id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6783	ISOLDE not listing clashes	andong.li@…	Tristan Croll	"{{{
The following bug report has been submitted:
Platform:        Linux-5.13.0-40-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
ISOLDE unable to resolve clashes for simulation but no clashes are displayed in validation tab.

Log:
> set selectionWidth 4

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/whitelab2/Desktop/Tony/NapBAsym/All_Isolde/Isolde6/Asym_Ad_test4.cif

Summary of feedback from opening
/home/whitelab2/Desktop/Tony/NapBAsym/All_Isolde/Isolde6/Asym_Ad_test4.cif  
---  
warnings | Unknown polymer entity '1' near line 377  
Unknown polymer entity '2' near line 155227  
Unknown polymer entity '3' near line 172436  
Unknown polymer entity '4' near line 177096  
Unknown polymer entity '5' near line 192199  
1 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Asym_Ad_test4.cif #1  
---  
Chain | Description  
A AA AB AC AD AE AF AG AH AI AJ AK AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ
Aa Ac Ad Ah Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax Ay Az B BB BC BD BE
BF BH BJ BK BL C D E F G H I J K L M N O P Q R S T U V W Y Z a b c d e f g i j
k l m o p q r s t u y z | ?  
Ab X h n | ?  
Ae v | ?  
Af Ag w x | ?  
Ai BA BI BM | ?  
BG | ?  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for Asym_Ad_test4.cif  
---  
Chain | Description  
1.2/A 1.2/AA 1.2/AB 1.2/AC 1.2/AD 1.2/AE 1.2/AF 1.2/AG 1.2/AH 1.2/AI 1.2/AJ
1.2/AK 1.2/AM 1.2/AN 1.2/AO 1.2/AP 1.2/AQ 1.2/AR 1.2/AS 1.2/AT 1.2/AU 1.2/AV
1.2/AW 1.2/AX 1.2/AY 1.2/AZ 1.2/Aa 1.2/Ac 1.2/Ad 1.2/Ah 1.2/Aj 1.2/Ak 1.2/Al
1.2/Am 1.2/An 1.2/Ao 1.2/Ap 1.2/Aq 1.2/Ar 1.2/As 1.2/At 1.2/Au 1.2/Av 1.2/Aw
1.2/Ax 1.2/Ay 1.2/Az 1.2/B 1.2/BB 1.2/BC 1.2/BD 1.2/BE 1.2/BF 1.2/BH 1.2/BJ
1.2/BK 1.2/BL 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L
1.2/M 1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V 1.2/W 1.2/Y 1.2/Z
1.2/a 1.2/b 1.2/c 1.2/d 1.2/e 1.2/f 1.2/g 1.2/i 1.2/j 1.2/k 1.2/l 1.2/m 1.2/o
1.2/p 1.2/q 1.2/r 1.2/s 1.2/t 1.2/u 1.2/y 1.2/z | ?  
1.2/Ab 1.2/X 1.2/h 1.2/n | ?  
1.2/Ae 1.2/v | ?  
1.2/Af 1.2/Ag 1.2/w 1.2/x | ?  
1.2/Ai 1.2/BA 1.2/BI 1.2/BM | ?  
1.2/BG | ?  
  

> open
> /home/whitelab2/Desktop/Tony/NapBAsym/All_Isolde/NapoleonB_sharpened_map.ccp4

Opened NapoleonB_sharpened_map.ccp4 as #2, grid size 800,800,800, pixel 1.45,
shown at step 1, values float32  

> clipper associate #2 toModel #1

Opened NapoleonB_sharpened_map.ccp4 as #1.1.1.1, grid size 800,800,800, pixel
1.45, shown at step 1, values float32  

> select /Ad

5736 atoms, 5783 bonds, 99 pseudobonds, 366 residues, 2 models selected  

> isolde sim start sel

ISOLDE: started sim  
ISOLDE: paused sim  




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: NVIDIA RTX A6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 64 Intel(R) Xeon(R) Gold 6226R CPU @ 2.90GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          376Gi       7.1Gi       353Gi        50Mi        16Gi       367Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	DeviceName: ASPEED Video AST2500	
	Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:096d]
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    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: 1.3
    ChimeraX-ItemsInspection: 1.0
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    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
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    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
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    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
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    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
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    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
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    Sphinx: 4.2.0
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    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
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    tables: 3.6.1
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    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

}}}
"	defect	closed	normal		Third Party		fixed						all	ChimeraX