#10323 closed defect (fixed)

fitmap search animation moving models does not take a direct route

Reported by: goddard@… Owned by:
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-13.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202311100228 (2023-11-10 02:28:59 UTC)
Description
Fit search list interpolation often sends the model into orbit far from the destination location even if only a small motion would be required to reach the fit location.

Log:
UCSF ChimeraX version: 1.8.dev202311100228 (2023-11-10)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/chimerax/src/bundles/map_fit/test.cxs format
> session

Opened emdb 12654 as #1, grid size 250,250,250, pixel 1.54, shown at level 2,
step 1, values float32  
Log from Mon Dec 11 15:12:35 2023Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.8.dev202311100228 (2023-11-10)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 12654 format ccp4 fromDatabase emdb

Opened emdb 12654 as #1, grid size 250,250,250, pixel 1.54, shown at level 2,
step 1, values float32, fit PDB 7nyu  

> open 7nyu format mmcif fromDatabase pdb

7nyu title:  
Respiratory complex I from Escherichia coli - conformation 2 [more info...]  
  
Chain information for 7nyu #2  
---  
Chain | Description | UniProt  
A | NADH-quinone oxidoreductase subunit A | NUOA_ECOLI 1-147  
B | NADH-quinone oxidoreductase subunit B | NUOB_ECOLI 1-220  
D | NADH-quinone oxidoreductase subunit C/D | NUOCD_ECOLI 1-596  
E | NADH-quinone oxidoreductase subunit E | NUOE_ECOLI 1-166  
F | NADH-quinone oxidoreductase subunit F | NUOF_ECOLI 1-445  
G | NADH-quinone oxidoreductase subunit G | NUOG_ECOLI 1-908  
H | NADH-quinone oxidoreductase subunit H | NUOH_ECOLI 1-325  
I | NADH-quinone oxidoreductase subunit I | NUOI_ECOLI 1-180  
J | NADH-quinone oxidoreductase subunit J | NUOJ_ECOLI 1-184  
K | NADH-quinone oxidoreductase subunit K | NUOK_ECOLI 1-100  
L | NADH-quinone oxidoreductase subunit L | A0A1V3W1N5_ECOLX 1-613  
M | NADH-quinone oxidoreductase subunit M | NUOM_ECOLI 1-509  
N | NADH-quinone oxidoreductase subunit N | NUON_ECOLI 1-485  
  
Non-standard residues in 7nyu #2  
---  
CA — calcium ion  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
SF4 — iron/sulfur cluster  
  

> open 3rko format mmcif fromDatabase pdb

3rko title:  
Crystal structure of the membrane domain of respiratory complex I from E. coli
at 3.0 angstrom resolution [more info...]  
  
Chain information for 3rko #3  
---  
Chain | Description | UniProt  
A E | NADH-QUINONE OXIDOREDUCTASE SUBUNIT A | C6E9R4_ECOBD 1-147  
B L | NADH-QUINONE OXIDOREDUCTASE SUBUNIT L | C6E9S4_ECOBD 1-613  
C M | NADH-QUINONE OXIDOREDUCTASE SUBUNIT M | C6E9S5_ECOBD 1-509  
D N | NADH-QUINONE OXIDOREDUCTASE SUBUNIT N | C6E9S6_ECOBD 1-485  
F J | NADH-QUINONE OXIDOREDUCTASE SUBUNIT J | C6E9S2_ECOBD 1-184  
G K | NADH-QUINONE OXIDOREDUCTASE SUBUNIT K | C6E9S3_ECOBD 1-100  
  
Non-standard residues in 3rko #3  
---  
CA7 — 7-cyclohexylheptyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside  
LFA — eicosane (lipid fragment)  
  
3rko mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete ~/L

> mmaker #3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7nyu, chain L (#2) with 3rko, chain L (#3), sequence alignment
score = 3003.3  
RMSD between 575 pruned atom pairs is 1.029 angstroms; (across all 612 pairs:
1.204)  
  

> hide atoms

> show cartoons

> hide #!1 models

> color #2 #17ceebff

> color #2 #17ce4cff

> delete :547-1000

> fitmap #3 inMap #1 search 100 radius 30

Found 96 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
1.444 (1), 1.24 (1), 1.208 (1), 1.2 (1), 1.179 (1), 1.158 (1), 1.151 (1),
1.148 (1), 1.141 (1), 1.14 (1), 1.13 (3), 1.13 (1), 1.13 (1), 1.125 (1), 1.117
(3), 1.116 (1), 1.116 (1), 1.113 (1), 1.109 (1), 1.103 (1), 1.093 (1), 1.093
(1), 1.092 (1), 1.088 (1), 1.087 (1), 1.086 (1), 1.086 (1), 1.081 (1), 1.081
(1), 1.08 (1), 1.078 (1), 1.077 (1), 1.071 (1), 1.067 (1), 1.065 (1), 1.064
(1), 1.058 (1), 1.057 (1), 1.056 (1), 1.051 (1), 1.047 (1), 1.046 (1), 1.046
(1), 1.046 (1), 1.045 (1), 1.045 (1), 1.044 (1), 1.043 (1), 1.04 (1), 1.039
(1), 1.037 (1), 1.036 (1), 1.035 (1), 1.034 (1), 1.033 (1), 1.031 (1), 1.029
(1), 1.029 (1), 1.027 (1), 1.026 (1), 1.026 (1), 1.025 (1), 1.024 (1), 1.024
(1), 1.022 (1), 1.018 (1), 1.014 (1), 1.01 (1), 1.006 (1), 1.005 (1), 1.003
(1), 1.002 (1), 0.9966 (1), 0.9957 (1), 0.993 (1), 0.9917 (1), 0.9872 (1),
0.9789 (1), 0.9728 (1), 0.9676 (1), 0.9624 (1), 0.9586 (1), 0.9548 (1), 0.9497
(1), 0.9442 (1), 0.9436 (1), 0.9379 (1), 0.9352 (1), 0.9197 (1), 0.918 (1),
0.8678 (1), 0.8646 (1), 0.8621 (1), 0.8414 (1), 0.8242 (1), 0.7459 (1)  
  
Best fit found:  
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms  
average map value = 1.444, steps = 96  
shifted from previous position = 2.75  
rotated from previous position = 27.4 degrees  
atoms outside contour = 2743, contour level = 2  
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:  
Matrix rotation and translation  
0.06497259 -0.16057875 -0.98488222 174.06774843  
-0.45505859 0.87360214 -0.17245541 117.10801015  
0.88808792 0.45938407 -0.01631256 168.13156167  
Axis 0.31615866 -0.93719331 -0.14735127  
Axis point 26.51958635 0.00000000 177.08106317  
Rotation angle (degrees) 92.22758609  
Shift along axis -79.49421665  
  
Found 96 fits.  

Populating font family aliases took 85 ms. Replace uses of missing font family
"Courier" with one that exists to avoid this cost.  

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/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 411, in mstep  
return move_step(mt, session)  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 427, in move_step  
c = m.scene_position.inverse() * scene # Center in model coordinates  
^^^^^  
NameError: name 'scene' is not defined  
  
Error processing trigger "new frame":  
NameError: name 'scene' is not defined  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 427, in move_step  
c = m.scene_position.inverse() * scene # Center in model coordinates  
^^^^^  
  
See log for complete Python traceback.  
  

> save test.cxs

——— End of log from Mon Dec 11 15:12:35 2023 ———

opened ChimeraX session  

> fitmap #3 inMap #1 search 100 radius 30

Found 92 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
1.444 (5), 1.233 (1), 1.226 (1), 1.203 (1), 1.2 (2), 1.184 (1), 1.183 (1),
1.182 (1), 1.18 (1), 1.174 (1), 1.166 (1), 1.165 (1), 1.16 (1), 1.155 (1),
1.154 (1), 1.142 (1), 1.14 (1), 1.137 (1), 1.133 (2), 1.13 (1), 1.12 (1),
1.113 (1), 1.11 (1), 1.109 (2), 1.108 (1), 1.105 (1), 1.103 (1), 1.099 (1),
1.096 (1), 1.096 (1), 1.091 (1), 1.083 (1), 1.08 (1), 1.078 (1), 1.074 (1),
1.073 (1), 1.068 (1), 1.067 (1), 1.066 (1), 1.059 (1), 1.058 (1), 1.056 (1),
1.054 (2), 1.052 (1), 1.046 (1), 1.045 (1), 1.043 (1), 1.042 (1), 1.042 (1),
1.041 (1), 1.041 (1), 1.039 (1), 1.033 (1), 1.032 (1), 1.032 (1), 1.031 (1),
1.029 (1), 1.027 (1), 1.027 (1), 1.026 (1), 1.024 (1), 1.022 (1), 1.019 (1),
1.019 (1), 1.016 (1), 1.013 (1), 1.01 (1), 1.009 (1), 0.9985 (1), 0.9925 (1),
0.9918 (1), 0.9916 (1), 0.9894 (1), 0.982 (1), 0.9794 (1), 0.9784 (1), 0.9684
(1), 0.9615 (1), 0.9537 (1), 0.9496 (1), 0.9427 (1), 0.9342 (1), 0.9328 (1),
0.9133 (1), 0.9011 (1), 0.8943 (1), 0.8907 (1), 0.8837 (1), 0.882 (1), 0.8666
(1), 0.8575 (1), 0.8545 (1)  
  
Best fit found:  
Fit molecule 3rko (#3) to map emdb 12654 (#1) using 4164 atoms  
average map value = 1.444, steps = 116  
shifted from previous position = 10.3  
rotated from previous position = 19.4 degrees  
atoms outside contour = 2745, contour level = 2  
Position of 3rko (#3) relative to emdb 12654 (#1) coordinates:  
Matrix rotation and translation  
0.06504250 -0.16044596 -0.98489924 174.07444595  
-0.45533495 0.87347605 -0.17236464 117.10082125  
0.88794115 0.45967017 -0.01624360 168.11747219  
Axis 0.31625632 -0.93712815 -0.14755597  
Axis point 26.53859698 0.00000000 177.07615129  
Rotation angle (degrees) 92.22721952  
Shift along axis -79.49306874  
  
Found 92 fits.  

Populating font family aliases took 85 ms. Replace uses of missing font family
"Courier" with one that exists to avoid this cost.  

> view




OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 522.0.0.0.0
      OS Loader Version: 577.140.2~15
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.6.1 (22G313)
      Kernel Version: Darwin 22.6.0
      Time since boot: 11 days, 23 hours, 39 minutes

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.13.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.12
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.51
    ChimeraX-AtomicLibrary: 12.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.10.5
    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: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    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.dev202311100228
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    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
    ChimeraX-DockPrep: 1.1.2
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.12
    ChimeraX-ModelPanel: 1.4
    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-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.2
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.14.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    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: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.44.0
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.0.0
    prompt-toolkit: 3.0.40
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.9
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (1)

comment:1 by Tom Goddard, 23 months ago

Component: UnassignedVolume Data
Platform: all
Project: ChimeraX
Resolution: fixed
Status: newclosed
Summary: ChimeraX bug report submissionfitmap search animation moving models does not take a direct route

Fixed in 1.8 daily and 1.7.

The interpolation code was using a center of rotation point in scene coordinates where it required a center point in fit model local coordinates. Fixed the coordinate system.

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