emplace_local error funning from ChimeraX with 2.2-6143
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
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
participants (2)
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Billy Poon -
Kevin M Jude