The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Something's a bit funky about the handling of hydrogen altlocs in histidines (this is the second ultra-high-res structure I've seen this in today).
open 7tgt
show
view /X:132
The histidine is shown as altloc B for all atoms other than HE2, which has altloc A shown, appearing with a very long bond to NE2. Playing with the altloc explorer, it looks like this might be because HE2 only appears in altloc A.
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7v5u structureFactors true
Summary of feedback from opening 7v5u fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
phase_calc, fom
Automatically choosing "F_meas_au, F_meas_sigma_au".
notes | Fetching compressed mmCIF 7v5u from
http://files.rcsb.org/download/7v5u.cif
Fetching CCD HA4 from http://ligand-expo.rcsb.org/reports/H/HA4/HA4.cif
Fetching CCD P6G from http://ligand-expo.rcsb.org/reports/P/P6G/P6G.cif
Fetching compressed 7v5u structure factors from
http://files.rcsb.org/download/7v5u-sf.cif
Resolution: 0.9190125273225865
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 82,84,80, pixel
0.303,0.289,0.301, shown at level 1.33, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 82,84,80, pixel
0.303,0.289,0.301, shown at level -0.225,0.225, step 1, values float32
Opened (LIVE) 2mFo-DFc_smooth_29 as #1.1.1.4, grid size 82,84,80, pixel
0.303,0.289,0.301, shown at level 0.244, step 1, values float32
Opened (STATIC) F_calc_au, phase_calc as #1.1.1.5, grid size 82,84,80, pixel
0.303,0.289,0.301, shown at level -1.69,1.69, step 1, values float32
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 82,84,80,
pixel 0.303,0.289,0.301, shown at level -0.373,0.373, step 1, values float32
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 82,84,80, pixel
0.303,0.289,0.301, shown at level -1.62,1.62, step 1, values float32
7v5u title:
The 0.92 angstrom X-ray structure of the human heart fatty acid-binding
protein complexed with 2-cyclohexadecylacetic acid (CYC16AA) [more info...]
Chain information for 7v5u
---
Chain | Description | UniProt
1.2/A | Fatty acid-binding protein, heart | FABPH_HUMAN
Non-standard residues in 7v5u #1.2
---
HA4 — 2-cyclohexadecylethanoic acid (2-cyclohexadecylacetic acid)
P6G — hexaethylene glycol (polyethylene glycol PEG400)
> set bgColor white
> cbo
Unknown command: cbo
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
> cbo
1308 atoms, 351 residues, atom occupancy range 0.29 to 1
> cbc
> cbo
1308 atoms, 351 residues, atom occupancy range 0.29 to 1
> select /A:1002@O
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> select /A:107@CD
1 atom, 1 residue, 1 model selected
> cbc
> close #1
Deleting Crystallographic maps(7v5u-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_smooth_29
> open 7th6 structureFactors true
Summary of feedback from opening 7th6 fetched from pdb
---
warning | Atom HCS is not in the residue template for I56 /A:301
notes | Fetching compressed mmCIF 7th6 from
http://files.rcsb.org/download/7th6.cif
Fetching CCD I56 from http://ligand-expo.rcsb.org/reports/I/I56/I56.cif
Fetching compressed 7th6 structure factors from
http://files.rcsb.org/download/7th6-sf.cif
Resolution: 0.9700031604813305
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 78,76,78, pixel
0.322,0.322,0.308, shown at level 1.47, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 78,76,78, pixel
0.322,0.322,0.308, shown at level -0.276,0.276, step 1, values float32
Opened (LIVE) 2mFo-DFc_smooth_28 as #1.1.1.4, grid size 78,76,78, pixel
0.322,0.322,0.308, shown at level 0.256, step 1, values float32
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 78,76,78,
pixel 0.322,0.322,0.308, shown at level -1.21,1.21, step 1, values float32
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 78,76,78, pixel
0.322,0.322,0.308, shown at level -4.28,4.28, step 1, values float32
7th6 title:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to
Macrocyclic Inhibitor B21 [more info...]
Chain information for 7th6
---
Chain | Description | UniProt
1.2/A | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | PPIF_HUMAN
Non-standard residues in 7th6 #1.2
---
I56 —
4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}-2-methyl[1,1'-biphenyl]-4-carboxylic
acid
> cbo
2785 atoms, 359 residues, atom occupancy range 0.402 to 1
> cbc
> close #1
Deleting Crystallographic maps(7th6-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_smooth_28
> open 7tgt structureFactors true
Summary of feedback from opening 7tgt fetched from pdb
---
notes | Fetching compressed mmCIF 7tgt from
http://files.rcsb.org/download/7tgt.cif
Fetching CCD I4F from http://ligand-expo.rcsb.org/reports/I/I4F/I4F.cif
Fetching compressed 7tgt structure factors from
http://files.rcsb.org/download/7tgt-sf.cif
Resolution: 1.0550024172682124
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 90,70,72, pixel
0.334,0.349,0.345, shown at level 1.29, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 90,70,72, pixel
0.334,0.349,0.345, shown at level -0.256,0.256, step 1, values float32
Opened (LIVE) 2mFo-DFc_smooth_28 as #1.1.1.4, grid size 90,70,72, pixel
0.334,0.349,0.345, shown at level 0.235, step 1, values float32
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 90,70,72,
pixel 0.334,0.349,0.345, shown at level -0.453,0.453, step 1, values float32
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 90,70,72, pixel
0.334,0.349,0.345, shown at level -1.59,1.59, step 1, values float32
7tgt title:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to
Macrocyclic Inhibitor A26 [more info...]
Chain information for 7tgt
---
Chain | Description | UniProt
1.2/X | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | PPIF_HUMAN
Non-standard residues in 7tgt #1.2
---
I4F —
(4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide
> cbo
2821 atoms, 421 residues, atom occupancy range 0.453 to 1
> cbc
> select /X:132@HE2
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> ui tool show Shell
Populating font family aliases took 189 ms. Replace uses of missing font
family "Monaco" with one that exists to avoid this cost.
> select /X:132@NE2
1 atom, 1 residue, 1 model selected
> close #1
Deleting Crystallographic maps(7tgt-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_smooth_28
> open 7tgt
7tgt title:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to
Macrocyclic Inhibitor A26 [more info...]
Chain information for 7tgt #1
---
Chain | Description | UniProt
X | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | PPIF_HUMAN
Non-standard residues in 7tgt #1
---
I4F —
(4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide
> show
> view /X:132
> select /X:132@NE2
1 atom, 1 residue, 1 model selected
> select up
18 atoms, 18 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
18 atoms, 18 bonds, 1 residue, 1 model selected
> ui tool show "Altloc Explorer"
> altlocs change A /X:132
Changed /X HIS 132 to alternate location A
> altlocs change B /X:132
Changed /X HIS 132 to alternate location B
> altlocs change A /X:132
Changed /X HIS 132 to alternate location A
> altlocs change B /X:132
Changed /X HIS 132 to alternate location B
> altlocs change A /X:132
Changed /X HIS 132 to alternate location A
> altlocs change B /X:132
Changed /X HIS 132 to alternate location B
> altlocs change A /X:132
Changed /X HIS 132 to alternate location A
> altlocs change B /X:132
Changed /X HIS 132 to alternate location B
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache: 20 MB
Memory: 32 GB
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 6 days 3:11
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
HP Z27k G3:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0.dev0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.4
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
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
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Tristan,
--Eric