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Opened 5 years ago
Closed 5 years ago
#4447 closed defect (fixed)
Wrong distance between atoms when models have different positions
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202104020052 (2021-04-02 00:52:32 UTC)
Description
If a model is opened, moved, and a centroid made, then the measured distance between that centroid and a centroid from another model can be implausibly large. It seems to report the distance as if the shifted model was in it's orginal position.
If a similar process is followed in Chimera, or if the shifted model is saved and reopened, the 'current' distance between the two centroids (i.e. after one model is moved) is reported.
Log:
UCSF ChimeraX version: 1.2.dev202104020052 (2021-04-02)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/crowe/Desktop/rqcH-DR-processing/modelling/combined-model-
> test.pdb format pdb
Chain information for combined-model-test.pdb
---
Chain | Description
1.1/0 | No description available
1.2/0 | No description available
1.1/1 1.2/1 | No description available
1.1/2 | No description available
1.2/2 | No description available
1.1/A | No description available
1.2/A | No description available
1.1/B 1.2/B | No description available
1.1/E 1.2/E | No description available
1.1/F 1.2/F | No description available
1.1/G 1.2/G | No description available
1.1/H | No description available
1.2/H | No description available
1.1/I 1.2/I | No description available
1.1/K 1.2/K | No description available
1.1/L 1.2/L | No description available
1.1/N 1.2/N | No description available
1.1/O 1.2/O | No description available
1.1/P 1.2/P | No description available
1.1/Q 1.2/Q | No description available
1.1/R 1.2/R | No description available
1.1/S 1.2/S | No description available
1.1/T 1.2/T | No description available
1.1/U 1.2/U | No description available
1.1/V 1.2/V | No description available
1.1/W 1.2/W | No description available
1.1/X 1.2/X | No description available
1.1/Y 1.2/Y | No description available
1.1/a 1.2/a | No description available
1.1/b 1.2/b | No description available
1.1/c 1.2/c | No description available
1.1/d 1.2/d | No description available
1.1/f 1.2/f | No description available
1.1/g 1.2/g | No description available
1.1/h 1.2/h | No description available
1.1/i 1.2/i | No description available
1.1/j 1.2/j | No description available
> hide #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> show #!1.1 models
> hide atoms
> style stick
Changed 187716 atom styles
> show atoms
> hide atoms
> show cartoons
> set bgColor white
> ui tool show "Show Sequence Viewer"
> sequence chain #1.1/0
Alignment identifier is 1.1/0
> select #1.1/0:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1.1/0:2-163
1297 atoms, 1326 bonds, 162 residues, 1 model selected
> name frozen DR sel
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2/0
Alignment identifier is 1.2/0
> select clear
> select #1.2/0:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1.2/0:2-163
1306 atoms, 1335 bonds, 162 residues, 1 model selected
> name frozen wt sel
> define centroid DR
Centroid 'centroid' placed at [223.65770239 120.10141712 109.87104472]
> define centroid wt
Centroid 'centroid' placed at [222.16657427 130.29441501 104.84159188]
> distance #1.1.2 #1.2.2
Distance between centroid #1.1.2/centroid centroid 1 cent and centroid
#1.2.2/centroid centroid 1 cent: 11.464Å
> open 7as8
7as8 title:
Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S
subunit with P-tRNA, RqcH, and RqcP/YabO [more info...]
Chain information for 7as8 #3
---
Chain | Description
0 | Rqc2 homolog RqcH
1 | Uncharacterized protein YabO
2 | tRNA-Ala-1-1
A | 23S rRNA
B | 5s rRNA
E | 50S ribosomal protein L2
F | 50S ribosomal protein L3
G | 50S ribosomal protein L4
H | 50S ribosomal protein L5
I | 50S ribosomal protein L6
K | 50S ribosomal protein L11
L | 50S ribosomal protein L10
N | 50S ribosomal protein L13
O | 50S ribosomal protein L14
P | 50S ribosomal protein L15
Q | 50S ribosomal protein L16
R | 50S ribosomal protein L17
S | 50S ribosomal protein L18
T | 50S ribosomal protein L19
U | 50S ribosomal protein L20
V | 50S ribosomal protein L21
W | 50S ribosomal protein L22
X | 50S ribosomal protein L23
Y | 50S ribosomal protein L24
a | 50S ribosomal protein L27
b | 50S ribosomal protein L28
c | 50S ribosomal protein L29
d | 50S ribosomal protein L30
f | 50S ribosomal protein L32
g | 50S ribosomal protein L33 1
h | 50S ribosomal protein L34
i | 50S ribosomal protein L35
j | 50S ribosomal protein L36
> mmaker #3/A to #1.1/A matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 combined-model-test.pdb, chain A (#1.1) with 7as8, chain A (#3),
sequence alignment score = 11106.6
RMSD between 2807 pruned atom pairs is 0.175 angstroms; (across all 2812
pairs: 0.205)
> ui tool show "Show Sequence Viewer"
> sequence chain #3/0
Alignment identifier is 3/0
> select clear
> select #3/0:2-170
1359 atoms, 1390 bonds, 169 residues, 1 model selected
> name frozen wt-cif sel
> define centroid wt-cif
Centroid 'centroid' placed at [264.08569831 172.17023988 195.48216777]
> distance #1.1.2 #3.3
Distance between centroid #1.1.2/centroid centroid 1 cent and centroid
#3.3/centroid centroid 1 cent: 108.050Å
> select clear
> save /Users/crowe/Desktop/7as8-aligned.cif models #!3 relModel #1.1
> hide #!3 models
> open /Users/crowe/Desktop/7as8-aligned.cif
Chain information for 7as8-aligned.cif #4
---
Chain | Description
0 | Rqc2 homolog RqcH
1 | Uncharacterized protein YabO
2 | tRNA-Ala-1-1
A | 23S rRNA
B | 5s rRNA
E | 50S ribosomal protein L2
F | 50S ribosomal protein L3
G | 50S ribosomal protein L4
H | 50S ribosomal protein L5
I | 50S ribosomal protein L6
K | 50S ribosomal protein L11
L | 50S ribosomal protein L10
N | 50S ribosomal protein L13
O | 50S ribosomal protein L14
P | 50S ribosomal protein L15
Q | 50S ribosomal protein L16
R | 50S ribosomal protein L17
S | 50S ribosomal protein L18
T | 50S ribosomal protein L19
U | 50S ribosomal protein L20
V | 50S ribosomal protein L21
W | 50S ribosomal protein L22
X | 50S ribosomal protein L23
Y | 50S ribosomal protein L24
a | 50S ribosomal protein L27
b | 50S ribosomal protein L28
c | 50S ribosomal protein L29
d | 50S ribosomal protein L30
f | 50S ribosomal protein L32
g | 50S ribosomal protein L33 1
h | 50S ribosomal protein L34
i | 50S ribosomal protein L35
j | 50S ribosomal protein L36
> hide #!4 models
> show #!3 models
> hide #3.3#1.1.2#1.2.2#!3#!1.1-2 atoms
> show #3.3#1.1.2#1.2.2#!3#!1.1-2 cartoons
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/0
Alignment identifier is 4/0
> select #4/0:2-170
1359 atoms, 1390 bonds, 169 residues, 1 model selected
> name frozen wt-cif-aligned sel
> define centroid wt-cif-aligned
Centroid 'centroid' placed at [222.44006181 131.03925975 104.55876895]
> distance #1.1.2 #4.3
Distance between centroid #1.1.2/centroid centroid 1 cent and centroid
#4.3/centroid centroid 1 cent: 12.220Å
> distance #1.1.2 #3.3
Distance already exists; modify distance properties with 'distance style'
> close #2
> distance #1.1.2 #3.3
Distance between centroid #1.1.2/centroid centroid 1 cent and centroid
#3.3/centroid centroid 1 cent: 108.050Å
> open 7as8
7as8 title:
Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S
subunit with P-tRNA, RqcH, and RqcP/YabO [more info...]
Chain information for 7as8 #5
---
Chain | Description
0 | Rqc2 homolog RqcH
1 | Uncharacterized protein YabO
2 | tRNA-Ala-1-1
A | 23S rRNA
B | 5s rRNA
E | 50S ribosomal protein L2
F | 50S ribosomal protein L3
G | 50S ribosomal protein L4
H | 50S ribosomal protein L5
I | 50S ribosomal protein L6
K | 50S ribosomal protein L11
L | 50S ribosomal protein L10
N | 50S ribosomal protein L13
O | 50S ribosomal protein L14
P | 50S ribosomal protein L15
Q | 50S ribosomal protein L16
R | 50S ribosomal protein L17
S | 50S ribosomal protein L18
T | 50S ribosomal protein L19
U | 50S ribosomal protein L20
V | 50S ribosomal protein L21
W | 50S ribosomal protein L22
X | 50S ribosomal protein L23
Y | 50S ribosomal protein L24
a | 50S ribosomal protein L27
b | 50S ribosomal protein L28
c | 50S ribosomal protein L29
d | 50S ribosomal protein L30
f | 50S ribosomal protein L32
g | 50S ribosomal protein L33 1
h | 50S ribosomal protein L34
i | 50S ribosomal protein L35
j | 50S ribosomal protein L36
> ui tool show "Show Sequence Viewer"
> sequence chain #5/0
Alignment identifier is 5/0
> select #5/0:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/0:2-170
1359 atoms, 1390 bonds, 169 residues, 1 model selected
> name frozen unaligned-7as8 sel
> define centroid unaligned-7as8
Centroid 'centroid' placed at [264.08569831 172.17023988 195.48216777]
> distance #1.1.2 #5.3
Distance between centroid #1.1.2/centroid centroid 1 cent and centroid
#5.3/centroid centroid 1 cent: 108.050Å
> distance #1.1.2 #4.3
Distance between centroid #1.1.2/centroid centroid 1 cent and centroid
#4.3/centroid centroid 1 cent: 12.220Å
> distance #1.1.2 #3.3
Distance already exists; modify distance properties with 'distance style'
> close #2
> distance #1.1.2 #3.3
Distance between centroid #1.1.2/centroid centroid 1 cent and centroid
#3.3/centroid centroid 1 cent: 108.050Å
> select clear
> name list
DR [1297 atoms, 2652 bonds]
unaligned-7as8 [1359 atoms, 2780 bonds]
wt [1306 atoms, 2670 bonds]
wt-cif [1359 atoms, 2780 bonds]
wt-cif-aligned [1359 atoms, 2780 bonds]
> color red wt*
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color wt* red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> hide #!5 models
> color wt-cif red
> color wt-cif-aligned red
> hide #!1 models
> show #!3 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!3 models
> hide #4.3#!4 atoms
> show #4.3#!4 cartoons
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> name list
DR [1297 atoms, 2652 bonds]
unaligned-7as8 [1359 atoms, 2780 bonds]
wt [1306 atoms, 2670 bonds]
wt-cif [1359 atoms, 2780 bonds]
wt-cif-aligned [1359 atoms, 2780 bonds]
> color wt orange
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3.7 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 32 GB
Boot ROM Version: 1554.80.3.0.0
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H524)
Kernel Version: Darwin 19.6.0
Time since boot: 5:38
Graphics/Displays:
Radeon Pro 580X:
Chipset Model: Radeon Pro 580X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A1X-009
EFI Driver Version: 01.B1.042
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 5120 x 2880 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
HP 24f:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 3CM9460GP9
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DVI or HDMI
Adapter Firmware Version: 0.00
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.5
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13
ChimeraX-AtomicLibrary: 3.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202104020052
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.2
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.0
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (3)
comment:1 by , 5 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Wrong distance between atoms when models have different positions |
comment:2 by , 5 years ago
| Status: | assigned → accepted |
|---|
comment:3 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
When the initial position of a Structure (which is what a centroid is) isn't the identity matrix, the C++ layer wasn't being informed.
Fix in tomorrow's build.
Note:
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I confirm that in the daily build the distance is computed incorrectly without taking account of the different model positions. Here are some commands that demonstrate the problem
open 1a0m
open 1a0m
move x 10 model #2
define centroid #1
define centroid #2
distance #1.1 #2.1
The reported and displayed distance is 0 instead of 10. If I then move one model "move x 5 model #2" the correct distance is shown.