March 2024 - phenixbb - phenix-online.org

Issue phenix.table1 macOS
by Xavier Brazzolotto 09 Mar '24

09 Mar '24

I am facing a strange issue with phenix.table1 Previously, I had generated a Table1 with the GUI that was ok. Recently, I have updated to Sonoma 14.4 and when I try to rerun phenix.table1 (or use similar model and with same reflections) do not get consistent results, especially in number of reflections, uniques, CC1/2, CC*... Besides, at the end of a refinement, I do also get an error when the program tries to auto-load the data (model and maps) in Coot… Any thoughts about this Xavier

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Macromolecular Crystallography - CSHL Course October 2024
by Paul Adams 07 Mar '24

07 Mar '24

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=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> 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=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> 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: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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map display after resolve_cryoem
by Valerie Biou 01 Mar '24

01 Mar '24

Hello, I ran resolve_cryoem for solvent flattening and obtained a ccp4 map that behaves like a mask both in Coot and Chimera. the histogram is just a single line and the dimensions are different from my original map, even though in a second run I used restore_full_size = true in a second run. To be clear, my original map has 480^3 dimensions, and the output one is 125x140x224, which boxes my protein but I can't see the inside of the map. I guess there is something I didn't understand. Can you please help me? All the best, Valerie Valérie Biou, Ph.D. valerie.biou(a)ibpc.fr Laboratoire de Biologie Physico-Chimique des Protéines Membranaires umr7099.ibpc.fr <http://umr7099.ibpc.fr/> UMR 7099 CNRS/Univ. Paris-Cité Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France Tel : +33 (0)1 5841 5099

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