer)
socket.error: (32, 'Broken pipe'
--
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology
Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909
http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.
Administrator: Delia Clark [ [EMAIL PROTECTED] ][ 1-510-486-6331 ]
--
[ccp4bb] Postodoctoral Position - Berkeley California
The Berkeley Center for Structural Biology (BCSB) has an opportunity for a Postdoc to develop hardware and software for the automated control of data collection instrumentation and methods for automated data collection and analysis. You will also provide technical and scientific help to users at the BCSB beamlines (http://bcsb.lbl.gov) at the Advanced Light Source in Berkeley California and participate on projects involving the structure determination of biological molecules and biomolecular complexes as required by users and other BCSB staff members. Responsibilities Under the direction of the Principal Investigator, you will: - Assist in the development of hardware and software for the automated control of data collection instrumentation and methods for automated data collection and analysis. - Participate in engineering projects to advance the capabilities of the beamlines, including robotics systems for sample handling. - Assist in the development of instrumentation and methodology for biological crystallography. - Participate in the design, implementation, and evaluation of collaborative experiments involving biological crystallography. - Participate in helping users regarding data collection, processing, archiving, and analysis. - Collaborate with colleagues both internal and external to the Berkeley Lab. Prepare documentation for beamline staff and users. - Prepare scientific data for publication in refereed journals and present findings at seminars and conferences. - Provide work oversight and direction to technical staff as needed (which will require occasional work off-hours and weekends). - Assist with developing research proposals that lead to continued funding in the area of biological crystallography for the BCSB/ALS. Key Qualifications - A recent Ph.D. in physics, biology, bioengineering, biophysics, or related field. - Experience working in the area of synchrotron science using complex instrumentation and computer controls. - Experience with robotics hardware and control systems. - Experience with the collection of experimental data for biological crystallography. - Demonstrated ability to conduct independent research and organize results for publication and presentation documented by publication record in either: physics, biology, bioengineering, biophysics, biochemistry or instrumentation fields. - Excellent written communication skills along with strong organizational, analytical, and interpersonal skills. - Experience in the use of computer programs required for biological crystallography. - The ability to work in a team environment and effectively interact with a broad range of colleagues. - Experience in UNIX computing is highly preferred. This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. How To Apply To apply please visit: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=21987p=1 Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Delia Clark [ [EMAIL PROTECTED] ][ 1-510-486-6331 ] --
[ccp4bb] Crystallographic Postdoctoral Research Position - Berkeley, USA
A postdoctoral research position is available immediately to work on challenging problems in structural biology: Postdoctoral Researcher Job ID: 21615 Division: Physical Biosciences Date Opened: 3/28/2008 This postdoctoral position will study the structure and function of macromolecular complexes and enzymes using X-ray crystallographic methods. This position will be joint between the Center for Protein Folding Machinery (proteinfoldingcenter.org) and the Joint BioEnergy Institute (www.jbei.org). The biological systems to be studied will include: Type-II chaperonins responsible for the refolding of unfolded proteins in archeal and mammalian cells, Glycosyl transferases responsible for the synthesis of hemicellulose in plants, and Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production. The candidate will have experience with using crystallographic methods to study macromolecules; robotic hardware for performing crystallization trials and imaging trays are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. Essential: Primary duties and responsibilities will include using robotic hardware to perform screens for crystallization conditions. Optimization of crystallization conditions. Biophysical characterization of protein samples using standard techniques, such as dynamic light scattering. Characterization of crystals using the Berkeley Center for Structural Biology beamlines at the Advanced Light Source. Collection and analysis of diffraction data, model building and structure refinement. Extensive email and verbal interaction with other researchers. Marginal: Use of small angle X-ray scattering methods to analyze macromolecular complexes in solution. Essential: Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using crystallographic methods. Experience with crystallization methods. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Marginal: Experience with the use of small angle scattering methods. Familiarity with robotic hardware for crystal growth. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the Center for Protein Folding Machinery visit: http://proteinfoldingcenter.org/ and the Joint BioEnergy Institute visit: http://www.jbei.org/. For more information about the Berkeley Center for Structural Biology visit: http://bcsb.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 21615. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
Re: [ccp4bb] refmac,tlsanl vs TLS, B and anisou
Some comments: - We (the PHENIX developers) are working with the PDB to come up with a more streamlined deposition of TLS information for PHENIX. There are some other issues that need to be resolved first that have slowed this down a little. - I am in agreement with George (not unusual). - As far as I remember Garib was supportive of the idea of no longer depositing residual B-factors in the atomic iso-B column. - What phenix.refine writes in the PDB file is almost exactly the same as you would get by running TLSANL on a REFMAC PDB file. - It is my understanding that the EBI runs TLSANL on REFMAC deposited PDB files to extract the ANISOU records so that R-factors can be calculated. It would seems that this information is then discarded. [I could be mistaken about this whole process though] - Allowing ANISOU records only when atomic anisotropic displacement parameters have been refined seems very restrictive. There may be multiple ways to arrive at anisotropic displacements other than the traditional method (TLS is one, George mentioned TLS restraints instead of constraints, and we have some ideas about ADP refinement that would also result in anisotropic displacements). - It is good to remember that TLS refinement is constrained anisotropic displacement parameter refinement. - If we want bioinformaticians to analyze our structures then we should be writing something in the iso-B column that they can understand - I favour the iso-B equivalent of the total atomic B-factor. This I assume they can handle. I very much doubt that anyone other than a crystallographer will go to the trouble of extracting the TLS information and recalculating atomic displacements. - The biologists looking at structures from the PDB do not care about TLS or ANISOU records. If they choose to look at anything it will be the iso-B column (probably by colouring the atoms by B-factor in a display program). I'd like to give them a fighting chance of seeing something meaningful such as the iso-B equivalent of the total atomic B-factor rather than a residual B-factor (which has no meaning to them). - I will not be holding my breath waiting for any of the popular display programs to start interpreting TLS header information. - I agree that it is best for everyone if we have some clear standards for deposition and tags that make it clear to anyone looking at files from the PDB what is meant by the contents. The PDB is very aware of this and I expect things to be straightened out fairly soon in collaboration with the developers of phenix.refine and REFMAC. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
[ccp4bb] Beamline Scientist Position, Berkeley California
= = = = = = = Beamline Biophysicist Scientist/Engineer, Lawrence Berkeley National Laboratory = = = = = = = Biophysicist Scientist/Engineer Division: Physical Biosciences SUMMARY: As a member of the Berkeley Center for Structural Biology (BCSB), provide technical and scientific support for users at the BCSB beamlines (http://bcsb.lbl.gov) at the Advanced Light Source in Berkeley California. Work with the BCSB group leader and other BCSB scientists and engineers to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation. Participate on projects involving the structure determination of biological molecules and biomolecular complexes. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. DUTIES: Essential - Provide support for users regarding data collection, processing, archiving, and analysis. Play a role in coordinating and participating in engineering projects to advance the capabilities of the beamlines, with a focus on robotics systems for sample handling. Participate in the development of instrumentation and methodology for biological crystallography. Participate in the design, implementation, and evaluation of collaborative experiments involving biological crystallography. Collaborate with colleagues both internal and external to the Berkeley Lab. Prepare documentation for beamline staff and users. Prepare scientific data for publication in refereed journals and present findings at seminars and conferences. Required to occasionally work off-hours and weekends to support users. Marginal - Assist with developing research proposals that lead to continued funding in the area of biological crystallography for the BCSB/ALS. QUALIFICATIONS: Essential - Substantial experience working in the area of synchrotron science using complex instrumentation and computer controls. Experience with robotics hardware and control systems. Experience with the collection of experimental data for biological crystallography. Demonstrated ability to conduct independent research and organize results for publication and presentation documented by publication record in either: physics, biology, bioengineering, biophysics, biochemistry or instrumentation fields. Excellent written communication skills along with strong organizational, analytical, and interpersonal skills. Experience in the use of computer programs required for biological crystallography. Ability to work in a team environment and effectively interact with a broad range of colleagues. Marginal – M.S. or Ph.D. in physics, biology, bioengineering, biophysics, or related field. Experience in UNIX computing. To apply: visit http://cjo.lbl.gov/ and search for the keyword BCSB or the job number 21576. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
[ccp4bb] Scientific Writer Position, Berkeley California
= = PSI Knowledgebase Scientific Writer, Lawrence Berkeley National Laboratory = = Scientific Writer/Editor Division: Physical Biosciences SUMMARY: We are seeking an intelligent and motivated structural biologist technology specialist to research, document, and communicate new technologies to the scientific community. This project is part of the NIH-funded Protein Structure Initiative (PSI) Knowledgebase. The position will require interactions with other groups in the Knowledgebase, members of the Protein Data Bank, researchers at NIH- funded PSI centers, scientific journals, and the broader biological research community. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities are promoting new PSI-developed technologies to the broader scientific community, and editing a web portal describing these technologies. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. DUTIES: Essential - Primary duties and responsibilities will include regular communication with researchers at the PSI-funded structural genomics centers and other programs. Interaction with other groups in the PSI Knowledgebase, members of the Protein Data Bank, researchers at NIH-funded PSI centers, scientific journals, and the broader biological research community. Collecting information describing technologies from other PSI-funded researchers and by the use of web and bibliographic search tools. Writing text that describes new technologies to the broad scientific community. Maintaining and editing written and graphical material on a web site devoted to technology dissemination. Extensive email and verbal interaction with other researchers. Marginal - Analysis of crystallographic data. QUALIFICATIONS: Essential - BS, MS or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using either computation or instrumentation. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Excellent spoken and written English skills are essential. Marginal - Experience with the solution of macromolecular structures using crystallographic or NMR methods. Practical computational analysis of crystallographic data. Familiarity with scripting languages such as Python. To apply: visit http://cjo.lbl.gov/ and search for the keyword PSI or the job number 21575. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
[ccp4bb] Collaborative Crystallography Program - Advanced Light Source
The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: == The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography. How To Apply: = To submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/ Initialize. For question 3 select Collaborative PX 501/502. For question 9, please describe a specific research project with a clear end point. In order to request CC time for January/February, 2008, proposals must be submitted by November 15, 2007. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
Re: [ccp4bb] SAD: Refine against anomalous data
Hi Ethan, if you want you can specify and refine both f' and f'' for any user selected atoms in phenix.refine: http://www.phenix-online.org/download/ Cheers, Paul On Aug 11, 2007, at 9:48 PM, Ethan A Merritt wrote: On Saturday 11 August 2007 21:41, Miller, Mitchell D. wrote: Hi Ethan, I have been wanting a way to instruct refmac to accept a user- defined f' term since about forever. According to Garib's latest release notes, a command was added to refmac 5.3.0015 and later to allow f' to be specified. I have not tried it myself yet.. see http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html Anomolous form factors anom formfactor [Name] [f'] [f''] It will modify form factor of the given atom and use f' part only goes off to install a newer refmac version/ Thanks, Ethan -- Paul Adams Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Laboratory Adjunct Professor, Department of Bioengineering, U.C. Berkeley Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
Re: [ccp4bb] SAD: Refine against anomalous data
Dear George, you are correct - this kind of refinement only makes sense if F+ and F- are kept unmerged. The refinement of f'/f'' is performed with the FFT (from what I recall - Ralf can confirm or deny). At the very least, structure factors from non-anomalous atoms are calculated using the FFT, and the anomalous atoms by direct summation. Either way, the inclusion of anomalous atoms doesn't add any perceptible cost to the refinement. The multi-wavelength f'/f'' refinement in SHELX sounds very interesting. We currently cannot do that in phenix.refine (refinement is limited to one dataset, thus one wavelength). Although it may be implemented in the future. Cheers, Paul George M. Sheldrick wrote: Dear Paul, That implies that phenix refine (like SHELXL, but unlike REFMAC) can refine against data for which I+ and I- (or F+ and F-) have not been merged. An attempt to refine f against Friedel merged data would be very poorly determined. Am I right in guessing that phenix refine can only do this when then structure factors are calculated by the classical summation and not by FFT? Given relatively high resolution MAD data, it is at least theoretically possible using SHELXL (and presumably also phenix refine) to refine against I+ and I- for all wavelengths at once, this should give much better occupancies for the selenium atoms (in the case of SHELXL it would be necessary to use HKLF 2 input format so that a wavelength is specified for each reflection, refine batch scale factors, use the LAUE instruction so that the program can work out f' and f for each reflection, and - at least when each site is assumed to be Se or S in different ratios - use 'free variables' for the Se occupancies). If anyone is MAD enough to try this, I would also recommend scaling against a reference dataset (e.g. high energy remote) rather than scaling the data for different wavelengths separately. There is a suitable option in SCALA and SADABS and possibly in other scaling programs as well. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Sat, 11 Aug 2007, Paul Adams wrote: Hi Ethan, if you want you can specify and refine both f' and f'' for any user selected atoms in phenix.refine: http://www.phenix-online.org/download/ Cheers, Paul On Aug 11, 2007, at 9:48 PM, Ethan A Merritt wrote: On Saturday 11 August 2007 21:41, Miller, Mitchell D. wrote: Hi Ethan, I have been wanting a way to instruct refmac to accept a user- defined f' term since about forever. According to Garib's latest release notes, a command was added to refmac 5.3.0015 and later to allow f' to be specified. I have not tried it myself yet.. see http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html Anomolous form factors anom formfactor [Name] [f'] [f''] It will modify form factor of the given atom and use f' part only goes off to install a newer refmac version/ Thanks, Ethan -- Paul Adams Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Laboratory Adjunct Professor, Department of Bioengineering, U.C. Berkeley Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. -- -- Paul Adams Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
[ccp4bb] Beam Time at ALS Sector 5.0
=== Synchrotron Beam Time available for Macromolecular Crystallography at upgraded ALS Sector 5.0 beamlines (5.0.1, 5.0.2 and 5.0.3). The ALS is now accepting General User applications for July/August. === The Berkeley Center for Structural Biology (BCSB) has recently completed a major upgrade of the Sector 5.0 wiggler beamline optics. A five- to ten-fold improvement in available flux has been achieved at the side-station beamlines (5.0.1 and 5.0.3), which now generate 1.5x10^11 photons per second at 1 Angstrom wavelength. The performance of 5.0.2 (the tunable beamline) has improved by a factor of 3 to 4. It now generates a peak flux of 8x10^11 photons per second. The upgrade has also extended the energy range of 5.0.2 to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to take advantage of the upgrades to these BCSB beamlines, submit a General User proposal by May 15, 2007 in order to be considered for the July-August schedules at the Advanced Light Source. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. You can also request open beam time by e-mailing our scheduler at [EMAIL PROTECTED] Any industrial or academic group interested in becoming part of the Participating Research Team for beamlines 5.0.1 and 5.0.2 should contact the Head of the BCSB (Paul Adams: [EMAIL PROTECTED], 510-486-4225). (Please note that executed user agreements and proprietary fees, if applicable, must be received at least five working days prior to scheduled beam time.) -- Paul Adams Senior Staff Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
