Opened 3 years ago

Closed 3 years ago

#8752 closed defect (duplicate)

Centroid distances

Reported by: dzyla@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.10.0-1050-oem-x86_64-with-glibc2.35
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

I am trying to measure distance between two centroids (I even have the XYZ coordinates) however chimerax is refusing measurment of the distance between them. I would appriciate adding this option. Thank you!

Log:
> lighting soft

UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /media/dzyla/Data/Data_exchange/pycharm/structures/structure_comparison/Fecto2M_fab.pdb

Chain information for Fecto2M_fab.pdb #1  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
G I K | No description available  
H J L | No description available  
  

> open
> /media/dzyla/Data/Data_exchange/pycharm/structures/structure_comparison/Fecto2M_fab_post.pdb

Summary of feedback from opening
/media/dzyla/Data/Data_exchange/pycharm/structures/structure_comparison/Fecto2M_fab_post.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 5 5 THR A 95
ASN A 97 1 3  
Start residue of secondary structure not found: HELIX 6 6 ALA B 128 SER B 140
1 13  
Start residue of secondary structure not found: HELIX 7 7 SER B 144 THR B 156
1 13  
Start residue of secondary structure not found: HELIX 8 8 GLN B 179 LEU B 186
1 8  
Start residue of secondary structure not found: HELIX 9 9 ILE B 187 SER B 189
1 3  
Start residue of secondary structure not found: HELIX 10 10 CYS B 195 LEU B
216 1 22  
8 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 23 23 THR C 95 ASN C 97 1
3  
Start residue of secondary structure not found: HELIX 24 24 ALA D 128 SER D
140 1 13  
Start residue of secondary structure not found: HELIX 25 25 SER D 144 THR D
156 1 13  
Start residue of secondary structure not found: HELIX 26 26 GLN D 179 LEU D
186 1 8  
Start residue of secondary structure not found: HELIX 27 27 CYS D 195 PHE D
217 1 23  
Start residue of secondary structure not found: HELIX 28 28 ASN D 243 LYS D
248 1 6  
165 messages similar to the above omitted  
  
Chain information for Fecto2M_fab_post.pdb  
---  
Chain | Description  
2.1/A 2.1/C 2.1/E | No description available  
2.2/A 2.2/B 2.2/C | No description available  
2.1/B 2.1/D 2.1/F | No description available  
2.1/G 2.1/I 2.1/K | No description available  
2.1/H 2.1/J 2.1/L | No description available  
2.2/a 2.2/b | No description available  
2.2/c | No description available  
  

> lighting soft

> hide atoms

> show #1/A-B cartoons

> show #2/A,a cartoons

> dssp

> define plane #1/B:290-370@ca radius 15

Plane 'plane' placed at [187.75307407 188.9252716 233.28654321] with normal
[0.8641664 0.41057632 0.29093558] and radius 15.0  

> define plane #2/a:290-370@ca radius 15

Plane 'plane' placed at [187.49185185 188.7354321 233.38016049] with normal
[0.85247164 0.42114287 0.30972695] and radius 15.0  

> define plane #1/B:375-432@ca

Plane 'plane' placed at [165.80291379 202.75893103 230.20910345] with normal
[-0.24680525 -0.87650248 0.41331656] and radius 15.3  

> define plane #2/a:375-432@ca

Plane 'plane' placed at [168.54212069 203.15043103 226.796 ] with normal
[-0.46498246 -0.87321514 0.14589937] and radius 13.7  

> define plane #1/A,B:70-96,254-285@ca radius 15

Plane 'plane' placed at [221.32591525 189.75086441 211.1520339 ] with normal
[-0.12750279 0.58948021 0.79765664] and radius 15.0  

> define plane #2/A,a:70-96,254-285@ca radius 15

Plane 'plane' placed at [216.39482353 191.98464706 200.88383529] with normal [
0.34645237 -0.87256682 -0.34438046] and radius 15.0  

> ui tool show Axes/Planes/Centroids

[Repeated 3 time(s)]

> angle #1.1 #2.2.1

Angle between plane #1.1 and plane #2.2.1: 1.405  

> angle #1.1 #1.2

Angle between plane #1.1 and plane #1.2: 63.070  

> angle #1.1 #1.3

Angle between plane #1.1 and plane #1.3: 68.660  

> set bgColor white

> set bgColor #ffffff00

> angle #1.1 #2.2.2

Angle between plane #1.1 and plane #2.2.2: 44.119  

> angle #1.1 #2.3

Angle between plane #1.1 and plane #2.3: 80.848  

> define centroid #1/B:290-373@ca

Centroid 'centroid' placed at [187.6197619 189.67114286 233.39760714]  

> define centroid #2/a:290-373@ca

Centroid 'centroid' placed at [187.29759524 189.53034524 233.68691667]  

> define centroid #1/B:375-432@ca

Centroid 'centroid' placed at [165.80291379 202.75893103 230.20910345]  

> define centroid #2/a:375-432@ca

Centroid 'centroid' placed at [168.54212069 203.15043103 226.796 ]  

> define centroid #1/A,B:70-96,254-285@ca

Centroid 'centroid' placed at [221.32591525 189.75086441 211.1520339 ]  

> define centroid #2/A,a:70-96,254-285@ca

Centroid 'centroid' placed at [216.39482353 191.98464706 200.88383529]  

> distance #1.4 #2.2.3

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance  
dist = object.distance(a, signed=signed)  
AttributeError: 'CentroidModel' object has no attribute 'distance'  
  
AttributeError: 'CentroidModel' object has no attribute 'distance'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance  
dist = object.distance(a, signed=signed)  
  
See log for complete Python traceback.  
  

> select #2.2.3/centroid:1@centroid

1 atom, 1 residue, 1 model selected  

> select add #1.4/centroid:1@centroid

2 atoms, 2 residues, 2 models selected  

> distance #2.2.3/centroid:1@centroid #1.4/centroid:1@centroid

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 254, in _create_distance  
run(self.session, "distance %s %s" % tuple(a.string(style="command") for a in
sel_atoms))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance  
dist = object.distance(a, signed=signed)  
AttributeError: 'CentroidModel' object has no attribute 'distance'  
  
AttributeError: 'CentroidModel' object has no attribute 'distance'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance  
dist = object.distance(a, signed=signed)  
  
See log for complete Python traceback.  
  

> ui tool show Distances

> dsitance #1.1 #2.2.1

Unknown command: dsitance #1.1 #2.2.1  

> distance #1.1 #2.2.1

Distance between plane #1.1 and plane #2.2.1: 0.000Å  

> distance #1.1 #1.2

Distance between plane #1.1 and plane #1.2: 0.000Å  
centroid #1.4 to centroid #1.5: distance: 25.640Å  

> distance #2.2.3/centroid:1#1.4/centroid:1 #1.4#1.5

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 145, in _apc_report_distance  
info = run(self.session, "distance %s %s" % (target_spec, item_spec))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance  
dist = object.distance(a, signed=signed)  
AttributeError: 'CentroidModel' object has no attribute 'distance'  
  
AttributeError: 'CentroidModel' object has no attribute 'distance'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance  
dist = object.distance(a, signed=signed)  
  
See log for complete Python traceback.  
  

> distance #1.1 #1.2

Distance between plane #1.1 and plane #1.2: 0.000Å  

> distance #1.4 #1.5

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance  
dist = object.distance(a, signed=signed)  
AttributeError: 'CentroidModel' object has no attribute 'distance'  
  
AttributeError: 'CentroidModel' object has no attribute 'distance'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance  
dist = object.distance(a, signed=signed)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 520.61.05
OpenGL renderer: Quadro T2000 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20TJS07400
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) W-10855M CPU @ 2.80GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        34Gi       3.5Gi       888Mi        24Gi        26Gi
	Swap:          2.0Gi       1.7Gi       288Mi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117GLM [Quadro T2000 Mobile / Max-Q] [10de:1fb8] (rev a1)	
	Subsystem: Lenovo TU117GLM [Quadro T2000 Mobile / Max-Q] [17aa:22c0]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-OpenCommands: 1.0
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    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: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Centroid distances

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Dawid,

Thanks for reporting this problem. It has been fixed in the 1.6 release candidate and the daily build, so if you get either of those you will be able to measure centroid distances.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Note: See TracTickets for help on using tickets.