![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16535 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5.2-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000002008c9280 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
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"build" : "22G91",
"releaseType" : "User"
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"captureTime" : "2024-12-26 14:58:51.9835 +0000",
"incident" : "D16EFC1D-CD5E-4EC1-9F6C-06B46CE1B1AA",
"pid" : 80805,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-26 14:39:52.1455 +0000",
"procStartAbsTime" : 565953996059,
"procExitAbsTime" : 593310238464,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"88086AAF-454D-532A-910F-AA3B3B3DC9A7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1627E5AC-823B-8143-2D56-E64802A179E2",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 3165,
"sleepWakeUUID" : "2B3C78B8-5FE3-4636-AB56-C44148E68EDD",
"sip" : "enabled",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/manuscript/multimedia_source_files/EC2LA_figure.cxs
Log from Fri Mar 10 08:32:53 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/EC2LA_figure.cxs
> format session
Log from Thu Mar 9 20:27:19 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/styli/Documents/Work/Projects/Side/CB2R/All_CBRs_comp_CB1_mutations_red_with_AS5.cxs
Log from Fri Dec 23 12:53:20 2022UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/styli/Documents/PhD
> Projects/CB2R/All_CBRs_comp_CB1_mutations_red_with_AS5.cxs" format session
Log from Wed Dec 21 18:04:16 2022UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/styli/Documents/PhD
> Projects/CB2R/All_CBRs_comp_CB1_mutations_red.cxs" format session
Log from Mon Dec 19 22:01:46 2022UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/styli/Documents/PhD
> Projects/CB2R/All_CBRs_comp_CB1_last_state.cxs"
Log from Thu Dec 8 17:21:45 2022UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/styli/Documents/PhD Projects/CB2R/All_CBRs_cleaned.cxs" format
> session
Log from Thu Dec 8 11:57:05 2022UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd "/Users/styli/Documents/PhD London/Projects/Side Projects/CB2R"
Current working directory is: /Users/styli/Documents/PhD London/Projects/Side
Projects/CB2R
> open 6KPC,6KPF,6PT0,5ZTY
'6KPC,6KPF,6PT0,5ZTY' has no suffix
> open 6KPC, 6KPF, 6PT0, 5ZTY
'6KPC,' has no suffix
> open 6KPC
Summary of feedback from opening 6KPC fetched from pdb
---
notes | Fetching compressed mmCIF 6kpc from http://files.rcsb.org/download/6kpc.cif
Fetching CCD E3R from http://ligand-expo.rcsb.org/reports/E/E3R/E3R.cif
6kpc title:
Crystal structure of an agonist bound GPCR [more info...]
Chain information for 6kpc #1
---
Chain | Description | UniProt
A | Cannabinoid receptor 2,Endolysin | CNR2_HUMAN
Non-standard residues in 6kpc #1
---
E3R —
7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]-
7-methyloctanenitrile
> open 6KPF
Summary of feedback from opening 6KPF fetched from pdb
---
note | Fetching compressed mmCIF 6kpf from http://files.rcsb.org/download/6kpf.cif
6kpf title:
Cryo-EM structure of a class A GPCR with G protein complex [more info...]
Chain information for 6kpf #2
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN
R | Cannabinoid receptor 2 | CNR2_HUMAN
S | scFv16 |
Non-standard residues in 6kpf #2
---
E3R —
7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]-
7-methyloctanenitrile
> open 6PT0
Summary of feedback from opening 6PT0 fetched from pdb
---
notes | Fetching compressed mmCIF 6pt0 from http://files.rcsb.org/download/6pt0.cif
Fetching CCD WI5 from http://ligand-expo.rcsb.org/reports/W/WI5/WI5.cif
Fetching CCD PLM from http://ligand-expo.rcsb.org/reports/P/PLM/PLM.cif
6pt0 title:
Cryo-EM structure of human cannabinoid receptor 2-Gi protein in complex with
agonist WIN 55,212-2 [more info...]
Chain information for 6pt0 #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN
E | scFv16 |
R | Cannabinoid receptor 2 | CNR2_HUMAN
Non-standard residues in 6pt0 #3
---
CLR — cholesterol
PLM — palmitic acid
WI5 —
{(3R)-5-methyl-3-[(morpholin-4-yl)methyl]-2,3-dihydro[1,4]oxazino[2,3,4-hi]indol-6-yl}(naphthalen-1-yl)methanone
> open 5ZTY
Summary of feedback from opening 5ZTY fetched from pdb
---
notes | Fetching compressed mmCIF 5zty from http://files.rcsb.org/download/5zty.cif
Fetching CCD 9JU from http://ligand-expo.rcsb.org/reports/9/9JU/9JU.cif
Fetching CCD PEG from http://ligand-expo.rcsb.org/reports/P/PEG/PEG.cif
5zty title:
Crystal structure of human G protein coupled receptor [more info...]
Chain information for 5zty #4
---
Chain | Description | UniProt
A | G protein coupled receptor,T4 lysozyme,G protein coupled receptor | CNR2_HUMAN
Non-standard residues in 5zty #4
---
9JU —
N-(adamantan-1-yl)-1-(5-hydroxypentyl)-4-methyl-5-phenyl-1H-pyrazole-3-carboxamide
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
SO4 — sulfate ion
> open P34972 fromDatabase uniprot
Summary of feedback from opening P34972 fetched from uniprot
---
notes | Fetching compressed P34972 UniProt info from https://www.uniprot.org/uniprot/P34972.xml
Alignment identifier is P34972
Associated 6kpf chain R to P34972 with 0 mismatches
Associated 6pt0 chain R to P34972 with 0 mismatches
Opened UniProt P34972
> open P34972 fromDatabase uniprot
Summary of feedback from opening P34972 fetched from uniprot
---
notes | Destroying pre-existing alignment with identifier P34972
Alignment identifier is P34972
Associated 6kpf chain R to P34972 with 0 mismatches
Associated 6pt0 chain R to P34972 with 0 mismatches
Opened UniProt P34972
> log metadata #4
Metadata for 5zty #4
---
Title | Crystal structure of human G protein coupled receptor
Citation | Li, X., Hua, T., Vemuri, K., Ho, J.H., Wu, Y., Wu, L., Popov, P., Benchama, O., Zvonok, N., Locke, K., Qu, L., Han, G.W., Iyer, M.R., Cinar, R., Coffey, N.J., Wang, J., Wu, M., Katritch, V., Zhao, S., Kunos, G., Bohn, L.M., Makriyannis, A., Stevens, R.C., Liu, Z.J. (2019). Crystal Structure of the Human Cannabinoid Receptor CB2. Cell, 176, 459-467.e13. PMID: 30639103. DOI: 10.1016/j.cell.2018.12.011
Non-standard residues | 9JU — N-(adamantan-1-yl)-1-(5-hydroxypentyl)-4-methyl-5-phenyl-1H-pyrazole-3-carboxamide
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
SO4 — sulfate ion
Gene sources | Homo sapiens (human)
Enterobacteria phage T4 (bacteriophage t4)
Experimental method | X-ray diffraction
Resolution | 2.8Å
> hide ~#1 models
> select #1:1001-1160
1275 atoms, 1295 bonds, 160 residues, 1 model selected
> delete #1:1001-1160
> hide #1 models
> show #2 models
> zoom #2
Expected a number > 0 or a keyword
> view #2
> hide #2 spheres
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2 sphere
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select #2
8775 atoms, 8965 bonds, 4 pseudobonds, 1136 residues, 2 models selected
> style sel stick
Changed 8775 atom styles
> style sel ball
Changed 8775 atom styles
> style sel sphere
Changed 8775 atom styles
> hide sel atoms
> show sel cartoons
> select clear
> select #2/E
Nothing selected
> select #2/S
1760 atoms, 1806 bonds, 1 pseudobond, 232 residues, 2 models selected
> delete #2/S
> delete ~#2/R
> undo
Undo failed, probably because structures have been modified.
> undo
[Repeated 1 time(s)]Undo failed, probably because structures have been
modified.
> delete all
> open 6KPC
6kpc title:
Crystal structure of an agonist bound GPCR [more info...]
Chain information for 6kpc #1
---
Chain | Description | UniProt
A | Cannabinoid receptor 2,Endolysin | CNR2_HUMAN
Non-standard residues in 6kpc #1
---
E3R —
7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]-
7-methyloctanenitrile
> open 6KPF
6kpf title:
Cryo-EM structure of a class A GPCR with G protein complex [more info...]
Chain information for 6kpf #2
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN
R | Cannabinoid receptor 2 | CNR2_HUMAN
S | scFv16 |
Non-standard residues in 6kpf #2
---
E3R —
7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]-
7-methyloctanenitrile
> open 6PT0
6pt0 title:
Cryo-EM structure of human cannabinoid receptor 2-Gi protein in complex with
agonist WIN 55,212-2 [more info...]
Chain information for 6pt0 #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN
E | scFv16 |
R | Cannabinoid receptor 2 | CNR2_HUMAN
Non-standard residues in 6pt0 #3
---
CLR — cholesterol
PLM — palmitic acid
WI5 —
{(3R)-5-methyl-3-[(morpholin-4-yl)methyl]-2,3-dihydro[1,4]oxazino[2,3,4-hi]indol-6-yl}(naphthalen-1-yl)methanone
> open 5ZTY
5zty title:
Crystal structure of human G protein coupled receptor [more info...]
Chain information for 5zty #4
---
Chain | Description | UniProt
A | G protein coupled receptor,T4 lysozyme,G protein coupled receptor | CNR2_HUMAN
Non-standard residues in 5zty #4
---
9JU —
N-(adamantan-1-yl)-1-(5-hydroxypentyl)-4-methyl-5-phenyl-1H-pyrazole-3-carboxamide
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
SO4 — sulfate ion
> hide ~#1 models
> delete #1:1001-1160
> hide #1 models
> show #2 models
> view #2
> hide #2 atoms
> show #2 cartoons
> delete #2/S
> delete #2/A,B,C
> hide #2 models
> show #3 models
> hide #3 atoms
> show #3 cartoons
> view #3
> rotate #3 10
Unknown command: rotate #3 10
> rotate #3 x10
Unknown command: rotate #3 x10
> rotate #3 x= 10
Unknown command: rotate #3 x= 10
> delete #3/A,B,C,E
> hide #3 models
> show #4 models
> view #4
> select #4:1001-1160
1271 atoms, 1291 bonds, 160 residues, 1 model selected
> delete #4:1001-1160
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
15 atoms, 15 bonds, 1 residue, 1 model selected
> show #!3 models
> show #!2 models
> show #!1 models
> help matchmaker
> matchermaker #1-3 to #4
Unknown command: matchermaker #1-3 to #4
> help matchmaker
> mmaker #1-3 to #4
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 5zty, chain A (#4) with 6kpc, chain A (#1), sequence alignment
score = 2237.2
RMSD between 273 pruned atom pairs is 0.895 angstroms; (across all 285 pairs:
1.049)
Matchmaker 5zty, chain A (#4) with 6kpf, chain R (#2), sequence alignment
score = 1122.9
RMSD between 232 pruned atom pairs is 1.079 angstroms; (across all 285 pairs:
2.662)
Matchmaker 5zty, chain A (#4) with 6pt0, chain R (#3), sequence alignment
score = 1278.6
RMSD between 234 pruned atom pairs is 1.009 angstroms; (across all 286 pairs:
2.675)
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/R
Alignment identifier is 2/R
> sequence chain #3/R
Alignment identifier is 3/R
> sequence chain #4/A
Alignment identifier is 4/A
> color #2 lightgreen
> color #3 forestgreen
> color #1 magenta
> color #4 darkmagenta
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select
> #1/A:22-26,30-66,68-95,102-137,140-166,187-220,235,237-271,274-300,303-310
1834 atoms, 1867 bonds, 238 residues, 1 model selected
> select #1/A:22-23
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:22-25
37 atoms, 37 bonds, 4 residues, 1 model selected
> select #1/A:21
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:19-21
19 atoms, 20 bonds, 3 residues, 1 model selected
> select
> #1/A:22-26,30-66,68-95,102-137,140-166,187-220,235,237-271,274-300,303-310
1834 atoms, 1867 bonds, 238 residues, 1 model selected
> select #1/A:19-21
19 atoms, 20 bonds, 3 residues, 1 model selected
> select #1/A:19-21
19 atoms, 20 bonds, 3 residues, 1 model selected
> select #1/A:21
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:21-71
383 atoms, 389 bonds, 51 residues, 1 model selected
> select #1/A:19
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:19-20
12 atoms, 12 bonds, 2 residues, 1 model selected
> select
> #1/A:22-26,30-66,68-95,102-137,140-166,187-220,235,237-271,274-300,303-310
1834 atoms, 1867 bonds, 238 residues, 1 model selected
> select #1/A:35
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:35-37
17 atoms, 16 bonds, 3 residues, 1 model selected
> select #1/A:43-44
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/A:43-47
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #1/A:28
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:28-30
18 atoms, 17 bonds, 3 residues, 1 model selected
> select #1/A:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:27-29
22 atoms, 21 bonds, 3 residues, 1 model selected
> select
> #1/A:22-26,30-66,68-95,102-137,140-166,187-220,235,237-271,274-300,303-310
1834 atoms, 1867 bonds, 238 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/R
Alignment identifier is 2/R
> sequence chain #3/R
Alignment identifier is 3/R
> sequence chain #4/A
Alignment identifier is 4/A
> hide #!1 models
> show #!3 models
> select #3/R:29-96,102-137,140-171,187-227,229-234,238-271,274-319
2036 atoms, 2079 bonds, 263 residues, 1 model selected
> select #3/R:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/R:29-31
17 atoms, 17 bonds, 3 residues, 1 model selected
> select #3/R:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/R:22-24
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #3/R:29-96,102-137,140-171,187-227,229-234,238-271,274-319
2036 atoms, 2079 bonds, 263 residues, 1 model selected
> select clear
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> save "/Users/styli/Documents/PhD London/Projects/Side
> Projects/CB2R/All_CB2Rs_cleaned.cxs"
> show #!1 models
> show #!4 models
> save "/Users/styli/Documents/PhD Projects/CB2R/All_CBRs_cleaned.cxs"
——— End of log from Thu Dec 8 11:57:05 2022 ———
opened ChimeraX session
> hide #!3 models
> hide #!2 models
> hide #!1 models
> select #2 & ligand
29 atoms, 31 bonds, 1 residue, 1 model selected
> select none
Expected an objects specifier or a keyword
> select
9494 atoms, 9692 bonds, 3 pseudobonds, 1237 residues, 7 models selected
> !sel
Unknown command: !sel
> ~select
Nothing selected
> select #4 & ligand
169 atoms, 161 bonds, 15 residues, 1 model selected
> select #4 & :9JU
31 atoms, 35 bonds, 1 residue, 1 model selected
> color #4 & :9JU & C salmon
> color #4 & :9JU & C byhetero
> color #4 & :9JU & C salmon
> open 6KQI
Summary of feedback from opening 6KQI fetched from pdb
---
notes | Fetching compressed mmCIF 6kqi from http://files.rcsb.org/download/6kqi.cif
Fetching CCD 9GF from http://ligand-expo.rcsb.org/reports/9/9GF/9GF.cif
Fetching CCD 9GL from http://ligand-expo.rcsb.org/reports/9/9GL/9GL.cif
6kqi title:
Structure of an allosteric modulator bound to the CB1 cannabinoid receptor
[more info...]
Chain information for 6kqi #5
---
Chain | Description | UniProt
A | Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1 | CNR1_HUMAN
Non-standard residues in 6kqi #5
---
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol
9GL —
5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PEG — di(hydroxyethyl)ether
> delete #5:1101-1196
> delete #5:1001-1196
> mmaker #5 to #1
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 6kpc, chain A (#1) with 6kqi, chain A (#5), sequence alignment
score = 840.7
RMSD between 240 pruned atom pairs is 1.022 angstroms; (across all 270 pairs:
1.565)
> select clear
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right zoom
> ui mousemode right translate
> select #5/A:1202@CAI
1 atom, 1 residue, 1 model selected
> select up
29 atoms, 32 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 29 atom styles
> color #5:1202 & lightcyan
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #5:1202 & C lightcyan
> surface zone #5 nearAtoms :1202 distance 8 maxComponents 1 (maximum 1
> component)
Expected a keyword
> surface zone #5 nearAtoms :1202 distance 8 maxComponents 1
No surfaces specified
> ui tool show Contacts
[Repeated 1 time(s)]
> contacts distanceOnly 3.8 ignoreHiddenModels true select true
2195 distances
> close #6
> select clear
> select #5/A:1202@CAK
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
29 atoms, 32 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 3.8 ignoreHiddenModels true select true
26 distances
> ui tool show Contacts
> contacts sel ignoreHiddenModels true select true
50 contacts
> show sel atoms
> select clear
> select #5/A:1202@CAA
1 atom, 1 residue, 1 model selected
> select up
29 atoms, 32 bonds, 1 residue, 1 model selected
> close #6
> ui tool show Contacts
> contacts sel ignoreHiddenModels true select true color #f6fa2d radius 0.115
29 contacts
> show sel atoms
> select up
91 atoms, 91 bonds, 9 residues, 1 model selected
> select down
33 atoms, 9 residues, 1 model selected
> select up
91 atoms, 91 bonds, 9 residues, 1 model selected
> show sel atoms
> select #5/A:1202@CAX
1 atom, 1 residue, 1 model selected
> undo
> select #5/A:1202@CAW
1 atom, 1 residue, 1 model selected
> undo
> select subtract #5/A:1202@NAV
90 atoms, 89 bonds, 9 residues, 1 model selected
> select subtract #5/A:1202@OAU
89 atoms, 88 bonds, 9 residues, 1 model selected
> select subtract #5/A:1202@CAE
88 atoms, 86 bonds, 9 residues, 1 model selected
> select subtract #5/A:1202@CAD
87 atoms, 85 bonds, 9 residues, 1 model selected
> select subtract #5/A:1202@CAX
86 atoms, 83 bonds, 9 residues, 1 model selected
> select add #5/A:1202@CAX
87 atoms, 83 bonds, 9 residues, 1 model selected
> select subtract #5/A:1202@CL
86 atoms, 82 bonds, 9 residues, 1 model selected
> select subtract #5/A:1202@CAZ
85 atoms, 80 bonds, 9 residues, 1 model selected
> select subtract #5/A:1202@CBB
84 atoms, 79 bonds, 9 residues, 1 model selected
> select down
84 atoms, 79 bonds, 9 residues, 1 model selected
> select down
84 atoms, 79 bonds, 9 residues, 1 model selected
> show sel surfaces
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
6kqi #5/A GLN 116
6kqi #5/A ARG 145
6kqi #5/A LYS 183
6kqi #5/A GLN 261
6kqi #5/A ARG 409
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6kqi_A SES surface #5.2: minimum, -12.88, mean 0.80,
maximum 12.49
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "6kqi_A SES surface": minimum -27.27, mean 1.244,
maximum 24.59
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> hide #5:1202
> ui tool show "Add Hydrogens"
> addh #!5
Summary of feedback from adding hydrogens to 6kqi #5
---
warnings | Not adding hydrogens to 6kqi #5/A GLN 116 CB because it is missing heavy-atom bond partners
Not adding hydrogens to 6kqi #5/A ARG 145 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6kqi #5/A LYS 183 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6kqi #5/A GLN 261 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6kqi #5/A ARG 409 CB because it is missing heavy-atom
bond partners
notes | Termini for 6kqi (#5) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6kqi #5/A ASN 101, 6kqi
#5/A ASP 333
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 6kqi #5/A ALA 301, 6kqi
#5/A PRO 413
249 hydrogen bonds
Adding 'H' to 6kqi #5/A ASN 101
Adding 'H' to 6kqi #5/A ASP 333
6kqi #5/A PRO 413 is not terminus, removing H atom from 'C'
2533 hydrogens added
> hide #5 hydrogens
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #5 hydrogen
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #5.2 models
> hide #6 models
> show #6 models
> hide #!5 models
> show #!5 models
> select clear
> show #!4 models
> show #5:1202 atoms
> show #5.2 models
> hide #!5 models
> show #!5 models
> name ligand_cb1 #5:1202
"#5:1202 ": contains extra trailing text
> name ligand_cb1 #5:1202
> hide ligand_cb1 atoms
> hide #5.2 models
> select #4/A:78
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
224 atoms, 231 bonds, 29 residues, 1 model selected
> select #4/A:78
8 atoms, 7 bonds, 1 residue, 1 model selected
> shoe sel atoms
Unknown command: shoe sel atoms
> show sel atoms
> select #4/A:158
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
162 atoms, 164 bonds, 21 residues, 1 model selected
> select down
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel byhetero
> select #4/A:155
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 4 atom styles
> select #4/A:159
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 7 atom styles
> select #5/A:158
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/A:75
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select #4/A:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #5/A:245
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #4/A:162
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> color sel byhetero
> select #5/A:234
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show ligand_cb1 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #4/A:151@CD2
1 atom, 1 residue, 1 model selected
> select #4/A:151@CD1
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4/A:151@CD2
1 atom, 1 residue, 1 model selected
> hide sel atoms
Mismatch between Cocoa '\u03c0' and Carbon 'p' for virtual key 35 with
QFlags(NoModifier)
Mismatch between Cocoa '\u03a0' and Carbon 'P' for virtual key 35 with
QFlags(ShiftModifier)
Mismatch between Cocoa 'P' and Carbon 'p' for virtual key 35 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\u2248' and Carbon '\u03c0' for virtual key 35 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u220f' for virtual key 35 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\u0399' and Carbon '\u03c0' for virtual key 35 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa 'P' and Carbon '\u220f' for virtual key 35 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
> save "/Users/styli/Documents/PhD Projects/CB2R/All_CBRs_comp_CB1.cxs"
> hide #!5 models
> select #4/A:158@CE2
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select #4/A:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!5 models
> hide #!5 models
> open 5XRA
Summary of feedback from opening 5XRA fetched from pdb
---
notes | Fetching compressed mmCIF 5xra from http://files.rcsb.org/download/5xra.cif
Fetching CCD FMN from http://ligand-expo.rcsb.org/reports/F/FMN/FMN.cif
Fetching CCD 8D3 from http://ligand-expo.rcsb.org/reports/8/8D3/8D3.cif
5xra title:
Crystal structure of the human CB1 in complex with agonist AM11542 [more
info...]
Chain information for 5xra #7
---
Chain | Description | UniProt
A | Cannabinoid receptor 1,Flavodoxin,Cannabinoid receptor 1 | CNR1_HUMAN
Non-standard residues in 5xra #7
---
8D3 — (6aR,10aR)-3-(8-bromanyl-2-methyl-
octan-2-yl)-6,6,9-trimethyl-6a,7,10,10a-tetrahydrobenzo[c]chromen-1-ol
CLR — cholesterol
FMN — flavin mononucleotide (riboflavin monophosphate)
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PEG — di(hydroxyethyl)ether
> view #6
No displayed objects specified.
> view #7
> ui mousemode right zoom
> close #7
> hide #!4 models
> show #!4 models
> show #!5 models
> view #5
> save "/Users/styli/Documents/PhD
> Projects/CB2R/All_CBRs_comp_CB1_last_state.cxs"
——— End of log from Thu Dec 8 17:21:45 2022 ———
opened ChimeraX session
> hide #!5 models
> select #5:201,197
28 atoms, 26 bonds, 2 residues, 1 model selected
> view #5:201,197
> show #5:201,197 atoms
> show #5:201,197 sticks
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #5:201,197 sticks
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #5:201,197 atoms
> view #5:201
> show #5:201 atoms
> style #!4 stick
Changed 2455 atom styles
> undo
> hide #5:201 atoms
> view #4:201 atoms
Expected an integer >= 1 or a keyword
> view #4:201
> show #4:201 atoms
> show #4:201,197 atoms
> show #4:201,197,157,156,133,129,126,125,72 atoms
> hide #4:201,197,157,156,133,129,126,125,72 atoms
> show #4:201,197,157,156,133,129,126,125,72 atoms
> color #4:201,197,157,156,133,129,126,125,72 & C red
> show #!5 models
> volume planes z style image imageMode "full region"
No volumes specified
> ui mousemode right "move planes"
> ui mousemode right clip
> ui mousemode right translate
> hide #!5 models
> show #!5 models
> hide #!5 models
> save "/Users/styli/Documents/PhD
> Projects/CB2R/All_CBRs_comp_CB1_mutations_red.cxs"
——— End of log from Mon Dec 19 22:01:46 2022 ———
opened ChimeraX session
> show #!5 models
> hide #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> open 6C1Q
6c1q title:
Crystal structure of human C5a receptor in complex with an orthosteric
antagonist PMX53 and an allosteric antagonist NDT9513727 [more info...]
Chain information for 6c1q #7
---
Chain | Description | UniProt
B | Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera | C5AR1_HUMAN
L | PMX53 |
Non-standard residues in 6c1q #7
---
9P2 —
1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-
imidazol-4-yl)methyl]methanamine
ACE — acetyl group
> matchmaker #7 to #1
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 6kpc, chain A (#1) with 6c1q, chain B (#7), sequence alignment
score = 222.9
RMSD between 87 pruned atom pairs is 1.158 angstroms; (across all 183 pairs:
6.476)
> select #7:10-115
613 atoms, 616 bonds, 1 pseudobond, 90 residues, 2 models selected
> delete #7:10-115
> select #7/A
Nothing selected
> select #7/A
Nothing selected
> select #7/B
2240 atoms, 2305 bonds, 2 pseudobonds, 285 residues, 2 models selected
> select clear
> select #7:9P2
43 atoms, 49 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 43 atom styles
> color #7:9P2 & C olive
> hide #!5 models
> show #!4 models
> hide #!7 models
> show #!7 models
> select #7 and ~:9P2
Expected a keyword
> select #7 & ~:9P2
2262 atoms, 2326 bonds, 2 pseudobonds, 291 residues, 2 models selected
> hide #!4 models
> hide #6 models
> show #!4 models
> hide #!4 models
> hide #7 & ~:9P2
> undo
> hide #7 & ~:9P2 cartoons
> hide #7 & ~:9P2 sticks
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #7 & ~:9P2 stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #7 & ~:9P2 atoms
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!7 models
> save "/Users/styli/Documents/PhD
> Projects/CB2R/All_CBRs_comp_CB1_mutations_red_with_AS5.cxs"
——— End of log from Wed Dec 21 18:04:16 2022 ———
opened ChimeraX session
> show #!5 models
> hide HC atoms
> save "/Users/styli/Documents/PhD
> Projects/CB2R/All_CBRs_comp_CB1_mutations_red_with_AS5.cxs"
——— End of log from Fri Dec 23 12:53:20 2022 ———
opened ChimeraX session
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> ui tool show "Side View"
> select #4:202
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4:20195
Nothing selected
> select #4:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4:262
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show sel surfaces
> hide sel surfaces
> hide #4.2 models
> select subtract #4.2
1 model selected
> surface #5
> surface #5 transparenct 50
Expected a keyword
> close #5.2
> surface #4
> surface style #4.2 mesh
> transparency #4.2 50
> surface style #4.2 solid
> color #4.2 #65edf280
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> select #4:197
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4:126
8 atoms, 7 bonds, 1 residue, 1 model selected
> save
> /Users/styli/Documents/Work/Projects/Side/CB2R/All_CBRs_comp_CB1_mutations_red_with_AS5.cxs
> close session
> cd /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara
Current working directory is:
/Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara
> open
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/ec2la.pdb
ec2la.pdb title:
Crystal structure of human G protein coupled receptor [more info...]
Chain information for ec2la.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in ec2la.pdb #1
---
ACE — (ACE)
NMA — (NMA)
UNK — (UNK)
> hbonds reveal true
278 hydrogen bonds found
> hbonds reveal true
278 hydrogen bonds found
> hide #1.1 models
> close session
> open
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/ec2la.pdb
> format pdb
ec2la.pdb title:
Crystal structure of human G protein coupled receptor [more info...]
Chain information for ec2la.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in ec2la.pdb #1
---
ACE — (ACE)
NMA — (NMA)
UNK — (UNK)
> save
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/test1.jpg
> width 1984 height 1155 supersample 3
> color /A green or byhetero
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /A green
> color /A byhetero
> ui tool show Shell
[Repeated 1 time(s)]
> label delete
Labels were deleted
> label #1/A:18 residues text 18
> label #1/A:19 residues text 19
> label #1/A:20 residues text 20
> label #1/A:21 residues text 21
> label #1/A:22 residues text 22
> label #1/A:23 residues text 23
> label #1/A:24 residues text 24
> label #1/A:25 residues text 25
> label #1/A:26 residues text 26
> label #1/A:27 residues text 27
> label #1/A:28 residues text 28
> label #1/A:29 residues text 1.28x28
> label #1/A:30 residues text 1.29x29
> label #1/A:31 residues text 1.30x30
> label #1/A:32 residues text 1.31x31
> label #1/A:33 residues text 1.32x32
> label #1/A:34 residues text 1.33x33
> label #1/A:35 residues text 1.34x34
> label #1/A:36 residues text 1.35x35
> label #1/A:37 residues text 1.36x36
> label #1/A:38 residues text 1.37x37
> label #1/A:39 residues text 1.38x38
> label #1/A:40 residues text 1.39x39
> label #1/A:41 residues text 1.40x40
> label #1/A:42 residues text 1.41x41
> label #1/A:43 residues text 1.42x42
> label #1/A:44 residues text 1.43x43
> label #1/A:45 residues text 1.44x44
> label #1/A:46 residues text 1.45x45
> label #1/A:47 residues text 1.46x46
> label #1/A:48 residues text 1.47x47
> label #1/A:49 residues text 1.48x48
> label #1/A:50 residues text 1.49x49
> label #1/A:51 residues text 1.50x50
> label #1/A:52 residues text 1.51x51
> label #1/A:53 residues text 1.52x52
> label #1/A:54 residues text 1.53x53
> label #1/A:55 residues text 1.54x54
> label #1/A:56 residues text 1.55x55
> label #1/A:57 residues text 1.56x56
> label #1/A:58 residues text 1.57x57
> label #1/A:59 residues text 1.58x58
> label #1/A:60 residues text 1.59x59
> label #1/A:61 residues text 1.60x60
> label #1/A:62 residues text 12.48x48
> label #1/A:63 residues text 12.49x49
> label #1/A:64 residues text 12.50x50
> label #1/A:65 residues text 12.51x51
> label #1/A:66 residues text 66
> label #1/A:67 residues text 2.37x37
> label #1/A:68 residues text 2.38x38
> label #1/A:69 residues text 2.39x39
> label #1/A:70 residues text 2.40x40
> label #1/A:71 residues text 2.41x41
> label #1/A:72 residues text 2.42x42
> label #1/A:73 residues text 2.43x43
> label #1/A:74 residues text 2.44x44
> label #1/A:75 residues text 2.45x45
> label #1/A:76 residues text 2.46x46
> label #1/A:77 residues text 2.47x47
> label #1/A:78 residues text 2.48x48
> label #1/A:79 residues text 2.49x49
> label #1/A:80 residues text 2.50x50
> label #1/A:81 residues text 2.51x51
> label #1/A:82 residues text 2.52x52
> label #1/A:83 residues text 2.53x53
> label #1/A:84 residues text 2.54x54
> label #1/A:85 residues text 2.55x55
> label #1/A:86 residues text 2.56x56
> label #1/A:87 residues text 2.57x57
> label #1/A:88 residues text 2.58x58
> label #1/A:89 residues text 2.59x59
> label #1/A:90 residues text 2.60x60
> label #1/A:91 residues text 2.61x61
> label #1/A:92 residues text 2.62x62
> label #1/A:93 residues text 2.63x63
> label #1/A:94 residues text 2.64x64
> label #1/A:95 residues text 2.65x65
> label #1/A:96 residues text 2.66x66
> label #1/A:97 residues text 97
> label #1/A:98 residues text 98
> label #1/A:99 residues text 99
> label #1/A:100 residues text 100
> label #1/A:101 residues text 101
> label #1/A:102 residues text 3.21x21
> label #1/A:103 residues text 3.22x22
> label #1/A:104 residues text 3.23x23
> label #1/A:105 residues text 3.24x24
> label #1/A:106 residues text 3.25x25
> label #1/A:107 residues text 3.26x26
> label #1/A:108 residues text 3.27x27
> label #1/A:109 residues text 3.28x28
> label #1/A:110 residues text 3.29x29
> label #1/A:111 residues text 3.30x30
> label #1/A:112 residues text 3.31x31
> label #1/A:113 residues text 3.32x32
> label #1/A:114 residues text 3.33x33
> label #1/A:115 residues text 3.34x34
> label #1/A:116 residues text 3.35x35
> label #1/A:117 residues text 3.36x36
> label #1/A:118 residues text 3.37x37
> label #1/A:119 residues text 3.38x38
> label #1/A:120 residues text 3.39x39
> label #1/A:121 residues text 3.40x40
> label #1/A:122 residues text 3.41x41
> label #1/A:123 residues text 3.42x42
> label #1/A:124 residues text 3.43x43
> label #1/A:125 residues text 3.44x44
> label #1/A:126 residues text 3.45x45
> label #1/A:127 residues text 3.46x46
> label #1/A:128 residues text 3.47x47
> label #1/A:129 residues text 3.48x48
> label #1/A:130 residues text 3.49x49
> label #1/A:131 residues text 3.50x50
> label #1/A:132 residues text 3.51x51
> label #1/A:133 residues text 3.52x52
> label #1/A:134 residues text 3.53x53
> label #1/A:135 residues text 3.54x54
> label #1/A:136 residues text 3.55x55
> label #1/A:137 residues text 3.56x56
> label #1/A:138 residues text 34.50x50
> label #1/A:139 residues text 34.51x51
> label #1/A:140 residues text 34.52x52
> label #1/A:141 residues text 34.53x53
> label #1/A:142 residues text 34.54x54
> label #1/A:143 residues text 34.55x55
> label #1/A:144 residues text 34.56x56
> label #1/A:145 residues text 34.57x57
> label #1/A:146 residues text 4.38x38
> label #1/A:147 residues text 4.39x39
> label #1/A:148 residues text 4.40x40
> label #1/A:149 residues text 4.41x41
> label #1/A:150 residues text 4.42x42
> label #1/A:151 residues text 4.43x43
> label #1/A:152 residues text 4.44x44
> label #1/A:153 residues text 4.45x45
> label #1/A:154 residues text 4.46x46
> label #1/A:155 residues text 4.47x47
> label #1/A:156 residues text 4.48x48
> label #1/A:157 residues text 4.49x49
> label #1/A:158 residues text 4.50x50
> label #1/A:159 residues text 4.51x51
> label #1/A:160 residues text 4.52x52
> label #1/A:161 residues text 4.53x53
> label #1/A:162 residues text 4.54x54
> label #1/A:163 residues text 4.55x55
> label #1/A:164 residues text 4.56x56
> label #1/A:165 residues text 4.57x57
> label #1/A:166 residues text 4.58x58
> label #1/A:167 residues text 4.59x59
> label #1/A:168 residues text 4.60x60
> label #1/A:169 residues text 4.61x61
> label #1/A:170 residues text 4.62x62
> label #1/A:171 residues text 4.63x63
> label #1/A:172 residues text 172
> label #1/A:173 residues text 173
> label #1/A:174 residues text 174
> label #1/A:175 residues text 175
> label #1/A:176 residues text 176
> label #1/A:177 residues text 177
> label #1/A:178 residues text 178
> label #1/A:179 residues text 179
> label #1/A:180 residues text 180
> label #1/A:181 residues text 181
> label #1/A:182 residues text 182
> label #1/A:183 residues text 183
> label #1/A:184 residues text 184
> label #1/A:185 residues text 185
> label #1/A:186 residues text 186
> label #1/A:187 residues text 5.36x36
> label #1/A:188 residues text 5.37x37
> label #1/A:189 residues text 5.38x38
> label #1/A:190 residues text 5.39x39
> label #1/A:191 residues text 5.40x40
> label #1/A:192 residues text 5.41x41
> label #1/A:193 residues text 5.42x42
> label #1/A:194 residues text 5.43x43
> label #1/A:195 residues text 5.44x44
> label #1/A:196 residues text 5.45x45
> label #1/A:197 residues text 5.46x46
> label #1/A:198 residues text 5.47x47
> label #1/A:199 residues text 5.48x48
> label #1/A:200 residues text 5.49x49
> label #1/A:201 residues text 5.50x50
> label #1/A:202 residues text 5.51x51
> label #1/A:203 residues text 5.52x52
> label #1/A:204 residues text 5.53x53
> label #1/A:205 residues text 5.54x54
> label #1/A:206 residues text 5.55x55
> label #1/A:207 residues text 5.56x56
> label #1/A:208 residues text 5.57x57
> label #1/A:209 residues text 5.58x58
> label #1/A:210 residues text 5.59x59
> label #1/A:211 residues text 5.60x60
> label #1/A:212 residues text 5.61x61
> label #1/A:213 residues text 5.62x62
> label #1/A:214 residues text 5.63x63
> label #1/A:215 residues text 5.64x64
> label #1/A:216 residues text 5.65x65
> label #1/A:217 residues text 5.66x66
> label #1/A:218 residues text 5.67x67
> label #1/A:219 residues text 5.68x68
> label #1/A:220 residues text 5.69x69
> label #1/A:221 residues text 5.70x70
> label #1/A:222 residues text 5.71x71
> label #1/A:235 residues text 235
> label #1/A:236 residues text 236
> label #1/A:237 residues text 237
> label #1/A:238 residues text 6.28x28
> label #1/A:239 residues text 6.29x29
> label #1/A:240 residues text 6.30x30
> label #1/A:241 residues text 6.31x31
> label #1/A:242 residues text 6.32x32
> label #1/A:243 residues text 6.33x33
> label #1/A:244 residues text 6.34x34
> label #1/A:245 residues text 6.35x35
> label #1/A:246 residues text 6.36x36
> label #1/A:247 residues text 6.37x37
> label #1/A:248 residues text 6.38x38
> label #1/A:249 residues text 6.39x39
> label #1/A:250 residues text 6.40x40
> label #1/A:251 residues text 6.41x41
> label #1/A:252 residues text 6.42x42
> label #1/A:253 residues text 6.43x43
> label #1/A:254 residues text 6.44x44
> label #1/A:255 residues text 6.45x45
> label #1/A:256 residues text 6.46x46
> label #1/A:257 residues text 6.47x47
> label #1/A:258 residues text 6.48x48
> label #1/A:259 residues text 6.49x49
> label #1/A:260 residues text 6.50x50
> label #1/A:261 residues text 6.51x51
> label #1/A:262 residues text 6.52x52
> label #1/A:263 residues text 6.53x53
> label #1/A:264 residues text 6.54x54
> label #1/A:265 residues text 6.55x55
> label #1/A:266 residues text 6.56x56
> label #1/A:267 residues text 6.57x57
> label #1/A:268 residues text 6.58x58
> label #1/A:269 residues text 6.59x59
> label #1/A:270 residues text 6.60x60
> label #1/A:271 residues text 6.61x61
> label #1/A:272 residues text 272
> label #1/A:273 residues text 273
> label #1/A:274 residues text 7.28x27
> label #1/A:275 residues text 7.29x28
> label #1/A:276 residues text 7.30x29
> label #1/A:277 residues text 7.31x30
> label #1/A:278 residues text 7.32x31
> label #1/A:279 residues text 7.33x32
> label #1/A:280 residues text 7.34x33
> label #1/A:281 residues text 7.35x34
> label #1/A:282 residues text 7.36x35
> label #1/A:283 residues text 7.37x36
> label #1/A:284 residues text 7.38x37
> label #1/A:285 residues text 7.39x38
> label #1/A:286 residues text 7.40x39
> label #1/A:287 residues text 7.41x40
> label #1/A:288 residues text 7.42x41
> label #1/A:289 residues text 7.43x42
> label #1/A:290 residues text 7.44x43
> label #1/A:291 residues text 7.45x45
> label #1/A:292 residues text 7.46x46
> label #1/A:293 residues text 7.47x47
> label #1/A:294 residues text 7.48x48
> label #1/A:295 residues text 7.49x49
> label #1/A:296 residues text 7.50x50
> label #1/A:297 residues text 7.51x51
> label #1/A:298 residues text 7.52x52
> label #1/A:299 residues text 7.53x53
> label #1/A:300 residues text 7.54x54
> label #1/A:301 residues text 7.55x55
> label #1/A:302 residues text 7.56x56
> label #1/A:303 residues text 8.47x47
> label #1/A:304 residues text 8.48x48
> label #1/A:305 residues text 8.49x49
> label #1/A:306 residues text 8.50x50
> label #1/A:307 residues text 8.51x51
> label #1/A:308 residues text 8.52x52
> label #1/A:309 residues text 8.53x53
> label #1/A:310 residues text 8.54x54
> label #1/A:311 residues text 8.55x55
> label #1/A:312 residues text 8.56x56
> label #1/A:313 residues text 8.57x57
> label #1/A:314 residues text 8.58x58
> label #1/A:315 residues text 8.59x59
> label #1/A:316 residues text 8.60x60
> label #1/A:317 residues text 8.61x61
> label #1/A:318 residues text 8.62x62
> label #1/A:319 residues text 8.63x63
Annotation completed
> hide labels
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> contacts :UNK reveal true showDist dist t
Invalid "showDist" argument: Expected true or false (or 1 or 0)
> contacts :UNK reveal true showDist true
126 contacts
> color /A magenta
> hide #!1.2 models
> hbonds :UNK reveal true interModel false showDist true color yellow radius
> .08
0 hydrogen bonds found
> contacts :UNK log true showDist true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
126 contacts
atom1 atom2 overlap distance
/? UNK 0 BR1 /A LEU 126 HD23 1.041 2.379
/? UNK 0 BR1 /A LEU 126 CD2 1.025 3.095
/? UNK 0 BR1 /A ILE 129 HD12 0.690 2.730
/? UNK 0 BR1 /A ILE 129 CD1 0.685 3.435
/? UNK 0 C1 /A LEU 125 HD23 0.567 2.133
/? UNK 0 C19 /A PHE 197 HZ 0.507 2.193
/? UNK 0 C18 /A LEU 201 HD13 0.482 2.218
/? UNK 0 C1 /A LEU 125 CD2 0.444 2.956
/? UNK 0 C18 /A PHE 197 HZ 0.402 2.298
/? UNK 0 H3 /A LEU 125 CD2 0.394 2.306
/? UNK 0 H22 /A LEU 160 C 0.368 2.332
/? UNK 0 H24 /A LEU 160 CB 0.364 2.336
/? UNK 0 C18 /A PHE 197 CZ 0.346 3.054
/? UNK 0 H24 /A LEU 160 HB2 0.338 1.662
/? UNK 0 C19 /A PHE 197 CZ 0.306 3.094
/? UNK 0 H3 /A LEU 125 HD23 0.304 1.696
/? UNK 0 C20 /A LEU 160 HB3 0.295 2.405
/? UNK 0 BR1 /A LEU 126 HD21 0.282 3.138
/? UNK 0 C21 /A LEU 160 CB 0.267 3.133
/? UNK 0 O2 /A MET 157 HA 0.264 2.216
/? UNK 0 C19 /A THR 118 CG2 0.252 3.148
/? UNK 0 BR1 /A LEU 126 HD22 0.235 3.185
/? UNK 0 H19 /A PHE 197 CZ 0.231 2.469
/? UNK 0 H14 /A MET 157 HG2 0.231 1.769
/? UNK 0 BR1 /A ILE 129 HD13 0.224 3.196
/? UNK 0 O2 /A MET 157 CB 0.220 2.960
/? UNK 0 H22 /A LEU 160 HB3 0.215 1.785
/? UNK 0 C20 /A LEU 160 CB 0.215 3.185
/? UNK 0 C21 /A LEU 160 HB2 0.196 2.504
/? UNK 0 H22 /A LEU 160 CB 0.194 2.506
/? UNK 0 C16 /A GLY 122 CA 0.180 3.220
/? UNK 0 H19 /A PHE 197 HZ 0.174 1.826
/? UNK 0 O2 /A MET 157 CG 0.173 3.007
/? UNK 0 H17 /A LEU 201 HD13 0.167 1.833
/? UNK 0 H17 /A PHE 197 HZ 0.163 1.837
/? UNK 0 H17 /A PHE 197 CZ 0.158 2.542
/? UNK 0 O2 /A MET 157 HG2 0.156 2.324
/? UNK 0 O2 /A MET 157 CA 0.156 3.024
/? UNK 0 H20 /A THR 118 HG22 0.149 1.851
/? UNK 0 C19 /A THR 118 HG22 0.135 2.565
/? UNK 0 C20 /A PHE 197 HZ 0.129 2.571
/? UNK 0 C18 /A LEU 201 CD1 0.122 3.278
/? UNK 0 H14 /A GLY 122 HA3 0.117 1.883
/? UNK 0 C16 /A GLY 122 HA3 0.117 2.583
/? UNK 0 H18 /A LEU 201 HD13 0.115 1.885
/? UNK 0 C1 /A LEU 126 HD23 0.114 2.586
/? UNK 0 C18 /A THR 118 CG2 0.090 3.310
/? UNK 0 C16 /A MET 157 HG2 0.083 2.617
/? UNK 0 H2 /A LEU 125 HD23 0.082 1.918
/? UNK 0 H14 /A MET 157 CG 0.080 2.620
/? UNK 0 H19 /A PHE 197 CE2 0.077 2.623
/? UNK 0 H23 /A MET 157 O 0.077 2.403
/? UNK 0 H14 /A GLY 122 CA 0.058 2.642
/? UNK 0 H1 /A LEU 126 CD2 0.051 2.649
/? UNK 0 H18 /A THR 118 CG2 0.050 2.650
/? UNK 0 H20 /A THR 118 CG2 0.049 2.651
/? UNK 0 H2 /A LEU 125 CD2 0.034 2.666
/? UNK 0 H20 /A SER 161 OG 0.033 2.467
/? UNK 0 C17 /A GLY 122 CA 0.028 3.372
/? UNK 0 C20 /A LEU 160 C 0.018 3.382
/? UNK 0 C18 /A PHE 197 CE2 0.013 3.387
/? UNK 0 C17 /A GLY 122 HA3 0.010 2.690
/? UNK 0 H18 /A THR 118 HG23 -0.027 2.027
/? UNK 0 C1 /A LEU 126 CD2 -0.032 3.432
/? UNK 0 C1 /A LEU 125 CG -0.033 3.433
/? UNK 0 C21 /A LEU 160 HB3 -0.043 2.743
/? UNK 0 C19 /A PHE 197 CE2 -0.045 3.445
/? UNK 0 H1 /A LEU 126 HD23 -0.049 2.049
/? UNK 0 H2 /A LEU 125 HG -0.050 2.050
/? UNK 0 H22 /A LEU 160 O -0.055 2.535
/? UNK 0 O1 /A LEU 160 CD1 -0.059 3.239
/? UNK 0 H2 /A LEU 125 CG -0.065 2.765
/? UNK 0 H18 /A LEU 201 CD1 -0.074 2.774
/? UNK 0 H21 /A PHE 197 HZ -0.076 2.076
/? UNK 0 C14 /A MET 157 HG2 -0.078 2.778
/? UNK 0 H22 /A SER 161 N -0.080 2.705
/? UNK 0 H20 /A SER 161 HA -0.093 2.093
/? UNK 0 C18 /A THR 118 HG22 -0.099 2.799
/? UNK 0 H15 /A GLY 122 CA -0.112 2.812
/? UNK 0 C21 /A MET 157 O -0.121 3.301
/? UNK 0 H17 /A LEU 201 CD1 -0.142 2.842
/? UNK 0 O2 /A MET 157 HB2 -0.145 2.625
/? UNK 0 C15 /A MET 157 HG2 -0.154 2.854
/? UNK 0 H20 /A SER 161 CA -0.158 2.858
/? UNK 0 H24 /A LEU 160 HB3 -0.158 2.158
/? UNK 0 C17 /A THR 118 O -0.162 3.342
/? UNK 0 C16 /A GLY 122 HA2 -0.164 2.864
/? UNK 0 C2 /A LEU 125 HD23 -0.175 2.875
/? UNK 0 H19 /A PHE 197 HE2 -0.176 2.176
/? UNK 0 H3 /A LEU 125 HD22 -0.177 2.177
/? UNK 0 C17 /A LEU 201 HD13 -0.181 2.881
/? UNK 0 C19 /A SER 161 HA -0.187 2.887
/? UNK 0 C20 /A SER 161 N -0.198 3.523
/? UNK 0 C16 /A MET 157 CG -0.199 3.599
/? UNK 0 H1 /A LEU 126 CG -0.200 2.900
/? UNK 0 H24 /A LEU 160 HD12 -0.214 2.214
/? UNK 0 C20 /A PHE 197 CZ -0.218 3.618
/? UNK 0 H18 /A PHE 197 CE2 -0.233 2.933
/? UNK 0 H15 /A GLY 122 N -0.238 2.863
/? UNK 0 H22 /A LEU 160 CA -0.238 2.938
/? UNK 0 H1 /A LEU 126 HG -0.241 2.241
/? UNK 0 C1 /A LEU 125 HG -0.251 2.951
/? UNK 0 C18 /A THR 118 HG23 -0.252 2.952
/? UNK 0 C19 /A PHE 197 HE2 -0.282 2.982
/? UNK 0 C14 /A MET 157 CG -0.286 3.686
/? UNK 0 C19 /A SER 161 OG -0.290 3.490
/? UNK 0 H16 /A SER 161 OG -0.297 2.797
/? UNK 0 H19 /A THR 118 CG2 -0.306 3.006
/? UNK 0 H24 /A LEU 160 CD1 -0.309 3.009
/? UNK 0 C18 /A PHE 197 HE2 -0.317 3.017
/? UNK 0 C19 /A SER 161 CA -0.322 3.722
/? UNK 0 C20 /A LEU 160 HB2 -0.335 3.035
/? UNK 0 C19 /A THR 118 HG21 -0.337 3.037
/? UNK 0 O1 /A LEU 160 HD13 -0.342 2.822
/? UNK 0 H23 /A SER 161 HG -0.348 2.348
/? UNK 0 H18 /A PHE 197 CZ -0.348 3.048
/? UNK 0 H21 /A PHE 197 CZ -0.372 3.072
/? UNK 0 H15 /A THR 118 O -0.374 2.854
/? UNK 0 C21 /A MET 157 HG2 -0.377 3.077
/? UNK 0 H16 /A THR 118 O -0.386 2.866
/? UNK 0 BR1 /A LEU 126 CG -0.390 4.510
/? UNK 0 H17 /A LEU 201 HD21 -0.390 2.390
/? UNK 0 H2 /A LEU 126 HD23 -0.391 2.391
/? UNK 0 H18 /A PHE 197 HE2 -0.393 2.393
/? UNK 0 H3 /A LEU 125 CG -0.396 3.096
/? UNK 0 C17 /A GLY 122 N -0.400 3.725
126 contacts
> select ~:126,129,125,197,201,125,160,157,122,118,161
4500 atoms, 4554 bonds, 282 residues, 3 models selected
> name ligand_binding :126,129,125,197,201,125,160,157,122,118,161
> hide ~ligand_binding label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide label ~ligand_binding
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide label ~ligand_binding
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~ligand_binding
> undo
> select ~ligand_binding
4500 atoms, 4554 bonds, 282 residues, 3 models selected
> hide sel
[Repeated 4 time(s)]
> name ligand_binding :126,129,125,197,201,125,160,157,122,118,161,UNK
> hide sel
> hide ~sel
> name ligand_binding :126,129,125,197,201,125,160,157,122,118,161,UNK
> select ligand_binding
215 atoms, 210 bonds, 126 pseudobonds, 11 residues, 2 models selected
> select ~ligand_binding
4449 atoms, 4501 bonds, 281 residues, 3 models selected
> hide sel
[Repeated 1 time(s)]
> hide sel labels
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide label sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label @@display
> label :UNK delete
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label :UNK 0 delete
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> select :UNK
51 atoms, 53 bonds, 1 residue, 1 model selected
> label sel delete
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> hide #!1.2 models
> hide HC atoms
> select ~ligands binding
Expected an objects specifier or a keyword
> select ~ligands binding
Expected an objects specifier or a keyword
> select ~ligand_binding
4449 atoms, 4501 bonds, 281 residues, 3 models selected
> label delete :UNK
> label delete sel
> undo
> color /A byhetero
> color /A cyan
> color /A byhetero
> contacts /A@C* restrict :UNK@C* distanceOnly 3.8 reveal true name vdW
19 distances
> cartoon suppressBackboneDisplay false
> name ligand_binding_no_ligand :126,129,125,197,201,125,160,157,122,118,161
> color ligand_binding_no_ligand & C salmon
> color ligand_binding_no_ligand & C olive
> ui tool show Shell
> label delete
> ui tool show Shell
> label delete
[Repeated 1 time(s)]Labels were deleted
> label #1/A:18 residues text 18
> label #1/A:19 residues text 19
> label #1/A:20 residues text 20
> label #1/A:21 residues text 21
> label #1/A:22 residues text 22
> label #1/A:23 residues text 23
> label #1/A:24 residues text 24
> label #1/A:25 residues text 25
> label #1/A:26 residues text 26
> label #1/A:27 residues text 27
> label #1/A:28 residues text 28
> label #1/A:29 residues text 1.28x28
> label #1/A:30 residues text 1.29x29
> label #1/A:31 residues text 1.30x30
> label #1/A:32 residues text 1.31x31
> label #1/A:33 residues text 1.32x32
> label #1/A:34 residues text 1.33x33
> label #1/A:35 residues text 1.34x34
> label #1/A:36 residues text 1.35x35
> label #1/A:37 residues text 1.36x36
> label #1/A:38 residues text 1.37x37
> label #1/A:39 residues text 1.38x38
> label #1/A:40 residues text 1.39x39
> label #1/A:41 residues text 1.40x40
> label #1/A:42 residues text 1.41x41
> label #1/A:43 residues text 1.42x42
> label #1/A:44 residues text 1.43x43
> label #1/A:45 residues text 1.44x44
> label #1/A:46 residues text 1.45x45
> label #1/A:47 residues text 1.46x46
> label #1/A:48 residues text 1.47x47
> label #1/A:49 residues text 1.48x48
> label #1/A:50 residues text 1.49x49
> label #1/A:51 residues text 1.50x50
> label #1/A:52 residues text 1.51x51
> label #1/A:53 residues text 1.52x52
> label #1/A:54 residues text 1.53x53
> label #1/A:55 residues text 1.54x54
> label #1/A:56 residues text 1.55x55
> label #1/A:57 residues text 1.56x56
> label #1/A:58 residues text 1.57x57
> label #1/A:59 residues text 1.58x58
> label #1/A:60 residues text 1.59x59
> label #1/A:61 residues text 1.60x60
> label #1/A:62 residues text 12.48x48
> label #1/A:63 residues text 12.49x49
> label #1/A:64 residues text 12.50x50
> label #1/A:65 residues text 12.51x51
> label #1/A:66 residues text 66
> label #1/A:67 residues text 2.37x37
> label #1/A:68 residues text 2.38x38
> label #1/A:69 residues text 2.39x39
> label #1/A:70 residues text 2.40x40
> label #1/A:71 residues text 2.41x41
> label #1/A:72 residues text 2.42x42
> label #1/A:73 residues text 2.43x43
> label #1/A:74 residues text 2.44x44
> label #1/A:75 residues text 2.45x45
> label #1/A:76 residues text 2.46x46
> label #1/A:77 residues text 2.47x47
> label #1/A:78 residues text 2.48x48
> label #1/A:79 residues text 2.49x49
> label #1/A:80 residues text 2.50x50
> label #1/A:81 residues text 2.51x51
> label #1/A:82 residues text 2.52x52
> label #1/A:83 residues text 2.53x53
> label #1/A:84 residues text 2.54x54
> label #1/A:85 residues text 2.55x55
> label #1/A:86 residues text 2.56x56
> label #1/A:87 residues text 2.57x57
> label #1/A:88 residues text 2.58x58
> label #1/A:89 residues text 2.59x59
> label #1/A:90 residues text 2.60x60
> label #1/A:91 residues text 2.61x61
> label #1/A:92 residues text 2.62x62
> label #1/A:93 residues text 2.63x63
> label #1/A:94 residues text 2.64x64
> label #1/A:95 residues text 2.65x65
> label #1/A:96 residues text 2.66x66
> label #1/A:97 residues text 97
> label #1/A:98 residues text 98
> label #1/A:99 residues text 99
> label #1/A:100 residues text 100
> label #1/A:101 residues text 101
> label #1/A:102 residues text 3.21x21
> label #1/A:103 residues text 3.22x22
> label #1/A:104 residues text 3.23x23
> label #1/A:105 residues text 3.24x24
> label #1/A:106 residues text 3.25x25
> label #1/A:107 residues text 3.26x26
> label #1/A:108 residues text 3.27x27
> label #1/A:109 residues text 3.28x28
> label #1/A:110 residues text 3.29x29
> label #1/A:111 residues text 3.30x30
> label #1/A:112 residues text 3.31x31
> label #1/A:113 residues text 3.32x32
> label #1/A:114 residues text 3.33x33
> label #1/A:115 residues text 3.34x34
> label #1/A:116 residues text 3.35x35
> label #1/A:117 residues text 3.36x36
> label #1/A:118 residues text 3.37x37
> label #1/A:119 residues text 3.38x38
> label #1/A:120 residues text 3.39x39
> label #1/A:121 residues text 3.40x40
> label #1/A:122 residues text 3.41x41
> label #1/A:123 residues text 3.42x42
> label #1/A:124 residues text 3.43x43
> label #1/A:125 residues text 3.44x44
> label #1/A:126 residues text 3.45x45
> label #1/A:127 residues text 3.46x46
> label #1/A:128 residues text 3.47x47
> label #1/A:129 residues text 3.48x48
> label #1/A:130 residues text 3.49x49
> label #1/A:131 residues text 3.50x50
> label #1/A:132 residues text 3.51x51
> label #1/A:133 residues text 3.52x52
> label #1/A:134 residues text 3.53x53
> label #1/A:135 residues text 3.54x54
> label #1/A:136 residues text 3.55x55
> label #1/A:137 residues text 3.56x56
> label #1/A:138 residues text 34.50x50
> label #1/A:139 residues text 34.51x51
> label #1/A:140 residues text 34.52x52
> label #1/A:141 residues text 34.53x53
> label #1/A:142 residues text 34.54x54
> label #1/A:143 residues text 34.55x55
> label #1/A:144 residues text 34.56x56
> label #1/A:145 residues text 34.57x57
> label #1/A:146 residues text 4.38x38
> label #1/A:147 residues text 4.39x39
> label #1/A:148 residues text 4.40x40
> label #1/A:149 residues text 4.41x41
> label #1/A:150 residues text 4.42x42
> label #1/A:151 residues text 4.43x43
> label #1/A:152 residues text 4.44x44
> label #1/A:153 residues text 4.45x45
> label #1/A:154 residues text 4.46x46
> label #1/A:155 residues text 4.47x47
> label #1/A:156 residues text 4.48x48
> label #1/A:157 residues text 4.49x49
> label #1/A:158 residues text 4.50x50
> label #1/A:159 residues text 4.51x51
> label #1/A:160 residues text 4.52x52
> label #1/A:161 residues text 4.53x53
> label #1/A:162 residues text 4.54x54
> label #1/A:163 residues text 4.55x55
> label #1/A:164 residues text 4.56x56
> label #1/A:165 residues text 4.57x57
> label #1/A:166 residues text 4.58x58
> label #1/A:167 residues text 4.59x59
> label #1/A:168 residues text 4.60x60
> label #1/A:169 residues text 4.61x61
> label #1/A:170 residues text 4.62x62
> label #1/A:171 residues text 4.63x63
> label #1/A:172 residues text 172
> label #1/A:173 residues text 173
> label #1/A:174 residues text 174
> label #1/A:175 residues text 175
> label #1/A:176 residues text 176
> label #1/A:177 residues text 177
> label #1/A:178 residues text 178
> label #1/A:179 residues text 179
> label #1/A:180 residues text 180
> label #1/A:181 residues text 181
> label #1/A:182 residues text 182
> label #1/A:183 residues text 183
> label #1/A:184 residues text 184
> label #1/A:185 residues text 185
> label #1/A:186 residues text 186
> label #1/A:187 residues text 5.36x36
> label #1/A:188 residues text 5.37x37
> label #1/A:189 residues text 5.38x38
> label #1/A:190 residues text 5.39x39
> label #1/A:191 residues text 5.40x40
> label #1/A:192 residues text 5.41x41
> label #1/A:193 residues text 5.42x42
> label #1/A:194 residues text 5.43x43
> label #1/A:195 residues text 5.44x44
> label #1/A:196 residues text 5.45x45
> label #1/A:197 residues text 5.46x46
> label #1/A:198 residues text 5.47x47
> label #1/A:199 residues text 5.48x48
> label #1/A:200 residues text 5.49x49
> label #1/A:201 residues text 5.50x50
> label #1/A:202 residues text 5.51x51
> label #1/A:203 residues text 5.52x52
> label #1/A:204 residues text 5.53x53
> label #1/A:205 residues text 5.54x54
> label #1/A:206 residues text 5.55x55
> label #1/A:207 residues text 5.56x56
> label #1/A:208 residues text 5.57x57
> label #1/A:209 residues text 5.58x58
> label #1/A:210 residues text 5.59x59
> label #1/A:211 residues text 5.60x60
> label #1/A:212 residues text 5.61x61
> label #1/A:213 residues text 5.62x62
> label #1/A:214 residues text 5.63x63
> label #1/A:215 residues text 5.64x64
> label #1/A:216 residues text 5.65x65
> label #1/A:217 residues text 5.66x66
> label #1/A:218 residues text 5.67x67
> label #1/A:219 residues text 5.68x68
> label #1/A:220 residues text 5.69x69
> label #1/A:221 residues text 5.70x70
> label #1/A:222 residues text 5.71x71
> label #1/A:235 residues text 235
> label #1/A:236 residues text 236
> label #1/A:237 residues text 237
> label #1/A:238 residues text 6.28x28
> label #1/A:239 residues text 6.29x29
> label #1/A:240 residues text 6.30x30
> label #1/A:241 residues text 6.31x31
> label #1/A:242 residues text 6.32x32
> label #1/A:243 residues text 6.33x33
> label #1/A:244 residues text 6.34x34
> label #1/A:245 residues text 6.35x35
> label #1/A:246 residues text 6.36x36
> label #1/A:247 residues text 6.37x37
> label #1/A:248 residues text 6.38x38
> label #1/A:249 residues text 6.39x39
> label #1/A:250 residues text 6.40x40
> label #1/A:251 residues text 6.41x41
> label #1/A:252 residues text 6.42x42
> label #1/A:253 residues text 6.43x43
> label #1/A:254 residues text 6.44x44
> label #1/A:255 residues text 6.45x45
> label #1/A:256 residues text 6.46x46
> label #1/A:257 residues text 6.47x47
> label #1/A:258 residues text 6.48x48
> label #1/A:259 residues text 6.49x49
> label #1/A:260 residues text 6.50x50
> label #1/A:261 residues text 6.51x51
> label #1/A:262 residues text 6.52x52
> label #1/A:263 residues text 6.53x53
> label #1/A:264 residues text 6.54x54
> label #1/A:265 residues text 6.55x55
> label #1/A:266 residues text 6.56x56
> label #1/A:267 residues text 6.57x57
> label #1/A:268 residues text 6.58x58
> label #1/A:269 residues text 6.59x59
> label #1/A:270 residues text 6.60x60
> label #1/A:271 residues text 6.61x61
> label #1/A:272 residues text 272
> label #1/A:273 residues text 273
> label #1/A:274 residues text 7.28x27
> label #1/A:275 residues text 7.29x28
> label #1/A:276 residues text 7.30x29
> label #1/A:277 residues text 7.31x30
> label #1/A:278 residues text 7.32x31
> label #1/A:279 residues text 7.33x32
> label #1/A:280 residues text 7.34x33
> label #1/A:281 residues text 7.35x34
> label #1/A:282 residues text 7.36x35
> label #1/A:283 residues text 7.37x36
> label #1/A:284 residues text 7.38x37
> label #1/A:285 residues text 7.39x38
> label #1/A:286 residues text 7.40x39
> label #1/A:287 residues text 7.41x40
> label #1/A:288 residues text 7.42x41
> label #1/A:289 residues text 7.43x42
> label #1/A:290 residues text 7.44x43
> label #1/A:291 residues text 7.45x45
> label #1/A:292 residues text 7.46x46
> label #1/A:293 residues text 7.47x47
> label #1/A:294 residues text 7.48x48
> label #1/A:295 residues text 7.49x49
> label #1/A:296 residues text 7.50x50
> label #1/A:297 residues text 7.51x51
> label #1/A:298 residues text 7.52x52
> label #1/A:299 residues text 7.53x53
> label #1/A:300 residues text 7.54x54
> label #1/A:301 residues text 7.55x55
> label #1/A:302 residues text 7.56x56
> label #1/A:303 residues text 8.47x47
> label #1/A:304 residues text 8.48x48
> label #1/A:305 residues text 8.49x49
> label #1/A:306 residues text 8.50x50
> label #1/A:307 residues text 8.51x51
> label #1/A:308 residues text 8.52x52
> label #1/A:309 residues text 8.53x53
> label #1/A:310 residues text 8.54x54
> label #1/A:311 residues text 8.55x55
> label #1/A:312 residues text 8.56x56
> label #1/A:313 residues text 8.57x57
> label #1/A:314 residues text 8.58x58
> label #1/A:315 residues text 8.59x59
> label #1/A:316 residues text 8.60x60
> label #1/A:317 residues text 8.61x61
> label #1/A:318 residues text 8.62x62
> label #1/A:319 residues text 8.63x63
Annotation completed
> label @@display
> label :UNK delete
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label delete :UNK
> name ligand_binding_no_ligand_extended
> :126,129,125,197,201,125,160,157,122,118,161,153,204
> show ligand_binding_no_ligand_extended stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show ligand_binding_no_ligand_extended atoms
> hide HC atoms
> select ~ligand_binding_no_ligand_extended&:UNK
51 atoms, 53 bonds, 1 residue, 1 model selected
> select ~ligand_binding_no_ligand_extended
4479 atoms, 4531 bonds, 280 residues, 2 models selected
> name ligand_binding_no_ligand_extended
> :126,129,125,197,201,125,160,157,122,118,161,153,204,UNK
> select ~ligand_binding_no_ligand_extended
4428 atoms, 4478 bonds, 279 residues, 2 models selected
> label delete sel
> lighting soft
> lighting full
> lighting soft
> select clear
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting simple
> ui tool show "Selection Inspector"
> select /?:0@C3
1 atom, 1 residue, 1 model selected
> select up
51 atoms, 53 bonds, 1 residue, 1 model selected
> style sel ball
Changed 51 atom styles
> view sel
> select clear
> view
> select add #1
4664 atoms, 4727 bonds, 145 pseudobonds, 292 residues, 4 models selected
> show sel surfaces
> select /?:0@C2
1 atom, 1 residue, 1 model selected
> select up
51 atoms, 53 bonds, 1 residue, 1 model selected
> view sel
> hide #!1.5 models
> hide #1.4 models
> surface ligand_binding_no_ligand
> save /Users/styli/Desktop/image1.png supersample 3
> select clear
> color #1.5 #c3b3f2ff
> ui mousemode right distance
> distance /A:153@CG2 /?:0@BR1
Distance between /A THR 153 CG2 and / UNK 0 BR1: 4.960Å
> distance /A:156@CG2 /?:0@C7
Distance between /A ILE 156 CG2 and / UNK 0 C7: 4.795Å
> ui mousemode right label
> label #1/A:204
[Repeated 3 time(s)]
> label #1/A:206
> undo
[Repeated 2 time(s)]
> label #1/A:204 residues text 5.53x53
> label #1/A:204 residues text 5.53^Thr
> label #1/A:204 residues text 5.53
> label #1/A:204 residues text Gly5.53
> label #1/A:206
> label delete residues
> undo
[Repeated 1 time(s)]
> ui mousemode right translate
> ui tool show Shell
> label delete
Labels were deleted
> label #1/A:18 residues text 18
> label #1/A:19 residues text 19
> label #1/A:20 residues text 20
> label #1/A:21 residues text 21
> label #1/A:22 residues text 22
> label #1/A:23 residues text 23
> label #1/A:24 residues text 24
> label #1/A:25 residues text 25
> label #1/A:26 residues text 26
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> label #1/A:36 residues text 1.35x35
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> label #1/A:185 residues text 185
> label #1/A:186 residues text 186
> label #1/A:187 residues text 5.36x36
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> label #1/A:319 residues text 8.63x63
Annotation completed
> label delete
> ui tool show Shell
> label delete
Labels were deleted
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> label #1/A:19 residues text 19
> label #1/A:20 residues text 20
> label #1/A:21 residues text 21
> label #1/A:22 residues text 22
> label #1/A:23 residues text 23
> label #1/A:24 residues text 24
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> label #1/A:98 residues text 98
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> label #1/A:100 residues text 100
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> label #1/A:250 residues text 6.40
> label #1/A:251 residues text 6.41
> label #1/A:252 residues text 6.42
> label #1/A:253 residues text 6.43
> label #1/A:254 residues text 6.44
> label #1/A:255 residues text 6.45
> label #1/A:256 residues text 6.46
> label #1/A:257 residues text 6.47
> label #1/A:258 residues text 6.48
> label #1/A:259 residues text 6.49
> label #1/A:260 residues text 6.50
> label #1/A:261 residues text 6.51
> label #1/A:262 residues text 6.52
> label #1/A:263 residues text 6.53
> label #1/A:264 residues text 6.54
> label #1/A:265 residues text 6.55
> label #1/A:266 residues text 6.56
> label #1/A:267 residues text 6.57
> label #1/A:268 residues text 6.58
> label #1/A:269 residues text 6.59
> label #1/A:270 residues text 6.60
> label #1/A:271 residues text 6.61
> label #1/A:272 residues text 272
> label #1/A:273 residues text 273
> label #1/A:274 residues text 7.28
> label #1/A:275 residues text 7.29
> label #1/A:276 residues text 7.30
> label #1/A:277 residues text 7.31
> label #1/A:278 residues text 7.32
> label #1/A:279 residues text 7.33
> label #1/A:280 residues text 7.34
> label #1/A:281 residues text 7.35
> label #1/A:282 residues text 7.36
> label #1/A:283 residues text 7.37
> label #1/A:284 residues text 7.38
> label #1/A:285 residues text 7.39
> label #1/A:286 residues text 7.40
> label #1/A:287 residues text 7.41
> label #1/A:288 residues text 7.42
> label #1/A:289 residues text 7.43
> label #1/A:290 residues text 7.44
> label #1/A:291 residues text 7.45
> label #1/A:292 residues text 7.46
> label #1/A:293 residues text 7.47
> label #1/A:294 residues text 7.48
> label #1/A:295 residues text 7.49
> label #1/A:296 residues text 7.50
> label #1/A:297 residues text 7.51
> label #1/A:298 residues text 7.52
> label #1/A:299 residues text 7.53
> label #1/A:300 residues text 7.54
> label #1/A:301 residues text 7.55
> label #1/A:302 residues text 7.56
> label #1/A:303 residues text 8.47
> label #1/A:304 residues text 8.48
> label #1/A:305 residues text 8.49
> label #1/A:306 residues text 8.50
> label #1/A:307 residues text 8.51
> label #1/A:308 residues text 8.52
> label #1/A:309 residues text 8.53
> label #1/A:310 residues text 8.54
> label #1/A:311 residues text 8.55
> label #1/A:312 residues text 8.56
> label #1/A:313 residues text 8.57
> label #1/A:314 residues text 8.58
> label #1/A:315 residues text 8.59
> label #1/A:316 residues text 8.60
> label #1/A:317 residues text 8.61
> label #1/A:318 residues text 8.62
> label #1/A:319 residues text 8.63
Annotation completed
> label delete
Labels were deleted
> label delete
Labels were deleted
> label delete
Labels were deleted
> label #1/A:18 residues text D18
> label #1/A:19 residues text S19
> label #1/A:20 residues text N20
> label #1/A:21 residues text P21
> label #1/A:22 residues text M22
> label #1/A:23 residues text K23
> label #1/A:24 residues text D24
> label #1/A:25 residues text Y25
> label #1/A:26 residues text M26
> label #1/A:27 residues text I27
> label #1/A:28 residues text L28
> label #1/A:29 residues text S1.28
> label #1/A:30 residues text G1.29
> label #1/A:31 residues text P1.30
> label #1/A:32 residues text Q1.31
> label #1/A:33 residues text K1.32
> label #1/A:34 residues text T1.33
> label #1/A:35 residues text A1.34
> label #1/A:36 residues text V1.35
> label #1/A:37 residues text A1.36
> label #1/A:38 residues text V1.37
> label #1/A:39 residues text L1.38
> label #1/A:40 residues text C1.39
> label #1/A:41 residues text T1.40
> label #1/A:42 residues text L1.41
> label #1/A:43 residues text L1.42
> label #1/A:44 residues text G1.43
> label #1/A:45 residues text L1.44
> label #1/A:46 residues text L1.45
> label #1/A:47 residues text S1.46
> label #1/A:48 residues text A1.47
> label #1/A:49 residues text L1.48
> label #1/A:50 residues text E1.49
> label #1/A:51 residues text N1.50
> label #1/A:52 residues text V1.51
> label #1/A:53 residues text A1.52
> label #1/A:54 residues text V1.53
> label #1/A:55 residues text L1.54
> label #1/A:56 residues text Y1.55
> label #1/A:57 residues text L1.56
> label #1/A:58 residues text I1.57
> label #1/A:59 residues text L1.58
> label #1/A:60 residues text S1.59
> label #1/A:61 residues text S1.60
> label #1/A:62 residues text H12.48
> label #1/A:63 residues text Q12.49
> label #1/A:64 residues text L12.50
> label #1/A:65 residues text R12.51
> label #1/A:66 residues text R66
> label #1/A:67 residues text K2.37
> label #1/A:68 residues text P2.38
> label #1/A:69 residues text S2.39
> label #1/A:70 residues text Y2.40
> label #1/A:71 residues text L2.41
> label #1/A:72 residues text F2.42
> label #1/A:73 residues text I2.43
> label #1/A:74 residues text G2.44
> label #1/A:75 residues text S2.45
> label #1/A:76 residues text L2.46
> label #1/A:77 residues text A2.47
> label #1/A:78 residues text G2.48
> label #1/A:79 residues text A2.49
> label #1/A:80 residues text D2.50
> label #1/A:81 residues text F2.51
> label #1/A:82 residues text L2.52
> label #1/A:83 residues text A2.53
> label #1/A:84 residues text S2.54
> label #1/A:85 residues text V2.55
> label #1/A:86 residues text V2.56
> label #1/A:87 residues text F2.57
> label #1/A:88 residues text A2.58
> label #1/A:89 residues text C2.59
> label #1/A:90 residues text S2.60
> label #1/A:91 residues text F2.61
> label #1/A:92 residues text V2.62
> label #1/A:93 residues text N2.63
> label #1/A:94 residues text F2.64
> label #1/A:95 residues text H2.65
> label #1/A:96 residues text V2.66
> label #1/A:97 residues text F97
> label #1/A:98 residues text H98
> label #1/A:99 residues text G99
> label #1/A:100 residues text V100
> label #1/A:101 residues text D101
> label #1/A:102 residues text S3.21
> label #1/A:103 residues text K3.22
> label #1/A:104 residues text A3.23
> label #1/A:105 residues text V3.24
> label #1/A:106 residues text F3.25
> label #1/A:107 residues text L3.26
> label #1/A:108 residues text L3.27
> label #1/A:109 residues text K3.28
> label #1/A:110 residues text I3.29
> label #1/A:111 residues text G3.30
> label #1/A:112 residues text S3.31
> label #1/A:113 residues text V3.32
> label #1/A:114 residues text T3.33
> label #1/A:115 residues text M3.34
> label #1/A:116 residues text T3.35
> label #1/A:117 residues text F3.36
> label #1/A:118 residues text T3.37
> label #1/A:119 residues text A3.38
> label #1/A:120 residues text S3.39
> label #1/A:121 residues text V3.40
> label #1/A:122 residues text G3.41
> label #1/A:123 residues text S3.42
> label #1/A:124 residues text L3.43
> label #1/A:125 residues text L3.44
> label #1/A:126 residues text L3.45
> label #1/A:127 residues text T3.46
> label #1/A:128 residues text A3.47
> label #1/A:129 residues text I3.48
> label #1/A:130 residues text D3.49
> label #1/A:131 residues text R3.50
> label #1/A:132 residues text Y3.51
> label #1/A:133 residues text L3.52
> label #1/A:134 residues text C3.53
> label #1/A:135 residues text L3.54
> label #1/A:136 residues text R3.55
> label #1/A:137 residues text Y3.56
> label #1/A:138 residues text P34.50
> label #1/A:139 residues text P34.51
> label #1/A:140 residues text S34.52
> label #1/A:141 residues text Y34.53
> label #1/A:142 residues text K34.54
> label #1/A:143 residues text A34.55
> label #1/A:144 residues text L34.56
> label #1/A:145 residues text L34.57
> label #1/A:146 residues text T4.38
> label #1/A:147 residues text R4.39
> label #1/A:148 residues text G4.40
> label #1/A:149 residues text R4.41
> label #1/A:150 residues text A4.42
> label #1/A:151 residues text L4.43
> label #1/A:152 residues text V4.44
> label #1/A:153 residues text T4.45
> label #1/A:154 residues text L4.46
> label #1/A:155 residues text G4.47
> label #1/A:156 residues text I4.48
> label #1/A:157 residues text M4.49
> label #1/A:158 residues text W4.50
> label #1/A:159 residues text V4.51
> label #1/A:160 residues text L4.52
> label #1/A:161 residues text S4.53
> label #1/A:162 residues text A4.54
> label #1/A:163 residues text L4.55
> label #1/A:164 residues text V4.56
> label #1/A:165 residues text S4.57
> label #1/A:166 residues text Y4.58
> label #1/A:167 residues text L4.59
> label #1/A:168 residues text P4.60
> label #1/A:169 residues text L4.61
> label #1/A:170 residues text M4.62
> label #1/A:171 residues text G4.63
> label #1/A:172 residues text W172
> label #1/A:173 residues text T173
> label #1/A:174 residues text C174
> label #1/A:175 residues text C175
> label #1/A:176 residues text P176
> label #1/A:177 residues text R177
> label #1/A:178 residues text P178
> label #1/A:179 residues text C179
> label #1/A:180 residues text S180
> label #1/A:181 residues text E181
> label #1/A:182 residues text L182
> label #1/A:183 residues text F183
> label #1/A:184 residues text P184
> label #1/A:185 residues text L185
> label #1/A:186 residues text I186
> label #1/A:187 residues text P5.36
> label #1/A:188 residues text N5.37
> label #1/A:189 residues text D5.38
> label #1/A:190 residues text Y5.39
> label #1/A:191 residues text L5.40
> label #1/A:192 residues text L5.41
> label #1/A:193 residues text S5.42
> label #1/A:194 residues text W5.43
> label #1/A:195 residues text L5.44
> label #1/A:196 residues text L5.45
> label #1/A:197 residues text F5.46
> label #1/A:198 residues text I5.47
> label #1/A:199 residues text A5.48
> label #1/A:200 residues text F5.49
> label #1/A:201 residues text L5.50
> label #1/A:202 residues text F5.51
> label #1/A:203 residues text S5.52
> label #1/A:204 residues text G5.53
> label #1/A:205 residues text I5.54
> label #1/A:206 residues text I5.55
> label #1/A:207 residues text Y5.56
> label #1/A:208 residues text T5.57
> label #1/A:209 residues text Y5.58
> label #1/A:210 residues text G5.59
> label #1/A:211 residues text H5.60
> label #1/A:212 residues text V5.61
> label #1/A:213 residues text L5.62
> label #1/A:214 residues text W5.63
> label #1/A:215 residues text K5.64
> label #1/A:216 residues text A5.65
> label #1/A:217 residues text H5.66
> label #1/A:218 residues text Q5.67
> label #1/A:219 residues text H5.68
> label #1/A:220 residues text V5.69
> label #1/A:221 residues text A5.70
> label #1/A:222 residues text S5.71
> label #1/A:235 residues text A235
> label #1/A:236 residues text R236
> label #1/A:237 residues text M237
> label #1/A:238 residues text R6.28
> label #1/A:239 residues text L6.29
> label #1/A:240 residues text D6.30
> label #1/A:241 residues text V6.31
> label #1/A:242 residues text R6.32
> label #1/A:243 residues text L6.33
> label #1/A:244 residues text A6.34
> label #1/A:245 residues text K6.35
> label #1/A:246 residues text T6.36
> label #1/A:247 residues text L6.37
> label #1/A:248 residues text G6.38
> label #1/A:249 residues text L6.39
> label #1/A:250 residues text V6.40
> label #1/A:251 residues text L6.41
> label #1/A:252 residues text A6.42
> label #1/A:253 residues text V6.43
> label #1/A:254 residues text L6.44
> label #1/A:255 residues text L6.45
> label #1/A:256 residues text I6.46
> label #1/A:257 residues text C6.47
> label #1/A:258 residues text W6.48
> label #1/A:259 residues text F6.49
> label #1/A:260 residues text P6.50
> label #1/A:261 residues text V6.51
> label #1/A:262 residues text L6.52
> label #1/A:263 residues text A6.53
> label #1/A:264 residues text L6.54
> label #1/A:265 residues text M6.55
> label #1/A:266 residues text A6.56
> label #1/A:267 residues text H6.57
> label #1/A:268 residues text S6.58
> label #1/A:269 residues text L6.59
> label #1/A:270 residues text A6.60
> label #1/A:271 residues text T6.61
> label #1/A:272 residues text T272
> label #1/A:273 residues text L273
> label #1/A:274 residues text S7.28
> label #1/A:275 residues text D7.29
> label #1/A:276 residues text Q7.30
> label #1/A:277 residues text V7.31
> label #1/A:278 residues text K7.32
> label #1/A:279 residues text K7.33
> label #1/A:280 residues text A7.34
> label #1/A:281 residues text F7.35
> label #1/A:282 residues text A7.36
> label #1/A:283 residues text F7.37
> label #1/A:284 residues text C7.38
> label #1/A:285 residues text S7.39
> label #1/A:286 residues text M7.40
> label #1/A:287 residues text L7.41
> label #1/A:288 residues text C7.42
> label #1/A:289 residues text L7.43
> label #1/A:290 residues text I7.44
> label #1/A:291 residues text N7.45
> label #1/A:292 residues text S7.46
> label #1/A:293 residues text M7.47
> label #1/A:294 residues text V7.48
> label #1/A:295 residues text N7.49
> label #1/A:296 residues text P7.50
> label #1/A:297 residues text V7.51
> label #1/A:298 residues text I7.52
> label #1/A:299 residues text Y7.53
> label #1/A:300 residues text A7.54
> label #1/A:301 residues text L7.55
> label #1/A:302 residues text R7.56
> label #1/A:303 residues text S8.47
> label #1/A:304 residues text G8.48
> label #1/A:305 residues text E8.49
> label #1/A:306 residues text I8.50
> label #1/A:307 residues text R8.51
> label #1/A:308 residues text S8.52
> label #1/A:309 residues text S8.53
> label #1/A:310 residues text A8.54
> label #1/A:311 residues text H8.55
> label #1/A:312 residues text H8.56
> label #1/A:313 residues text C8.57
> label #1/A:314 residues text L8.58
> label #1/A:315 residues text A8.59
> label #1/A:316 residues text H8.60
> label #1/A:317 residues text W8.61
> label #1/A:318 residues text K8.62
> label #1/A:319 residues text K8.63
Annotation completed
> name ligand_binding_no_ligand_extended
> :126,129,125,197,201,125,160,157,122,118,161,153,204
> name ligand_binding_no_ligand :126,129,125,197,201,125,160,157,122,118,161
> color ligand_binding_no_ligand & C olive
> hide #1.5 models
> select ~ligand_binding_no_ligand_extended
4479 atoms, 4531 bonds, 1 pseudobond, 280 residues, 3 models selected
> label delete sel
> select clear
> select /A:164@CB
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right "move label"
> lighting simple
> lighting soft
> lighting simple
> save /Users/styli/Desktop/image2.png supersample 3
> cofr sel
> view myview
Expected an objects specifier or a view name or a keyword
> save
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/EC2LA_figure.cxs
> select clear
> ui mousemode right translate
> ui mousemode right "move label"
> hide #2 models
> save /Users/styli/Desktop/image3.png supersample 3
> view matrix
view matrix camera
-0.88247,-0.23264,0.4088,47.378,-0.46623,0.3177,-0.82565,-69.713,0.062208,-0.91921,-0.38883,-70.718
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> windowsize 1200 1200
> ui mousemode right translate
> ui mousemode right "move label"
> view matrix camera
Missing "camera" keyword's argument
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/styli/Desktop/movie1.mp4
Movie saved to /Users/styli/Desktop/movie1.mp4
> save /Users/styli/Desktop/image4.png supersample 3
> label #1/A:156 residues text I4.48
> save /Users/styli/Desktop/image5.png supersample 3
> mlp
Map values for surface "ec2la.pdb_A SES surface": minimum -23.85, mean 1.628,
maximum 24.45
> ui mousemode right "color key"
> ui mousemode right "move label"
> ui mousemode right "color key"
> key delete
> ui mousemode right "move label"
> hide #!1.5 models
> coulombic protein
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue NMA (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/37/1pzfrg0d7tx64kkb_y_xb0mc0000gn/T/tmpc7u75s0f/ante.in.mol2 -fi
mol2 -o
/var/folders/37/1pzfrg0d7tx64kkb_y_xb0mc0000gn/T/tmpc7u75s0f/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(NMA) ``
(NMA) `Welcome to antechamber 20.0: molecular input file processor.`
(NMA) ``
(NMA) `Info: Finished reading file
(/var/folders/37/1pzfrg0d7tx64kkb_y_xb0mc0000gn/T/tmpc7u75s0f/ante.in.mol2);
atoms read (12), bonds read (11).`
(NMA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NMA) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NMA) ``
(NMA) ``
(NMA) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NMA) `Info: Total number of electrons: 40; net charge: 0`
(NMA) ``
(NMA) `Running: /Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NMA) ``
(NMA) `Running: /Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(NMA) ``
(NMA) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(NMA) ``
Charges for residue NMA determined
Coulombic values for ec2la.pdb_A SES surface #1.5: minimum, -8.95, mean 2.99,
maximum 18.84
> hide #!1.5 models
> select /A:163
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
302 atoms, 303 bonds, 19 residues, 2 models selected
> show (#!1 & sel) target ab
> undo
> select down
19 atoms, 18 bonds, 1 residue, 2 models selected
> show (#!1 & sel) target ab
> hide (#!1 & sel) target a
> ui mousemode right translate
> label height 1.0
> label height 0.8
> label height 0.9
> label height 0.85
> save
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/EC2LA_figure.cxs
——— End of log from Thu Mar 9 20:27:19 2023 ———
opened ChimeraX session
> select :156,204
26 atoms, 24 bonds, 2 residues, 1 model selected
> hide sel atoms
> label delete sel
> select :72
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> hide HC atoms
> label :72 text F2.42
> label height 0.85
> save
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/EC2LA_figure.cxs
> ui mousemode right "move label"
> select clear
> label height 0.80
> label height 0.85
> select /A:121@CB
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> select :121,198
35 atoms, 33 bonds, 2 residues, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right "move label"
> save
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/EC2LA_figure.cxs
> select clear
> save /Users/styli/Desktop/image2.png supersample 3
> view matrix
view matrix camera
-0.9094,-0.27284,0.31392,35.608,-0.41386,0.51871,-0.7481,-49.192,0.041277,-0.81024,-0.58464,-72.701
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0
> save
> /Users/styli/Documents/Work/Projects/Side/CB2R/Paper_with_Zara/EC2LA_figure.cxs
——— End of log from Fri Mar 10 08:32:53 2023 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close
> open 6kqi format mmcif fromDatabase pdb
6kqi title:
Structure of an allosteric modulator bound to the CB1 cannabinoid receptor
[more info...]
Chain information for 6kqi #1
---
Chain | Description | UniProt
A | Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1 | CNR1_HUMAN 94-301 333-413, Q9V2J8_PYRAB 1001-1196
Non-standard residues in 6kqi #1
---
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol
9GL —
5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PEG — di(hydroxyethyl)ether
> select #1:1008-1195
1434 atoms, 1456 bonds, 188 residues, 1 model selected
> delete sel
> open
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/data/docking/ec2la_pose.pdb
ec2la_pose.pdb title:
Crystal structure of human G protein coupled receptor [more info...]
Chain information for ec2la_pose.pdb #2
---
Chain | Description
A | No description available
Non-standard residues in ec2la_pose.pdb #2
---
ACE — (ACE)
NMA — (NMA)
UNK — (UNK)
29 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #2 to #1
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 6kqi, chain A (#1) with ec2la_pose.pdb, chain A (#2), sequence
alignment score = 712.2
RMSD between 263 pruned atom pairs is 0.951 angstroms; (across all 278 pairs:
1.173)
> select :OLA,OLC,PEG
89 atoms, 81 bonds, 8 residues, 1 model selected
> delete sel
> select #1 & protein
2249 atoms, 2305 bonds, 1 pseudobond, 285 residues, 2 models selected
> select ~sel & ##selected
56 atoms, 60 bonds, 2 residues, 1 model selected
> select #1 & protein
2249 atoms, 2305 bonds, 1 pseudobond, 285 residues, 2 models selected
> hide sel atoms
> select #1 & protein
2249 atoms, 2305 bonds, 1 pseudobond, 285 residues, 2 models selected
> hide sel atoms
> hide #2 models
> show #2 models
> hide #!1 models
> select #2 & protein
4613 atoms, 4674 bonds, 291 residues, 1 model selected
> hide sel atoms
> view #1
> lighting full
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #2/A:76
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:156
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
302 atoms, 303 bonds, 19 residues, 1 model selected
> select up
4613 atoms, 4674 bonds, 291 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #2/?:0@C13
1 atom, 1 residue, 1 model selected
> select #2/?:0@C11
1 atom, 1 residue, 1 model selected
> select up
51 atoms, 53 bonds, 1 residue, 1 model selected
> color sel cyan
> style sel sphere
Changed 51 atom styles
> style sel stick
Changed 51 atom styles
> color sel byhetero
> ui tool show "Side View"
> view
> select clear
> lighting full
> lighting soft
> lighting simple
> lighting soft
> save
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/image/0_image1.png
> 1500
Expected a keyword
> save image
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/image/0_image1.png
> 1500
Cannot determine format for 'image'
> save image
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/image/0_image1.png
> width 1500
Cannot determine format for 'image'
> save
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/image/0_image1.png
> width 1500
> show #!1 models
> hide #2 models
> select #1/A:1202@CAB
1 atom, 1 residue, 1 model selected
> select up
29 atoms, 32 bonds, 1 residue, 1 model selected
> select up
2305 atoms, 2365 bonds, 287 residues, 1 model selected
> select down
29 atoms, 32 bonds, 1 residue, 1 model selected
> color sel & C peru
> select #1/A:1201@CAI
1 atom, 1 residue, 1 model selected
> select #1/A:1201@CAG
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 28 bonds, 1 residue, 1 model selected
> select up
2305 atoms, 2365 bonds, 287 residues, 1 model selected
> select down
27 atoms, 28 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
2278 atoms, 2337 bonds, 1 pseudobond, 286 residues, 2 models selected
> select ~sel & ##selected
27 atoms, 28 bonds, 1 residue, 1 model selected
> color sel & C brown
> color sel byhetero
> select clear
> save
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/image/0_image2.png
> width 1500
> show #2 models
> save
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/image/0_image3.png
> width 1500
> save
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/image/0_image4.png
> width 1500
> save
> /Users/styli/Documents/Work/projects/0_redock_zara_manuscript_peter/result/image/0_image5.png
> width 1500
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15G0029KB/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 3 days, 3 hours, 41 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
P27FBA-RAGL:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 100.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
GPCR-generic-numbering-annotation: 0.2
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
pandas: 2.2.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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