June 2025 - phenixbb - phenix-online.org

Refine pixel size for EM map?
by Oliver Clarke 01 Aug '25

01 Aug '25

Hi, I remember asking about this some time ago, but I am not sure if it was ever implemented. Is there a way to refine just pixel size for an EM map in phenix.real_space refine (or another phenix utility)? Even just automatically rigid-body fitting a crystal structure and calculating the pixel size with max correlation would be handy. We do this at the moment using Chimera/ChimeraX, but an automated way to do it in phenix would be handy. In the absence of a crystal structure, I wonder if directly refining pixel size during real space refinement would be possible/reasonable at higher resolution (<2Å)? Cheers Oli

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Data uncertainty: Minimising it and characterising the uncertainty that remains
by John R Helliwell 30 Jun '25

30 Jun '25

Dear Colleagues, I imagine you will be interested in my post at the IUCr Committee on Data Public Forum on this topic of data uncertainty:- https://forums.iucr.org/viewtopic.php?f=39&t=6464&sid=7966a823f22e445ad1a3c… All best wishes, John -- Professor John R Helliwell DSc

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phenix install/splash screen issue
by Hekstra, Doeke Romke 15 Jun '25

15 Jun '25

Hi, After an ostensibly error-free installation of phenix-2.0-5716 on linux within an HPC environment, when starting the Phenix GUI, I get the following error: [dhekstra@holygpu7c26105 phenix]$ phenix Error in sys.excepthook: Traceback (most recent call last): File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 972, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 136, in OnInit self.start_gui() File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 151, in start_gui self.get_screen_params() File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 263, in get_screen_params self.set_window_height(self.prefs.get_root().gui.max_dialog_height) File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 266, in set_window_height if (max_height < self.screen_height) : TypeError: '<' not supported between instances of 'NoneType' and 'int' OnInit returned false, exiting... ==== The same error occurred with phenix-2.0-5716 (both using the Linux-x86_64 installer). Could you please advise? Thanks, Doeke

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phenix.map_sharpening - sequence file required?
by Oliver Clarke 04 Jun '25

04 Jun '25

Hi, The new-ish map_sharpening utility seems to absolutely require a sequence file (at least on the CLI), whereas using auto_sharpen one could directly provide solvent content or estimated molecular mass. This option - molecular_mass - is still present in map_sharpening, but the program still terminates with an error - "Sorry: Need a sequence file". Is this intended? I run using the following command: phenix.map_sharpening cryosparc_P4_J199_002_volume_map.mrc resolution=2.3 molecular_mass=50000 Cheers Oli

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Reminder: Macromolecular Crystallography - CSHL Course October 2025
by Paul Adams 02 Jun '25

02 Jun '25

Dear Colleagues, A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th 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. Many applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> Macromolecular Crystallography <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> October 12 - 28, 2025 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 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://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road | Cold Spring Harbor, NY 11724 US Unsubscribe <https://visitor.constantcontact.com/do?p=un&m=001S3f9XM7Br7nKhcnZ-APDwA%3D&…> | Update Profile <https://visitor.constantcontact.com/do?p=oo&m=001S3f9XM7Br7nKhcnZ-APDwA%3D&…> | Constant Contact Data Notice <https://www.constantcontact.com/legal/customer-contact-data-notice> -- 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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