Hi Kevin, Try 2.2.1. The point release should have a fix for this bug. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 92R0129 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Sep 30, 2026 at 12:21 PM Kevin M Jude via phenixbb < [email protected]> wrote:
Running Tools>Phenix>Local EM Fitting from ChimeraX 1.12, using phenix 2.2-6143, I get the failure pasted below. When I point ChimeraX to phenix 2.1-6048, the search is successful.
phenix.voyager.emplace_local exited with error code 1
Command: /programs/i386-mac/phenix/2.2-6143/phenix_bin/phenix.voyager.emplace_local map1=half_map1.mrc map2=half_map2.mrc d_min=3.4 model_file=model.pdb sphere_center=(121.216,117.898,130.99) --json --json-filename emplace_local_result.json
stdout: Starting phenix.voyager.emplace_local on Wed Sep 30 11:54:00 2026 by kjude
===============================================================================
Processing files:
-------------------------------------------------------------------------------
No files found
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL: ------------------------- map1=half_map1.mrc map2=half_map2.mrc d_min=3.4 model_file=model.pdb sphere_center=(121.216,117.898,130.99)
Final processed PHIL parameters:
------------------------------------------------------------------------------- model_file = model.pdb map1 = half_map1.mrc map2 = half_map2.mrc d_min = 3.4 sphere_center = (121.216,117.898,130.99)
Starting job
=============================================================================== Traceback (most recent call last): File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/New_Voyager/scripts/em_placement_script.py", line 729, in em_placement_code results = prepare_docking_sphere( ^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/New_Voyager/_prepare_docking_sphere.py", line 55, in prepare_docking_sphere results = prepare_map_for_docking.assess_cryoem_errors( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/cctbx/maptbx/prepare_map_for_docking.py", line 1952, in assess_cryoem_errors total_ordered_volume = flex.mean(ordered_mm.map_data()) * unit_cell.volume() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'map_data'
stderr: AttributeError: 'NoneType' object has no attribute 'map_data'
During handling of the above exception, another exception occurred:
Sorry: Search failed
-- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 https://www.google.com/maps/search/279+Campus+Drive,+Stanford+CA+94305?entry=gmail&source=g _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s