The following bug report has been submitted:
Platform: Windows-7-6.1.7601-SP1
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
changechins command can not use.
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-1.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-2.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-3.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-4.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-5.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-6.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-7.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-8.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-9.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-10.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-11.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-12.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-13.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-14.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-15.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_Sp-16.pdb
> D:/0-HWei/BaseWorks/20230830_candidate_cas/3-chimera_spCas9_outs_selected/SpCas9_chimera_SpCas9.pdb
Chain information for SpCas9_chimera_Sp-1.pdb #1
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-2.pdb #2
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-3.pdb #3
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-4.pdb #4
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-5.pdb #5
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-6.pdb #6
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-7.pdb #7
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-8.pdb #8
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-9.pdb #9
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-10.pdb #10
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-11.pdb #11
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-12.pdb #12
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-13.pdb #13
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-14.pdb #14
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-15.pdb #15
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_Sp-16.pdb #16
---
Chain | Description
A | No description available
Chain information for SpCas9_chimera_SpCas9.pdb #17
---
Chain | Description
A | No description available
> open 5b2r
Summary of feedback from opening 5b2r fetched from pdb
---
notes | Fetching compressed mmCIF 5b2r from
http://files.rcsb.org/download/5b2r.cif
Fetching CCD K from http://ligand-expo.rcsb.org/reports/K/K/K.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD EDO from http://ligand-expo.rcsb.org/reports/E/EDO/EDO.cif
Fetching CCD ACT from http://ligand-expo.rcsb.org/reports/A/ACT/ACT.cif
5b2r title:
Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex
with sgRNA and target DNA (TGA PAM) [more info...]
Chain information for 5b2r #18
---
Chain | Description
A | Guide RNA
B | CRISPR-associated endonuclease Cas9
C | Target DNA
D | Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3')
Non-standard residues in 5b2r #18
---
ACT — acetate ion
EDO — 1,2-ethanediol (ethylene glycol)
K — potassium ion
MG — magnesium ion
> mmaker #1-17 to #18
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 5b2r, chain B (#18) with SpCas9_chimera_Sp-1.pdb, chain A (#1),
sequence alignment score = 5151.9
RMSD between 721 pruned atom pairs is 1.048 angstroms; (across all 1006 pairs:
2.045)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-2.pdb, chain A (#2),
sequence alignment score = 5562.8
RMSD between 819 pruned atom pairs is 0.907 angstroms; (across all 1108 pairs:
2.091)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-3.pdb, chain A (#3),
sequence alignment score = 5433.6
RMSD between 818 pruned atom pairs is 0.865 angstroms; (across all 1113 pairs:
2.298)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-4.pdb, chain A (#4),
sequence alignment score = 5860.6
RMSD between 900 pruned atom pairs is 0.919 angstroms; (across all 1149 pairs:
1.867)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-5.pdb, chain A (#5),
sequence alignment score = 5616.4
RMSD between 870 pruned atom pairs is 0.896 angstroms; (across all 1173 pairs:
2.588)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-6.pdb, chain A (#6),
sequence alignment score = 6089.2
RMSD between 973 pruned atom pairs is 0.841 angstroms; (across all 1316 pairs:
2.394)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-7.pdb, chain A (#7),
sequence alignment score = 6078.6
RMSD between 980 pruned atom pairs is 0.897 angstroms; (across all 1316 pairs:
2.372)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-8.pdb, chain A (#8),
sequence alignment score = 5845.6
RMSD between 917 pruned atom pairs is 0.841 angstroms; (across all 1316 pairs:
2.516)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-9.pdb, chain A (#9),
sequence alignment score = 6111.5
RMSD between 973 pruned atom pairs is 0.868 angstroms; (across all 1316 pairs:
2.374)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-10.pdb, chain A (#10),
sequence alignment score = 5977.2
RMSD between 960 pruned atom pairs is 0.865 angstroms; (across all 1316 pairs:
2.466)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-11.pdb, chain A (#11),
sequence alignment score = 5975.8
RMSD between 955 pruned atom pairs is 0.839 angstroms; (across all 1316 pairs:
2.498)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-12.pdb, chain A (#12),
sequence alignment score = 6115.6
RMSD between 980 pruned atom pairs is 0.895 angstroms; (across all 1316 pairs:
2.386)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-13.pdb, chain A (#13),
sequence alignment score = 6065.4
RMSD between 985 pruned atom pairs is 0.859 angstroms; (across all 1316 pairs:
2.327)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-14.pdb, chain A (#14),
sequence alignment score = 6099.6
RMSD between 982 pruned atom pairs is 0.874 angstroms; (across all 1316 pairs:
2.358)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-15.pdb, chain A (#15),
sequence alignment score = 6105.4
RMSD between 978 pruned atom pairs is 0.881 angstroms; (across all 1316 pairs:
2.426)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_Sp-16.pdb, chain A (#16),
sequence alignment score = 5943.3
RMSD between 967 pruned atom pairs is 0.837 angstroms; (across all 1316 pairs:
2.395)
Matchmaker 5b2r, chain B (#18) with SpCas9_chimera_SpCas9.pdb, chain A (#17),
sequence alignment score = 6706.5
RMSD between 1065 pruned atom pairs is 0.866 angstroms; (across all 1319
pairs: 1.805)
> hide #1-17#!18 target m
> show #1 models
> select #1:1105-1400
Nothing selected
> hide #1 models
> show #2 models
> select #1:1105-1400
Nothing selected
> select #2:1105-1400
753 atoms, 761 bonds, 46 residues, 1 model selected
> show #!18 models
> hide #!18 models
> delete #2:1-1105
> delete #4:1-1105
> delete #5:1-1106
> delete #3,6-16:1-1104
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> hide #17 models
> open D:/0-HWei/BaseWorks/20230830_candidate_cas/SpCas9_Protein_model.pdb
SpCas9_Protein_model.pdb title:
SpCas9_Protein_model [more info...]
Chain information for SpCas9_Protein_model.pdb #19
---
Chain | Description
A | No description available
> open D:/0-HWei/BaseWorks/20230830_candidate_cas/SpCas9_DNA_RNA.pdb
SpCas9_DNA_RNA.pdb title:
SpCas9_DNA_RNA [more info...]
Chain information for SpCas9_DNA_RNA.pdb #20
---
Chain | Description
A | No description available
C | No description available
D | No description available
Non-standard residues in SpCas9_DNA_RNA.pdb #20
---
ACT — (ACT)
EDO — (EDO)
K — (K)
MG — (MG)
> hide #2-17 target m
> ~select #2
Nothing selected
> help changechain
No help found for 'changechain'
> help changechainId
No help found for 'changechainId'
> changechains #19 A B
Unknown command: changechains #19 A B
> help changechains
No help found for 'changechains'
> help changechain
No help found for 'changechain'
> select #19
22462 atoms, 22660 bonds, 1363 residues, 1 model selected
> toolshed show
> hide #19 models
> ~select #19
Nothing selected
> hide #20.1 models
> show #20.1 models
> close #20.1
> close #19
> open D:/0-HWei/BaseWorks/20230830_candidate_cas/SpCas9_Protein_model.pdb
Summary of feedback from opening
D:/0-HWei/BaseWorks/20230830_candidate_cas/SpCas9_Protein_model.pdb
---
warning | Ignored bad PDB record found on line 33012
END
SpCas9_Protein_model.pdb title:
SpCas9_Protein_model [more info...]
Chain information for SpCas9_Protein_model.pdb #19
---
Chain | Description
B | No description available
> help combine
No help found for 'combine'
> show #1 models
> hide #1 models
> show #2 models
> hide #2 models
> hide #19 models
> hide #20 models
> show #2 models
OpenGL version: 3.3.0 NVIDIA 441.22
OpenGL renderer: Quadro K5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 30B8A03KCW
OS: Microsoft Windows 7 Professional (Build 7601)
Memory: 137,327,489,024
MaxProcessMemory: 8,589,934,464
CPU: 28 Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
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: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
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: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
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: 2.0
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: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
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-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
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: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
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: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
changechains first appeared in 1.5