fitmap: self.data is None fitting atomic model into simulated map

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202405132341 (2024-05-13 23:41:14 UTC)
Description
Fitting an atomic model into a map computed by molmap  for that model with the fitmap resolution option generates this error apparently because the fitmap code replaces the current molmap.


Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9.dev202405132341 (2024-05-13)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
2024-07-08 10:58:47,013 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x309d78910>: Failed to establish a new connection: [Errno 61] Connection
refused')':
/cxservices/api/v1/chimerax/updates?uuid=4f1238ff-f8a6-5cec-a689-f3fe8a976599&OS=macosx&OSVersion=14.5&ChimeraXVersion=1.9.dev202405132341  
2024-07-08 10:58:47,015 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x3294f42d0>: Failed to establish a new connection: [Errno 61] Connection
refused')':
/cxservices/api/v1/chimerax/updates?uuid=4f1238ff-f8a6-5cec-a689-f3fe8a976599&OS=macosx&OSVersion=14.5&ChimeraXVersion=1.9.dev202405132341  
2024-07-08 10:58:47,016 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x16f750550>: Failed to establish a new connection: [Errno 61] Connection
refused')':
/cxservices/api/v1/chimerax/updates?uuid=4f1238ff-f8a6-5cec-a689-f3fe8a976599&OS=macosx&OSVersion=14.5&ChimeraXVersion=1.9.dev202405132341  

> open 3ny5 format mmcif fromDatabase pdb

3ny5 title:  
Crystal structure of the RBD domain of serine/threonine-protein kinase B-raf
from Homo sapiens. Northeast Structural Genomics Consortium Target HR4694F
[more info...]  
  
Chain information for 3ny5 #1  
---  
Chain | Description | UniProt  
A B C D | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 153-237  
  
3ny5 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_defined_assembly  
  
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> molmap #1 4

Opened 3ny5 map 4 as #2, grid size 57,86,65, pixel 1.33, shown at level
0.0952, step 1, values float32  

> fitmap #1 inMap #2 resolution 5

Opened 3ny5 map 5 as #2, grid size 49,72,56, pixel 1.67, shown at level
0.0898, step 1, values float32  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3209, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 141, in fitmap  
fits = [fit_map_in_map(v, volume, metric, envelope, zeros,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 317, in fit_map_in_map  
move_tf, stats = F.motion_to_maximum(points, point_weights, volume,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitmap.py", line 104, in motion_to_maximum  
volume.matrix_and_transform(identity(), subregion = None, step = 1)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1641, in matrix_and_transform  
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1363, in
matrix_indices_to_xyz_transform  
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1420, in ijk_aligned_region  
return self.step_aligned_region(r)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1450, in step_aligned_region  
for o,s,lim in zip(origin, size, self.data.size)]  
^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'size'  
  
AttributeError: 'NoneType' object has no attribute 'size'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1450, in step_aligned_region  
for o,s,lim in zip(origin, size, self.data.size)]  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 20 days, 14 hours, 31 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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[Tom Goddard]

Using fitmap with resolution specified computes a simulated map with molmap that replaces any existing simulated map for those atoms. In this case I was trying to fit into a molmap simulated map (for testing) and so the map I was fitting into got deleted. Oops.

Not sure how or whether to fix this. It is useful that the previous molmap created by a previous fit at a different resolution is deleted. Probably the fitmap code itself should delete the molmap from a previous fit instead of letting the molmap replace true do the deletion since the replace true will delete all molmaps for those atoms even ones not created by fitmap.

[Tom Goddard]

While it would be desirable to fix this, the case of fitting an atomic model using a simulated map into a simulated map is absurd, and not useful, I was just trying to do a quick test so I didn't open a real experimental map. So I think I'll ignore this problem unless a real user reports it.