The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202012310239 (2020-12-31 02:39:02 UTC)
Description
open 6pt2
then click on chain A in Log chain table to select chain A. It selects nothing and issues the command
select #2/A:999-329
that shows why residue 999-329. Oops. Likewise chain B selects nothing.
Log:
UCSF ChimeraX version: 1.2.dev202012310239 (2020-12-31)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> open 6ddf
6ddf title:
μ Opioid Receptor-Gi Protein Complex [more info...]
Chain information for 6ddf #1
---
Chain | Description
A | Guanine nucleotide-binding protein G(i) subunit alpha-1
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
D | DAMGO
R | Mu-type opioid receptor
Non-standard residues in 6ddf #1
---
ETA — ethanolamine
> close
> open 4n6h
4n6h title:
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]
Chain information for 4n6h #1
---
Chain | Description
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein
Non-standard residues in 4n6h #1
---
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)
NA — sodium ion
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PGE — triethylene glycol
TLA — L(+)-tartaric acid
> surface
> mlp
Map values for surface "4n6h_A SES surface": minimum -26.77, mean -0.8566,
maximum 23.81
> lighting soft
> lighting simple
> hide surfaces
> delete :1002-1106
> hbonds
581 hydrogen bonds found
> hbonds :EJ4
10 hydrogen bonds found
> color :EJ4 orange
> color byhetero
> hide cartoons
> clip off
> hide atoms
> show :EJ4 :< 4
> addh
Summary of feedback from adding hydrogens to 4n6h #1
---
warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy-
atom bond partners
Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond
partners
10 messages similar to the above omitted
notes | Termini for 4n6h (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLY 36
Chain-final residues that are actual C termini: /A GLY 338
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A GLY 338
580 hydrogen bonds
Adding 'H' to /A GLY 36
3076 hydrogens added
> open 4n6h fromDatabase eds
Opened eds 4n6h as #2, grid size 114,100,190, pixel 0.599,0.607,0.603, shown
at level 0.799, step 1, values float32
> volume #2 showOutlineBox true
> volume #2 showOutlineBox false
> volume zone #2 nearAtoms :EJ4 range 6 newMap false
> volume #2 level 0.6601
> delete H
> volume level .5
> close #2
> style :EJ4 sphere
Changed 31 atom styles
> surface :EJ4 :< 4
> transparency 50
> open 6pt2
6pt2 title:
Crystal structure of the active δ opioid receptor in complex with the peptide
agonist KGCHM07 [more info...]
Chain information for 6pt2 #2
---
Chain | Description
A B | δ opioid receptor
C D | Peptide agonist KGCHM07
Non-standard residues in 6pt2 #2
---
CLR — cholesterol
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
OXJ — 1-[3,5-bis(trifluoromethyl)phenyl]-N-methylmethanamine
> hide #1 models
> view
> select #2/A:999-329
Nothing selected
> select #2/A:999-329
Nothing selected
> select #2/B:1002-333
Nothing selected
> select #2/B:1002-333
Nothing selected
> select #2/B:1002-333
Nothing selected
OpenGL version: 4.1 ATI-3.10.18
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
Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2)
Kernel Version: Darwin 19.6.0
Time since boot: 20 days 19:04
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: Supported, feature set macOS GPUFamily2 v1
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: Supported, feature set macOS GPUFamily2 v1
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: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PySide2 version: 5.15.2
Qt version: 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
biopython: 1.78
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.3.0
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.10
ChimeraX-AtomicLibrary: 1.1
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: 2.2
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-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202012310239
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 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: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
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: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.4
ChimeraX-PDB: 2.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-Read-Pbonds: 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: 1.3
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: 1.2.2
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Tempy: 0.6.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.3.2
ChimeraX-uniprot: 2.1
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: 4.4.2
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: 4.7.0
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.5.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
MolecularDynamicsViewer: 1.1
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.2
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.8
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 20.3.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.8
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
PySide2: 5.15.2
python-dateutil: 2.8.1
pytz: 2020.5
pyzmq: 20.0.0
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
Send2Trash: 1.5.0
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
shiboken2: 5.15.2
six: 1.15.0
snowballstemmer: 2.0.0
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: 1.2.0
Chain-selection table entry now handles circular permutations.