EMAN2 HDF5 file: cannot import name '_broken_hdf5_long_double' from 'tables.utilsextension'

[btn1@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202403290055 (2024-03-29 00:55:10 UTC)
Description
Version 1.71 opens an hdf map generated by EMAN2 subtomogram averaging. Converting it to mrc format (using e2proc3d.py) allows it to still be opened in Version 1.71. Version 1.8dev fails to open hdf formatted file, with error as reported. Version 1.8dev opens the mrc file no problem. 

Log:
UCSF ChimeraX version: 1.8.dev202403290055 (2024-03-29)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/T7/mark/sarah/crystal/threed_09.mrc

Opened threed_09.mrc as #1, grid size 56,56,56, pixel 2.63, shown at level
5.62, step 1, values float32  

> open /Volumes/T7/mark/sarah/crystal/AFmodel.pdb

Chain information for AFmodel.pdb #2  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> transparency 50

> volume #1 level 0.8099

> ui tool show "Fit in Map"

Already setting window visible!  

Opened AFmodel.pdb map 20 as #3, grid size 38,37,37, pixel 6.67, shown at
level 0.0217, step 1, values float32  

> fitmap #2 inMap #1 resolution 20

Fit map AFmodel.pdb map 20 in map threed_09.mrc using 1521 points  
correlation = 0.6666, correlation about mean = 0.6412, overlap = 398.1  
steps = 104, shift = 0.742, angle = 3.65 degrees  
  
Position of AFmodel.pdb map 20 (#3) relative to threed_09.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99821068 0.04411912 -0.04036013 0.01897479  
-0.04322020 0.99880353 0.02288056 -0.39596352  
0.04132131 -0.02109525 0.99892319 -0.20598429  
Axis -0.34514579 -0.64107985 -0.68548597  
Axis point -3.29930267 -3.60309893 0.00000000  
Rotation angle (degrees) 3.65256585  
Shift along axis 0.38849451  
  
Average map value = 2.287 for 8561 atoms, 3748 outside contour  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 2/A  

> select /A:24

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:24-132

851 atoms, 868 bonds, 109 residues, 1 model selected  
Opened AFmodel.pdb map 20 as #4, grid size 25,25,28, pixel 6.67, shown at
level 0.0125, step 1, values float32  

> fitmap sel inMap #1 resolution 20

Fit map AFmodel.pdb map 20 in map threed_09.mrc using 235 points  
correlation = 0.8204, correlation about mean = 0.527, overlap = 114  
steps = 172, shift = 42.9, angle = 40.2 degrees  
  
Position of AFmodel.pdb map 20 (#4) relative to threed_09.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.75847365 0.25315684 -0.60052421 -21.00353498  
-0.39026826 0.91441123 -0.10743735 17.04554257  
0.52192759 0.31585394 0.79235591 -31.92011867  
Axis 0.31095209 -0.82455923 -0.47266359  
Axis point 45.99614556 0.00000000 -50.62742004  
Rotation angle (degrees) 42.89347664  
Shift along axis -5.49867460  
  
Average map value = 6.672 for 851 atoms, 29 outside contour  

> fitmap sel inMap #1 resolution 20 moveWholeMolecules false

Fit map AFmodel.pdb map 20 in map threed_09.mrc using 235 points  
correlation = 0.8204, correlation about mean = 0.527, overlap = 114  
steps = 172, shift = 42.9, angle = 40.2 degrees  
  
Position of AFmodel.pdb map 20 (#4) relative to threed_09.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.75847365 0.25315684 -0.60052421 -21.00353498  
-0.39026826 0.91441123 -0.10743735 17.04554257  
0.52192759 0.31585394 0.79235591 -31.92011867  
Axis 0.31095209 -0.82455923 -0.47266359  
Axis point 45.99614556 0.00000000 -50.62742004  
Rotation angle (degrees) 42.89347664  
Shift along axis -5.49867460  
  
Average map value = 6.672 for 851 atoms, 29 outside contour  

> open /Volumes/T7/mark/sarah/crystal/AFmodel_adj2.pdb

Chain information for AFmodel_adj2.pdb #5  
---  
Chain | Description  
A | No description available  
  
Opened AFmodel_adj2.pdb map 20 as #6, grid size 38,34,36, pixel 6.67, shown at
level 0.0257, step 1, values float32  

> fitmap #5 inMap #1 resolution 20 moveWholeMolecules false

Fit map AFmodel_adj2.pdb map 20 in map threed_09.mrc using 1196 points  
correlation = 0.7019, correlation about mean = 0.6519, overlap = 413.6  
steps = 48, shift = 0.458, angle = 1.96 degrees  
  
Position of AFmodel_adj2.pdb map 20 (#6) relative to threed_09.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99964187 0.00459849 -0.02636276 -0.06837213  
-0.00403924 0.99976651 0.02122753 -0.20578623  
0.02645421 -0.02111344 0.99942703 -0.27758498  
Axis -0.62045120 -0.77396330 -0.12657458  
Axis point 9.42166914 0.00000000 2.85227054  
Rotation angle (degrees) 1.95537502  
Shift along axis 0.23682777  
  
Average map value = 2.611 for 7827 atoms, 2617 outside contour  

> hide #!1 models

> show #!1 models

> hide #!5 models

> hide #2 models

> show #2 models

> select #2/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> fitmap #2 inMap #1 resolution 20 moveWholeMolecules false

Fit map AFmodel.pdb map 20 in map threed_09.mrc using 1521 points  
correlation = 0.6666, correlation about mean = 0.6412, overlap = 398.1  
steps = 84, shift = 0.0303, angle = 0.0222 degrees  
  
Position of AFmodel.pdb map 20 (#3) relative to threed_09.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99820406 0.04403488 -0.04061503 0.02369345  
-0.04311907 0.99880156 0.02315579 -0.41720148  
0.04158602 -0.02136292 0.99890652 -0.22556411  
Axis -0.34832641 -0.64316330 -0.68191618  
Axis point -3.39217365 -3.95038891 0.00000000  
Rotation angle (degrees) 3.66390973  
Shift along axis 0.41389145  
  
Average map value = 2.288 for 8561 atoms, 3749 outside contour  

> hide #2 models

> movie record

> turn y 2 360

> movie stop

> movie reset

> movie record

> turn y 2 180

> show #2 models

> turn y 2 180

> show #!5 models

> hide #2 models

> turn y 2 180

> movie stop

> movie encode

Movie saved to /Users/nixon/Desktop/movie.mp4  
  
Opened AFmodel.pdb map 20 as #3, grid size 38,37,37, pixel 6.67, shown at
level 0.0217, step 1, values float32  

> fitmap #2 inMap #1 resolution 20 moveWholeMolecules false

Fit map AFmodel.pdb map 20 in map threed_09.mrc using 1521 points  
correlation = 0.6666, correlation about mean = 0.6411, overlap = 398.1  
steps = 64, shift = 0.0205, angle = 0.0291 degrees  
  
Position of AFmodel.pdb map 20 (#3) relative to threed_09.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99820432 0.04410646 -0.04053100 0.00402302  
-0.04322382 0.99881423 0.02240163 -0.39692675  
0.04147100 -0.02060950 0.99892713 -0.19319403  
Axis -0.33791833 -0.64425141 -0.68611321  
Axis point -3.32855676 -3.19103866 0.00000000  
Rotation angle (degrees) 3.64884434  
Shift along axis 0.38691414  
  
Average map value = 2.287 for 8561 atoms, 3748 outside contour  
Opened AFmodel.pdb map 20 as #3, grid size 38,37,37, pixel 6.67, shown at
level 0.0215, step 1, values float32  

> fitmap #2 inMap #1 resolution 20 moveWholeMolecules false

Fit map AFmodel.pdb map 20 in map threed_09.mrc using 1521 points  
correlation = 0.6666, correlation about mean = 0.6419, overlap = 398  
steps = 60, shift = 0.0774, angle = 0.284 degrees  
  
Position of AFmodel.pdb map 20 (#3) relative to threed_09.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99849424 0.04025499 -0.03726647 0.05661764  
-0.03941935 0.99896046 0.02289337 -0.33938301  
0.03814930 -0.02138988 0.99904309 -0.23269344  
Axis -0.37430796 -0.63745826 -0.67345417  
Axis point -2.79345456 -4.78269425 0.00000000  
Rotation angle (degrees) 3.39122560  
Shift along axis 0.35185844  
  
Average map value = 2.287 for 8561 atoms, 3741 outside contour  
Opened AFmodel_adj2.pdb map 20 as #6, grid size 38,34,36, pixel 6.67, shown at
level 0.0265, step 1, values float32  

> fitmap #5 inMap #1 resolution 20 moveWholeMolecules false

Fit map AFmodel_adj2.pdb map 20 in map threed_09.mrc using 1194 points  
correlation = 0.7023, correlation about mean = 0.6501, overlap = 413.8  
steps = 44, shift = 0.0787, angle = 0.289 degrees  
  
Position of AFmodel_adj2.pdb map 20 (#6) relative to threed_09.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99998968 -0.00388168 0.00236083 -0.00482954  
0.00388680 0.99999009 -0.00217022 0.07873962  
-0.00235239 0.00217937 0.99999486 -0.01618906  
Axis 0.43176972 0.46786641 0.77115234  
Axis point -17.58684259 -3.67459950 -0.00000000  
Rotation angle (degrees) 0.28859598  
Shift along axis 0.02227014  
  
Average map value = 2.61 for 7826 atoms, 2615 outside contour  

> show #2 models

> hide #!5 models

> select add #2

8579 atoms, 8808 bonds, 1081 residues, 1 model selected  

> select subtract #2

Nothing selected  

> open /Volumes/T7/mark/sarah/crystal/6wlb_relativetothreed09.pdb

Chain information for 6wlb_relativetothreed09.pdb #7  
---  
Chain | Description  
A B C | No description available  
  

> open /Volumes/T7/mark/sarah/crystal/attempt2.pdb

Chain information for attempt2.pdb #8  
---  
Chain | Description  
A B C | No description available  
  

> volume #1 level 0.3656

> ui tool show "Show Volume Menu"

> open /Users/nixon/Downloads/6wlbfittothreed09.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 752, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/session.py", line 231, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/session.py", line 412, in grid_data_from_state  
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/session.py", line 483, in open_data  
grids, error_message = opendialog.open_grid_files(paths_and_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/opendialog.py", line 38, in open_grid_files  
glist = open_file(path, file_type, log = log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 171, in open_file  
data = open_func(apath, **okw)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 55, in __init__  
import warnings, tables  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in <module>  
from .utilsextension import _broken_hdf5_long_double  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
opened ChimeraX session  

> open /Users/nixon/Downloads/6wlbfittothreed09.cxs format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 752, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/session.py", line 231, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/session.py", line 412, in grid_data_from_state  
dlist = open_data(path, gid, file_type, dbfetch, gdcache, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/session.py", line 483, in open_data  
grids, error_message = opendialog.open_grid_files(paths_and_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/opendialog.py", line 38, in open_grid_files  
glist = open_file(path, file_type, log = log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 171, in open_file  
data = open_func(apath, **okw)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 55, in __init__  
import warnings, tables  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in <module>  
from .utilsextension import _broken_hdf5_long_double  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
opened ChimeraX session  

> open /Volumes/T7/mark/sarah/crystal/threed_09.mrc

Opened threed_09.mrc as #1, grid size 56,56,56, pixel 2.63, shown at level
5.62, step 1, values float32  

> open 6wlb

Summary of feedback from opening 6wlb fetched from pdb  
---  
note | Fetching compressed mmCIF 6wlb from http://files.rcsb.org/download/6wlb.cif  
  
6wlb title:  
Structure of homotrimeric poplar cellulose synthase isoform 8 [more info...]  
  
Chain information for 6wlb #2  
---  
Chain | Description | UniProt  
A B C | Cellulose synthase | Q6J8X0_POPPZ 1-978  
  
Non-standard residues in 6wlb #2  
---  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
  

> select add #2

34441 atoms, 34957 bonds, 6 pseudobonds, 2175 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-202.43,0,1,0,-167.32,0,0,1,-231.58

> select subtract #2

Nothing selected  

> volume #1 level 0.7103

> ui tool show "Fit in Map"

Opened 6wlb map 15 as #3, grid size 43,42,37, pixel 5, shown at level 0.0623,
step 1, values float32  

> fitmap #2 inMap #1 resolution 15

Fit map 6wlb map 15 in map threed_09.mrc using 4204 points  
correlation = 0.415, correlation about mean = 0.2437, overlap = 1028  
steps = 2000, shift = 29.3, angle = 29.7 degrees  
  
Position of 6wlb map 15 (#3) relative to threed_09.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90391052 -0.37563017 -0.20456723 -84.95528972  
0.41701476 0.88029571 0.22622589 -293.32993466  
0.09510238 -0.28979552 0.95235188 -199.64218702  
Axis -0.52010308 -0.30203996 0.79891467  
Axis point 602.94001388 -417.39357988 0.00000000  
Rotation angle (degrees) 29.74073429  
Shift along axis -26.71420087  
  
Average map value = 1.061 for 33089 atoms, 25758 outside contour  

> fitmap #2 inMap #1 resolution 15

Fit map 6wlb map 15 in map threed_09.mrc using 4204 points  
correlation = 0.4148, correlation about mean = 0.2411, overlap = 1029  
steps = 2000, shift = 0.779, angle = 1.53 degrees  
  
Position of 6wlb map 15 (#3) relative to threed_09.mrc (#1) coordinates:  
Matrix rotation and translation  
0.91450307 -0.35399305 -0.19589044 -92.32948736  
0.39457452 0.88738168 0.23846321 -292.83690361  
0.08941527 -0.29536871 0.95118990 -197.20005334  
Axis -0.55453389 -0.29636985 0.77759699  
Axis point 629.02189456 -436.79788534 0.00000000  
Rotation angle (degrees) 28.77255709  
Shift along axis -15.35430901  
  
Average map value = 1.06 for 33147 atoms, 25712 outside contour  

> transparency #1.1 50

> select /B

11428 atoms, 11596 bonds, 2 pseudobonds, 720 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select /C

11417 atoms, 11585 bonds, 2 pseudobonds, 720 residues, 2 models selected  

> select /A

11428 atoms, 11596 bonds, 2 pseudobonds, 720 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 56 atoms, 60 bonds  

> delete atoms sel

> delete bonds sel

Drag select of 56 atoms, 60 bonds  

> delete atoms sel

> delete bonds sel

> select add #2

11473 atoms, 11645 bonds, 2 pseudobonds, 725 residues, 2 models selected  
Opened 6wlb map 15 as #3, grid size 32,32,37, pixel 5, shown at level 0.0511,
step 1, values float32  

> view matrix models
> #2,0.9145,-0.35399,-0.19589,-92.953,0.39457,0.88738,0.23846,-293.48,0.089415,-0.29537,0.95119,-199.66

> fitmap #2 inMap #1 resolution 15

Fit map 6wlb map 15 in map threed_09.mrc using 1494 points  
correlation = 0.7675, correlation about mean = 0.6282, overlap = 1091  
steps = 412, shift = 6.27, angle = 118 degrees  
  
Position of 6wlb map 15 (#3) relative to threed_09.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.74223117 -0.66517418 0.08146285 245.02910559  
0.64925965 -0.74387835 -0.15845162 17.15303342  
0.16599637 -0.06471719 0.98400045 -258.57363351  
Axis 0.07098510 -0.06401725 0.99542097  
Axis point 131.40866990 49.91012475 0.00000000  
Rotation angle (degrees) 138.68180764  
Shift along axis -241.09429213  
  
Average map value = 3.267 for 11473 atoms, 2813 outside contour  

> view matrix models
> #2,-0.74223,-0.66517,0.081463,242.26,0.64926,-0.74388,-0.15845,13.292,0.166,-0.064717,0.984,-257.48

> fitmap #2 inMap #1 resolution 15

Fit map 6wlb map 15 in map threed_09.mrc using 1494 points  
correlation = 0.7675, correlation about mean = 0.6282, overlap = 1091  
steps = 52, shift = 4.9, angle = 0.0586 degrees  
  
Position of 6wlb map 15 (#3) relative to threed_09.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.74266412 -0.66465063 0.08178971 244.95243762  
0.64860849 -0.74431389 -0.15907188 17.53687720  
0.16660444 -0.06508748 0.98387325 -258.60696873  
Axis 0.07123555 -0.06428539 0.99538580  
Axis point 131.34432764 50.00776849 0.00000000  
Rotation angle (degrees) 138.72502892  
Shift along axis -241.09174660  
  
Average map value = 3.267 for 11473 atoms, 2810 outside contour  

> view matrix models
> #2,-0.74266,-0.66465,0.08179,241.45,0.64861,-0.74431,-0.15907,15.397,0.1666,-0.065087,0.98387,-258.89

> view matrix models
> #2,-0.74266,-0.66465,0.08179,241.91,0.64861,-0.74431,-0.15907,16.925,0.1666,-0.065087,0.98387,-260.79

> fitmap #2 inMap #1 resolution 15

Fit map 6wlb map 15 in map threed_09.mrc using 1494 points  
correlation = 0.7676, correlation about mean = 0.6281, overlap = 1091  
steps = 48, shift = 3.8, angle = 0.0469 degrees  
  
Position of 6wlb map 15 (#3) relative to threed_09.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.74281389 -0.66448824 0.08174911 244.97508643  
0.64858211 -0.74450546 -0.15828097 17.34796004  
0.16603850 -0.06455230 0.98400418 -258.61181443  
Axis 0.07105464 -0.06389883 0.99542362  
Axis point 131.35064908 49.94636333 0.00000000  
Rotation angle (degrees) 138.73416786  
Shift along axis -241.13020613  
  
Average map value = 3.267 for 11473 atoms, 2815 outside contour  

> fitmap #2 inMap #1 resolution 15

Fit map 6wlb map 15 in map threed_09.mrc using 1494 points  
correlation = 0.7676, correlation about mean = 0.6281, overlap = 1091  
steps = 40, shift = 0.00547, angle = 0.0189 degrees  
  
Position of 6wlb map 15 (#3) relative to threed_09.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.74299761 -0.66427214 0.08183565 244.95956321  
0.64833985 -0.74469128 -0.15839930 17.45293833  
0.16616253 -0.06463299 0.98397794 -258.61773736  
Axis 0.07110749 -0.06394912 0.99541661  
Axis point 131.33263865 49.96933759 0.00000000  
Rotation angle (degrees) 138.75136165  
Shift along axis -241.13003291  
  
Average map value = 3.267 for 11473 atoms, 2814 outside contour  

> volume #1 level 1.241

> fitmap #2 inMap #1 resolution 15

Fit map 6wlb map 15 in map threed_09.mrc using 1494 points  
correlation = 0.7675, correlation about mean = 0.6281, overlap = 1091  
steps = 40, shift = 0.00993, angle = 0.0162 degrees  
  
Position of 6wlb map 15 (#3) relative to threed_09.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.74282719 -0.66447278 0.08175387 244.97267083  
0.64855343 -0.74451423 -0.15835724 17.37748396  
0.16609099 -0.06461031 0.98399151 -258.61013091  
Axis 0.07107061 -0.06393693 0.99542003  
Axis point 131.34761030 49.95461982 0.00000000  
Rotation angle (degrees) 138.73567677  
Shift along axis -241.12641070  
  
Average map value = 3.267 for 11473 atoms, 3576 outside contour  

> hide #!2 models

> open /Users/nixon/Downloads/threed_09.hdf

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 191, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open  
return open_map(session, path, format=_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3604, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 175, in open_file  
data.extend(open_func(p, **okw))  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 55, in __init__  
import warnings, tables  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in <module>  
from .utilsextension import _broken_hdf5_long_double  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in  
from .utilsextension import _broken_hdf5_long_double  
  
See log for complete Python traceback.  
  

> open /Users/nixon/Downloads/threed_09.hdf

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 191, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open  
return open_map(session, path, format=_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3604, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 175, in open_file  
data.extend(open_func(p, **okw))  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 55, in __init__  
import warnings, tables  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in <module>  
from .utilsextension import _broken_hdf5_long_double  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in  
from .utilsextension import _broken_hdf5_long_double  
  
See log for complete Python traceback.  
  

> open /Users/nixon/Downloads/threed_09(1).hdf

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 191, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open  
return open_map(session, path, format=_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3604, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 175, in open_file  
data.extend(open_func(p, **okw))  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 55, in __init__  
import warnings, tables  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in <module>  
from .utilsextension import _broken_hdf5_long_double  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in  
from .utilsextension import _broken_hdf5_long_double  
  
See log for complete Python traceback.  
  

> open /Users/nixon/Downloads/threed_09(1).hdf

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 191, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open  
return open_map(session, path, format=_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3604, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 175, in open_file  
data.extend(open_func(p, **okw))  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 55, in __init__  
import warnings, tables  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in <module>  
from .utilsextension import _broken_hdf5_long_double  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
ImportError: cannot import name '_broken_hdf5_long_double' from
'tables.utilsextension'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 135, in  
from .utilsextension import _broken_hdf5_long_double  
  
See log for complete Python traceback.  
  

> view matrix models
> #2,-0.74283,-0.66447,0.081754,247.59,0.64855,-0.74451,-0.15836,16.443,0.16609,-0.06461,0.98399,-262.02

> view matrix models
> #2,-0.74283,-0.66447,0.081754,245.65,0.64855,-0.74451,-0.15836,17.036,0.16609,-0.06461,0.98399,-259.81




OpenGL version: 4.1 ATI-5.2.4
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2020.61.1.0.0 (iBridge: 21.16.2057.0.0,0)
      OS Loader Version: 580~1053

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 4 hours, 53 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG UltraFine:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.1.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403290055
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
File attachment: threed_09.hdf

threed_09.hdf​

[btn1@…]

Added by email2trac

[Eric Pettersen]

Reported by Tracy Nixon

[Tom Goddard]

In my testing the ChimeraX 1.8 daily build on Intel Mac gives an error reading any HDF5 file while the ARM Mac (M1,M2,M3) works for all HDF5 files including the one attached to this report.

This is a problem with the PyTables library version 3.9.2 that ChimeraX daily builds are using, that is not present in the PyTables version 3.8.0 that ChimeraX 1.7.1 uses. Also the daily build Mac ARM version still uses the 3.8.0 version and that is why it is working.

I have reverted the ChimeraX daily build to use the working PyTables version 3.8.0.

[Tom Goddard]

Fixed.

PyTables 3.9.2 has problems so I reverted to the working 3.8.0 version.