Fit in map gives wrong position if moved model has a moved parent

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202108251821 (2021-08-25 18:21:58 UTC)
Description
Fit in map tool does not move map fit to map to correct location if the source map is a child model and the parent group had a non-identity transformation.  Probably it is not taking account of the parent model transoformations and only works correct if the parent model transform is the identity.

I also observed this fitting selected atoms when the structure the atoms belonged to has a different transform than the map being fit to.

Log:
UCSF ChimeraX version: 1.3.dev202108251821 (2021-08-25)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 30495 format ccp4 fromDatabase emdb

Opened emdb 30495 as #1, grid size 220,220,220, pixel 1.09, shown at level
0.000223, step 1, values float32  

> volume #1 level 1.806

> open 30495 format ccp4 fromDatabase emdb

Opened emdb 30495 as #2, grid size 220,220,220, pixel 1.09, shown at level
0.000223, step 1, values float32  

> volume #2 level 1.764

> rename #1,2 id #3

> rename #3.2 id #1

> move x 50 coordinateSystem #1 models #3

> move x -50 coordinateSystem #1 models #3.1

> ui tool show "Fit in Map"

Fit map emdb 30495 in map emdb 30495 using 5199 points  
correlation = 1, correlation about mean = 0.9997, overlap = 3.427e+04  
steps = 48, shift = 0.0169, angle = 0.0135 degrees  
  
Position of emdb 30495 (#3.1) relative to emdb 30495 (#1) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00007117 0.00012733 -50.02455381  
0.00007115 0.99999998 0.00018499 -0.03532166  
-0.00012734 -0.00018498 0.99999997 0.04789174  
Axis -0.78523311 0.54052639 0.30205991  
Axis point 0.00000000 -63893.55291316 114949.23954883  
Rotation angle (degrees) 0.01349743  
Shift along axis 39.27630963  
  

> volume #3.1 level 1.827

> volume #1 level 1.66

> turn y 10 models #3 coordinateSystem #1

Fit map emdb 30495 in map emdb 30495 using 5041 points  
correlation = 0.4619, correlation about mean = 0.03588, overlap = 6167  
steps = 92, shift = 0.58, angle = 4.03 degrees  
  
Position of emdb 30495 (#3.1) relative to emdb 30495 (#1) coordinates:  
Matrix rotation and translation  
0.99980179 0.00004414 -0.01990907 -47.92618312  
0.00130034 0.99771756 0.06751277 -8.69167932  
0.01986661 -0.06752527 0.99751975 4.88502083  
Axis -0.95921455 -0.28253819 0.00892318  
Axis point 0.00000000 68.57522414 -71.78876035  
Rotation angle (degrees) 4.03638233  
Shift along axis 48.47081335  
  

> volume #3.1 level 1.121

> volume #1 level 0.7058

Fit map emdb 30495 in map emdb 30495 using 12725 points  
correlation = 0.4281, correlation about mean = 0.06704, overlap = 9950  
steps = 72, shift = 1.2, angle = 1.46 degrees  
  
Position of emdb 30495 (#3.1) relative to emdb 30495 (#1) coordinates:  
Matrix rotation and translation  
0.99917473 0.01622678 -0.03723634 -47.65975093  
-0.01331804 0.99693629 0.07707568 -7.56951171  
0.03837295 -0.07651615 0.99632966 4.14847874  
Axis -0.88411285 -0.43522588 -0.17006737  
Axis point 0.00000000 160.72264590 -147.95571363  
Rotation angle (degrees) 4.98311250  
Shift along axis 44.72552457  
  




OpenGL version: 4.1 ATI-4.6.20
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 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: 32 GB
      System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 11.5.2 (20G95)
      Kernel Version: Darwin 20.6.0
      Time since boot: 3 days 2:39

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 Family: Supported, Metal GPUFamily macOS 2

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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[Tom Goddard]

Fixed.

Code that moved atomic structures, maps or atoms into another map assumed the moved object parent models all had identity transform. Surprised this has not been reported earlier. Made the motions correctly use scene coordinates.