![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9702 closed defect (can't reproduce)
Crash handling text input
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.5-arm64-arm-64bit
ChimeraX Version: 1.6rc202304202331 (2023-04-20 23:31:10 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 0x00000001009f0580 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 480000,
"procLaunch" : "2023-08-29 18:46:46.5094 +0800",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"procStartAbsTime" : 5559962758681,
"coalitionID" : 656,
"osVersion" : {
"train" : "macOS 12.5",
"build" : "21G72",
"releaseType" : "User"
},
"captureTime" : "2023-09-03 14:30:24.7192 +0800",
"incident" : "1F2CDD66-DC18-4EDD-B979-7B601F11052E",
"bug_type" : "309",
"pid" : 39326,
"procExitAbsTime" : 11562096572978,
"translated" : false,
"cpuType" : "ARM-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6-rc2023.04.20.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3AFED439-0FD2-5851-9C38-71652745F93E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1FE36C33-9CCF-B3F5-8006-378077B2E675",
"wakeTime" : 1370,
"sleepWakeUUID" : "8D5267D0-0684-4BC4-9C58-314B7D8E9527",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105553518919656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 105553518919656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
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"faultingThread" : 0,
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"uuid" : "1b766dc4-2490-3425-8726-45387675bc14",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7077134336,
"size" : 290816,
"uuid" : "035d23d9-4cb5-3759-9059-1f7878f89fee",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7164665856,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4046848,
"uuid" : "73d946b4-c187-3095-bc77-59ad2d0da9bc",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5054332928,
"size" : 6373376,
"uuid" : "e580e17d-2c19-39bf-bdd1-9f96d62b6172",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"sharedCache" : {
"base" : 7075676160,
"size" : 3144695808,
"uuid" : "ffede77c-d90b-366b-96f2-665c2f50ee59"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1280K 10 \nActivity Tracing 256K 1 \nCG backing stores 2176K 4 \nCG image 736K 37 \nColorSync 640K 28 \nCoreAnimation 544K 20 \nCoreGraphics 32K 2 \nCoreServices 624K 2 \nCoreUI image data 5120K 38 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.3G 399 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 464.0M 7 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 170.4M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 220.4M 443 \nVM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated)\n__AUTH 2624K 311 \n__AUTH_CONST 20.6M 511 \n__CTF 756 1 \n__DATA 23.6M 656 \n__DATA_CONST 28.0M 664 \n__DATA_DIRTY 1804K 216 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 606.6M 152 \n__OBJC_CONST 3665K 282 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 738.2M 682 \n__UNICODE 592K 1 \ndyld private memory 1024K 1 \nmapped file 530.6M 88 \nshared memory 3184K 27 \n=========== ======= ======= \nTOTAL 4.5G 4688 \nTOTAL, minus reserved VM space 3.7G 4688 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "5f72dc58705eff005a46b3a9",
"factorPackIds" : {
},
"deploymentId" : 240000015
}
],
"experiments" : [
{
"treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
"experimentId" : "64406ba83deb637ac8a04419",
"deploymentId" : 900000017
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/Fig2. AS structure and binding pocket/ligand overlap.cxs"
opened ChimeraX session
> hide #!5 models
> hide #!6 models
> select #4:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> ui tool show "Side View"
> select #4:93,234,238
32 atoms, 32 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 32 atom styles
> select add #3
50 atoms, 51 bonds, 4 residues, 3 models selected
> select add #4
2256 atoms, 2310 bonds, 1 pseudobond, 291 residues, 5 models selected
> select subtract #4
18 atoms, 19 bonds, 1 residue, 2 models selected
> style sel sphere
Changed 18 atom styles
> style sel stick
Changed 18 atom styles
> show #!6 models
> select #6/R:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/R:235
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/pocket/AS pocket.cxs"
opened ChimeraX session
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/pocket/oleamide pocket.cxs"
opened ChimeraX session
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/结构/pdb7xz5.ent"
pdb7xz5.ent title:
GPR119-GS-LPC complex [more info...]
Chain information for pdb7xz5.ent #2
---
Chain | Description | UniProt
A | guanine nucleotide-binding protein G(S) subunit α isoforms short |
B | transducin β chain 1 | GBB1_HUMAN 2-340
G | G γ-I | GBG2_HUMAN 1-71
N | NANOBODY35 |
R | soluble cytochrome B562,glucose-dependent insulinotropic receptor |
C562_ECOLX -121--17, GP119_HUMAN 1-335
Non-standard residues in pdb7xz5.ent #2
---
LSC —
(4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium
4-oxide
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> matchmaker #!2 to #1.1
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 119-oleamide receptor.pdb, chain R (#1.1) with pdb7xz5.ent, chain R
(#2), sequence alignment score = 1453.9
RMSD between 272 pruned atom pairs is 0.802 angstroms; (across all 287 pairs:
1.184)
> select add #2
16508 atoms, 16673 bonds, 3 pseudobonds, 1053 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select ligand
107 atoms, 105 bonds, 2 residues, 2 models selected
> show sel atoms
> select H
8241 atoms, 1053 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> delete sel
> select clear
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select proteins
Expected an objects specifier or a keyword
> select cartoon proteins
Expected an objects specifier or a keyword
> select cartoon
Expected an objects specifier or a keyword
> hide cartoons
> select add #1
2260 atoms, 2313 bonds, 2 pseudobonds, 290 residues, 5 models selected
> hide sel atoms
> select ligand
55 atoms, 53 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> select add #1.1/R:401@C02
1 atom, 1 bond, 1 residue, 2 models selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
3 atoms, 1 bond, 2 residues, 2 models selected
> select up
55 atoms, 53 bonds, 2 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 1 residue, 2 models selected
> color sel #f095bc
> select clear
> select #2/R:401@C35
1 atom, 1 residue, 1 model selected
> select #2/R:401@C35
1 atom, 1 residue, 1 model selected
> select #2/R:401@N32
1 atom, 1 residue, 1 model selected
> select #2/R:401@N32
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #2/R:401@O33
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #2/R:401@C21
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #2/R:401@O25
1 atom, 1 residue, 1 model selected
> select add #2/R:401@O34
2 atoms, 1 residue, 2 models selected
> select add #2/R:401@P24
3 atoms, 1 residue, 2 models selected
> color sel byelement
> select add #2/R:401@O23
4 atoms, 1 residue, 2 models selected
> select add #2/R:401@O35
5 atoms, 1 residue, 2 models selected
> color sel byelement
> select #2/R:401@O32
1 atom, 1 residue, 1 model selected
> select add #2/R:401@O19
2 atoms, 1 residue, 2 models selected
> color sel byelement
> select C2
1521 atoms, 2 bonds, 1342 residues, 2 models selected
> show sel atoms
> hide sel atoms
> undo
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 1521 atom styles
> style sel sphere
Changed 1521 atom styles
> undo
No visible atoms selected
> select #1.1/R:401@C12
1 atom, 1 residue, 1 model selected
> label (#!1.1 & sel) atoms attribute idatm_type
> select clear
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
4 atoms, 2 bonds, 2 residues, 2 models selected
> select up
55 atoms, 53 bonds, 2 residues, 4 models selected
> select C2
1521 atoms, 2 bonds, 1342 residues, 2 models selected
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color sel yellow
> select add #2/R:401@C10
1 atom, 2 bonds, 1 residue, 2 models selected
> select add #2/R:401@C9
2 atoms, 2 bonds, 1 residue, 3 models selected
> select add #1.1/R:401@C12
3 atoms, 2 bonds, 2 residues, 3 models selected
> select add #1.1/R:401@C11
4 atoms, 2 bonds, 2 residues, 4 models selected
> select subtract #2/R:401@C10
3 atoms, 1 bond, 2 residues, 4 models selected
> select clear
> select add #2/R:401@C10
1 atom, 1 residue, 1 model selected
> select add #1.1/R:401@C11
2 atoms, 2 residues, 3 models selected
> select add #1.1/R:401@C12
3 atoms, 2 residues, 4 models selected
> select add #2/R:401@C9
4 atoms, 2 residues, 4 models selected
> color sel yellow
> select clear
> show cartoons
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> transparency 70 cartoons
> transparency 80 cartoons
> select #2/R:163
7 atoms, 7 bonds, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
87 atoms, 90 bonds, 11 residues, 1 model selected
> select up
1595 atoms, 1632 bonds, 210 residues, 1 model selected
> color sel #71afe0
> select clear
> select #2/R:255
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 4 residues, 1 model selected
> select up
664 atoms, 682 bonds, 82 residues, 1 model selected
> color sel #71afe0
> select clear
> transparency 90 cartoons
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> lighting soft
> select #1.1/R:157
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
165 atoms, 171 bonds, 20 residues, 2 models selected
> select up
1582 atoms, 1619 bonds, 208 residues, 2 models selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
165 atoms, 171 bonds, 20 residues, 2 models selected
> hide cartoons sel
Expected ',' or a keyword
> hide sel cartoons
> select #2/R:157
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
147 atoms, 152 bonds, 18 residues, 1 model selected
> hide sel cartoons
> select #2/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1.1/R:86
14 atoms, 12 bonds, 2 residues, 2 models selected
> select up
532 atoms, 536 bonds, 70 residues, 3 models selected
> hide sel cartoons
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/Fig1. overall structure of oleamide-bingding
> complex/配体结构比较.tif" width 1200 height 931 supersample 3
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/Fig1. overall structure of oleamide-bingding
> complex/配体结构比较.cxs"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/Fig1. overall structure of oleamide-bingding
> complex/配体结构比较.cxs"
Log from Sun Sep 3 14:30:22 2023UCSF ChimeraX version: 1.6rc202304202331
(2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/pocket/oleamide pocket.cxs"
Log from Fri Jun 9 15:40:14 2023UCSF ChimeraX version: 1.6rc202304202331
(2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/pocket/oleamide pocket.cxs"
Log from Fri May 5 17:54:14 2023UCSF ChimeraX version: 1.6rc202304202331
(2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.cxs"
Frozen name "oleamide pocker" not restored: nothing is selected by specifier
Log from Fri May 5 17:18:04 2023UCSF ChimeraX version: 1.6rc202304202331
(2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/apo69-230410-oleamide.pdb"
Chain information for apo69-230410-oleamide.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
R | No description available
> sequence chain #1/A
Alignment identifier is 1/A
> hide surfaces
> select add #1
8196 atoms, 8359 bonds, 3 pseudobonds, 1048 residues, 2 models selected
> hide sel surfaces
[Repeated 1 time(s)]
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 8196 atom styles
> style sel ball
Changed 8196 atom styles
> style sel sphere
Changed 8196 atom styles
> hide sel atoms
> show sel cartoons
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> show sel surfaces
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select chain A
Expected an objects specifier or a keyword
> select /A
1947 atoms, 1983 bonds, 2 pseudobonds, 235 residues, 2 models selected
> select /A
1947 atoms, 1983 bonds, 2 pseudobonds, 235 residues, 2 models selected
> select /R
2260 atoms, 2313 bonds, 1 pseudobond, 290 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 1/R
> select add #1
8196 atoms, 8359 bonds, 3 pseudobonds, 1048 residues, 4 models selected
> select subtract #1
6 models selected
> select /R:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> style sel stick
Changed 9 atom styles
> show sel atoms
> undo
[Repeated 3 time(s)]
> select /R
2260 atoms, 2313 bonds, 1 pseudobond, 290 residues, 2 models selected
> color sel
> color sel pink
> ui tool show "Color Actions"
> color sel light blue
> color sel light steel blue
> color /A misty rose
> color /B misty rose
> color /B dark sea green
> color /C dark sea green
> color /C bisque
> color /D bisque
> color /G bisque
> color /N thisle
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /N Thisle
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /N Thistle
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /N Thistle
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /N old lace
> color sel thistle
[Repeated 1 time(s)]
> color /N lavender
> select add #1
8196 atoms, 8359 bonds, 3 pseudobonds, 1048 residues, 4 models selected
> select subtract #1
6 models selected
> ui tool show "Color Actions"
> color bychain
[Repeated 1 time(s)]
> color medium purple
> color dark orchid
> color magenta
> color dark slate blue
> color bychain
> color light blue
> color bychain
> set bgColor white
> help help:user/tools/coloractions.html
> save /R
Cannot determine format for '/R'
> select /R
2260 atoms, 2313 bonds, 1 pseudobond, 290 residues, 2 models selected
> color #1 #bad077ff
> color #1 #bccbe5ff
> color /R #BCCBE5
> color /A #FFD5AB
> color /B #B1D0A9
> color /C #E5CDCC
> color /N #C1BCBF
> select add #1
8196 atoms, 8359 bonds, 3 pseudobonds, 1048 residues, 4 models selected
> select subtract #1
6 models selected
> hide cartoons
> hide surfaces
[Repeated 1 time(s)]
> show surfaces
> hide cartoons
> show cartoons
> hide surfaces
> cartoon
> cartoon style xsection oval modeHelix default
> cartoon style modeHelix tube sides 20
> cartoon style xsection oval modeHelix default
> ui tool show "Selection Inspector"
> view
> ui tool show "Side View"
> view
[Repeated 1 time(s)]
> view orient
> ui tool show "Side View"
[Repeated 1 time(s)]
> view orient
> ui tool show "Side View"
[Repeated 1 time(s)]
> lighting simple
> view
> lighting soft
> color /N #b5aabd
> color /C #cf9198
> color /B #99bdbd
> color /B #509579
> color /B #c6e3d8
> color /B #99bdbd
> color /R #8d9fbb
> color /C #c8ccc1
> color /C #b5aabd
> color /A #cf9198
> color /N #d89c7c
> color /N #ecd6bc
> color /N #e7dbc
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /N #e7dbc1
> color /N #fad888
> color /N #f9d099
[Repeated 1 time(s)]
> color /N #9ab777
> color /N #d2bb7e
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> show sel surfaces
> color ligand #d2bb7e
> color /R #6378a7
> color ligand #d2bb7e
> select add #1
8196 atoms, 8359 bonds, 3 pseudobonds, 1048 residues, 3 models selected
> select subtract #1
6 models selected
> view
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> undo
[Repeated 3 time(s)]
> color ligand #d2bb7e
> view sel
> select add #1
8196 atoms, 8359 bonds, 3 pseudobonds, 1048 residues, 3 models selected
> view
> select subtract #1
6 models selected
> cartoon style xsection oval modeHelix default
> lighting simple
> lighting soft
> color /R #C1BCBF
> color /R #ffccc3
> color /R #b5aabd
> color ligand ##d2bb7e
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ligand #d2bb7e
> color /C #6378a7
> color /C #bccbe5
> color /C #d9b5ca
> color /B #95acbd
> color /A #f2d5b9
> color /C #f2d99d
> color /R #3a795e
> color /R #87b9bb
> color /R #729b8b
> color /A #c68463
> color /A #a6755a
> color /A #deb3a3
> redo
> color /R #deb3a3
> color /R #8f423b
> color /R #ce8f8b
> color /R #d29380
> color /R #e3beb4
> color /R #cf9198
> color /A #99bdbd
> color /B #b5aabd
> color /C #c8ccc1
> color /C #aabdc4
> color /R #eebabb
> color /R #f18d91
> color /R #ef9493
> color /R #d6bbc1
> color /R #ceb5b9
> color /A #aebfce
> redo
> color /C #98a1b1
> color /N #98a1b1
> color /N #f0e6e4
> color /N #b3d6ad
> color /R #ffc6d0
> color /R #edcfco
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /R #edcfc0
> color /N #c1bcbf
> color /C #ffccc3
> color /R #e5cdcc
> color /R #9ec4b2
> color ligand #d16d74
> redo
> undo
> redo
[Repeated 8 time(s)]
> undo
[Repeated 1 time(s)]
> redo
[Repeated 2 time(s)]
> undo
[Repeated 9 time(s)]
> redo
[Repeated 6 time(s)]
> color /B #aac078
> color /B #b1d0a9
> lighting simple
> lighting soft
> lighting full
> lighting flat
> show surfaces
> hide surfaces
> color ligand #edc39a
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel surfaces
> color /R #f2a7a0
> color /R #f2a0a0
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> select /A:13
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /R:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> undo
> select /R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /R:37
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /R:181
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel surfaces
> undo
> hide sel surfaces
> hbonds sel reveal true
0 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
0 hydrogen bonds found
> style sel stick
Changed 9 atom styles
> hide sel surfaces
> show sel surfaces
> undo
[Repeated 1 time(s)]
> hide sel surfaces
> hbonds sel reveal true
0 hydrogen bonds found
> undo
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> hide sel surfaces
> undo
> ~hbonds
> hbonds sel reveal true
1 hydrogen bonds found
> style sel stick
Changed 20 atom styles
> ~hbonds
> undo
[Repeated 3 time(s)]
> contacts sel select true makePseudobonds false
1 contacts
> show sel surfaces
> select /R
2260 atoms, 2313 bonds, 1 pseudobond, 290 residues, 2 models selected
> contacts sel select true makePseudobonds false
1459 contacts
> show sel surfaces
> undo
[Repeated 2 time(s)]
> hide sel surfaces
[Repeated 1 time(s)]
> undo
[Repeated 4 time(s)]
> hide sel surfaces
> select /R
2260 atoms, 2313 bonds, 1 pseudobond, 290 residues, 2 models selected
> hide sel surfaces
> style sel stick
Changed 2260 atom styles
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> contacts sel select true makePseudobonds false
48 contacts
> hide sel cartoons
> show sel atoms
> undo
[Repeated 2 time(s)]
> transparency 75
> undo
> transparency /R 75
> transparency cartoon /R 75
Missing or invalid "percent" argument: Expected a number
> transparency /R 100
> transparency /R 25
> undo
[Repeated 3 time(s)]
> hbonds sel reveal true
5 hydrogen bonds found
> ~hbonds
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> ui tool show "Check Waters"
> hbonds interModel false reveal true restrict any name "water H-bonds"
917 hydrogen bonds found
> ~select
Nothing selected
> help help:user/preferences.html#startup
> ~hbonds
> undo
[Repeated 1 time(s)]
> ~hbonds
> select /R
2260 atoms, 2313 bonds, 251 pseudobonds, 290 residues, 3 models selected
> ~hbonds
[Repeated 1 time(s)]
> undo
Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> redo
> undo
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select /R
2260 atoms, 2313 bonds, 251 pseudobonds, 290 residues, 3 models selected
> ~hbonds
> hbonds sel reveal true
255 hydrogen bonds found
> ~hbonds
> ui tool show Contacts
> contacts ignoreHiddenModels true
4351 contacts
> select add #1
8196 atoms, 8359 bonds, 5271 pseudobonds, 1048 residues, 6 models selected
> select subtract #1
6 models selected
> undo
[Repeated 1 time(s)]
> select add #1
8196 atoms, 8359 bonds, 5271 pseudobonds, 1048 residues, 6 models selected
> select subtract #1
6 models selected
> undo
[Repeated 2 time(s)]
> redo
[Repeated 2 time(s)]
> hbonds reveal true
917 hydrogen bonds found
> select add #1
8196 atoms, 8359 bonds, 6188 pseudobonds, 1048 residues, 5 models selected
> ~hbonds
[Repeated 1 time(s)]
> hbonds sel reveal true
917 hydrogen bonds found
> ~hbonds
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> hide target m
[Repeated 1 time(s)]
> show target m
> select sideonly
3987 atoms, 3151 bonds, 1890 pseudobonds, 979 residues, 3 models selected
> undo
> select backbone
4189 atoms, 4181 bonds, 1551 pseudobonds, 1047 residues, 4 models selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select add #1
8196 atoms, 8359 bonds, 5271 pseudobonds, 1048 residues, 9 models selected
> select subtract #1
6 models selected
> ~hbonds
[Repeated 1 time(s)]
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select hbond
Expected an objects specifier or a keyword
> select hbonds
Nothing selected
> ~hbonds
> contacts sel select true makePseudobonds false
No atoms match given atom specifier
> contacts sel distanceOnly 4.0 select true makePseudobonds false
No atoms match given atom specifier
> select /R
2260 atoms, 2313 bonds, 1650 pseudobonds, 290 residues, 4 models selected
> contacts sel select true makePseudobonds false
1459 contacts
> hide sel cartoons
> hide sel atoms
> undo
[Repeated 2 time(s)]Undo failed, probably because structures have been
modified.
> ui tool show Contacts
> hide contacts
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide contact
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select clear
> hide atoms
> show cartoons
> show ligand
> rlab ligand
Unknown command: rlab ligand
> label ligand
> undo
> show ligand
> unlab ligand
Unknown command: unlab ligand
> ~label ligand
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> show sel surfaces
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/apo-119-TM(1).mrc"
Opened apo-119-TM(1).mrc as #2, grid size 280,280,280, pixel 0.851, shown at
level 0.00515, step 2, values float32
> hide #!1 models
> hide #!2 models
> show #!2 models
> ui tool show "Show Volume Menu"
> volume #2 level 0.01357
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/apo119-267post.mrc"
Opened apo119-267post.mrc as #3, grid size 280,280,280, pixel 0.851, shown at
level 0.0142, step 2, values float32
> volume #3 level 0.01733
> hide #!2 models
> volume #3 level 0.02494
> volume #3 level 0.02404
> volume #3 level 0.02091
> hide #!3 models
> show #!1 models
> hide sel cartoons
> hide sel atoms
> transparency ligand 0
> hbonds sel reveal true
1 hydrogen bonds found
> show sel atoms
> undo
> ~hbonds
> hide sel atoms
> hbonds sel reveal true
1 hydrogen bonds found
> hide sel atoms
> select /R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel cartoons
> select /R:261
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> ~select
Nothing selected
> view
[Repeated 3 time(s)]
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> color ligand #5abf9a
> color ligand #54bfb5
> color ligand #d9ab82
> color ligand #edcc86
> color /C #a9b76b
> color /C #9ab077
> color /C #256b48
> color /C #6a9949
> lighting soft
> lighting flat
> view
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/overall oleamide bond to GPR119-Gs complex.tif" width 864 height
> 723 supersample 3
> view
[Repeated 2 time(s)]
> ui tool show "Side View"
> view
[Repeated 3 time(s)]
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overall.tif" width 864 height 723 supersample 3
> set bgColor black
> lighting soft
> set bgColor white
> lighting flat
> view
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overall.png" width 864 height 723 supersample 3
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> view
> lighting simple
> lighting soft
> view
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overal.pdb"
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overal.pdb"
Chain information for oleamide overal.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
R | No description available
> hide #!1 models
> hide #!4 models
> show #!1 models
> show #!4 models
> hide #!4 models
> lighting flat
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/ol.tif" width 864 height 723 supersample 3
> view
[Repeated 1 time(s)]
> lighting soft
> lighting flat
> view
[Repeated 1 time(s)]
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide.png" width 1434 height 1200 supersample 3
> transparentBackground true
> view
[Repeated 1 time(s)]
> lighting soft
> lighting flat
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overall.tif" width 2100 height 1757 supersample 3
> transparentBackground true
> hide #!1 models
> hide #!4 target m
> log metadata #4
No models had metadata
> log chains #4
Chain information for oleamide overal.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
R | No description available
> close session
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overal.pdb" format pdb
No such file/path: /Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
AS+oleamide/作图/oleamide overal.pdb
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/apo119-267post.mrc" format mrc
Opened apo119-267post.mrc as #1, grid size 280,280,280, pixel 0.851, shown at
level 0.0142, step 2, values float32
> volume #1 level 0.02807
> volume #1 level 0.01957
> volume #1 level -0.006832
> volume #1 level 0.001669
> volume #1 level 0.01599
> volume #1 level 0.02628
> volume #1 level 0.01957
> close session
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/apo69-230410-oleamide.pdb" format pdb
Chain information for apo69-230410-oleamide.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
R | No description available
> hide #!1 models
> show #!1 models
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/apo119-267post.mrc"
Opened apo119-267post.mrc as #2, grid size 280,280,280, pixel 0.851, shown at
level 0.0142, step 2, values float32
> ui tool show Matchmaker
> ui tool show "Surface Color"
> color radial #2.1 palette #ff0000:#ffffff:#0000ff
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.02046
> ui tool show "Color Zone"
> ui tool show "Fit to Segments"
Density map not found or not selected
[Repeated 2 time(s)]
> ui tool show "Volume Viewer"
> lighting soft
> lighting full
> lighting flat
> volume #2 level 0.0227
> hide #!2 models
> show #!1 models
> hide surfaces
> style stick
Changed 8196 atom styles
> hide cartoons
> show cartoons
> hide atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 1/R
> select
> /R:6-35,39-65,75-108,110-116,119-142,163-209,222-235,239-250,254-281,284-299
1833 atoms, 1863 bonds, 239 residues, 1 model selected
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> show sel surfaces
> fecth by ID 7WCN
Unknown command: fecth by ID 7WCN
> fecth 7WCN
Unknown command: fecth 7WCN
> fetch 7WCN
Unknown command: fetch 7WCN
> fetch by id 7WCN
Unknown command: fetch by id 7WCN
> open 7WCN
Cannot open '7WCN': Remote end closed connection without response
> open 7wcn
Cannot open '7wcn': Remote end closed connection without response
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/pdb7wcn (1).ent"
pdb7wcn (1).ent title:
Cryo-em structure of GPR119-GS complex with small molecule agonist AR231453
[more info...]
Chain information for pdb7wcn (1).ent #3
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394
B | transducin β chain 1 | GBB1_HUMAN 13-351
C | G γ-I | GBG2_HUMAN 1-71
N | NB35 |
R | G-protein coupled receptor 119 | GP119_HUMAN 1-335
Non-standard residues in pdb7wcn (1).ent #3
---
8WL — N-(2-fluoranyl-4-methylsulfonyl-
phenyl)-5-nitro-6-[4-(3-propan-2-yl-1,2,4-oxadiazol-5-yl)piperidin-1-yl]pyrimidin-4-amine
(AR231453)
> hide #!1 models
> hide #!3 surfaces
[Repeated 1 time(s)]
> hide #!3 atoms
> show #!3 cartoons
> ui tool show Matchmaker
> matchmaker #!3 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 apo69-230410-oleamide.pdb, chain B (#1) with pdb7wcn (1).ent, chain
B (#3), sequence alignment score = 1722.5
RMSD between 337 pruned atom pairs is 0.373 angstroms; (across all 339 pairs:
0.408)
> show #!1 models
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> hide sel surfaces
> show sel atoms
> hide #!1 models
> select
> #1/R:6-35,39-65,75-108,110-116,119-142,163-209,222-235,239-250,254-281,284-299
1833 atoms, 1863 bonds, 239 residues, 1 model selected
> select #1/R:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select #1/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/R
Alignment identifier is 3/R
> select #3/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> style sel ball
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> ui tool show Rotamers
> swapaa interactive sel PHE rotLib Dunbrack
pdb7wcn (1).ent #3/R VAL 85: phi -62.6, psi -44.9 trans
Changed 162 bond radii
> show #!1 models
> hide #!3 models
> select #1/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> open 7wcn
Cannot open '7wcn': Remote end closed connection without response
> swapaa interactive sel PHE rotLib Dunbrack
apo69-230410-oleamide.pdb #1/R VAL 85: phi -60.7, psi -38.9 trans
Changed 162 bond radii
> hide #!1 models
> show #!3 models
> select #3/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel PHE rotLib Dunbrack
pdb7wcn (1).ent #3/R VAL 85: phi -62.6, psi -44.9 trans
Changed 162 bond radii
> select sel @< 5
278 atoms, 265 bonds, 46 residues, 20 models selected
> select sel @< 5
441 atoms, 404 bonds, 81 residues, 2 models selected
> undo
[Repeated 1 time(s)]Undo failed, probably because structures have been
modified.
> select clear
> select #3/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel @< 5
116 atoms, 103 bonds, 28 residues, 2 models selected
> undo
[Repeated 1 time(s)]
> select #3/R:6-36,38-66,74-116,118-143,163-210,222-250,255-280,283-300
1915 atoms, 1948 bonds, 250 residues, 1 model selected
> select clear
> select #3/R:113-114
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/R:113-114
20 atoms, 20 bonds, 2 residues, 1 model selected
> undo
> select clear
> select #3/R:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/R:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/R:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/R:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> mlp sel
Map values for surface "pdb7wcn (1).ent_R SES surface": minimum -27.76, mean
0.4888, maximum 23.39
To also show corresponding color key, enter the above mlp command and add key
true
> undo
[Repeated 1 time(s)]
> hide sel surfaces
> ui tool show Rotamers
> open 7wcn
Cannot open '7wcn': Remote end closed connection without response
> swapaa interactive sel MET rotLib Dunbrack
pdb7wcn (1).ent #3/R LEU 11: phi -64.6, psi -42.7 trans
Changed 135 bond radii
> style sel stick
Changed 8 atom styles
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> select sel @< 4
2435 atoms, 186 bonds, 328 residues, 29 models selected
> undo
> swapaa #!3/R:11 MET criteria 1 rotLib Dunbrack
Using Dunbrack library
pdb7wcn (1).ent #!3/R LEU 11: phi -64.6, psi -42.7 trans
Applying MET rotamer (chi angles: -69.1 174.7 69.8) to pdb7wcn (1).ent #!3/R
MET 11
> hbonds sel reveal true
3 hydrogen bonds found
> ~hbonds
> mlp sel
Map values for surface "pdb7wcn (1).ent_R SES surface": minimum -27.76, mean
0.5471, maximum 23.39
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for pdb7wcn (1).ent_R SES surface #3.2: minimum, -11.95, mean
0.92, maximum 15.92
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
> hide sel surfaces
> rainbow sel
> color sel byhetero
[Repeated 1 time(s)]
> coulombic sel
Coulombic values for pdb7wcn (1).ent_R SES surface #3.2: minimum, -11.95, mean
0.92, maximum 15.92
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color (#!3 & sel) byelement
> undo
[Repeated 3 time(s)]
> redo
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> redo
> undo
[Repeated 6 time(s)]
> ui tool show Rotamers
> swapaa interactive sel LEU rotLib Dunbrack
pdb7wcn (1).ent #3/R MET 11: phi -64.6, psi -42.7 trans
Changed 45 bond radii
> swapaa #!3/R:11 LEU criteria 1 rotLib Dunbrack
Using Dunbrack library
pdb7wcn (1).ent #!3/R MET 11: phi -64.6, psi -42.7 trans
Applying LEU rotamer (chi angles: -69.2 172.7) to pdb7wcn (1).ent #!3/R LEU 11
> hide sel surfaces
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> style sel ball
Changed 4 atom styles
> select #3/R:60-61
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/R:60-61
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/R:6-36,38-66,74-116,118-143,163-210,222-250,255-280,283-300
1915 atoms, 1948 bonds, 250 residues, 1 model selected
> select #3/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!3 models
> show #!1 models
> select #3/R:6-36,38-66,74-116,118-143,163-210,222-250,255-280,283-300
1915 atoms, 1948 bonds, 250 residues, 1 model selected
> select #3/R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!3 models
> hide #!1 models
> show sel surfaces
> mlp sel
Map values for surface "pdb7wcn (1).ent_R SES surface": minimum -27.76, mean
0.5646, maximum 23.39
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> show sel atoms
> style sel stick
Changed 9 atom styles
> color (#!3 & sel) byelement
> ui tool show Rotamers
> swapaa interactive sel LEU rotLib Dunbrack
pdb7wcn (1).ent #3/R GLN 65: phi -62.8, psi -39.9 trans
Changed 45 bond radii
> swapaa #!3/R:65 LEU criteria 1 rotLib Dunbrack
Using Dunbrack library
pdb7wcn (1).ent #!3/R GLN 65: phi -62.8, psi -39.9 trans
Applying LEU rotamer (chi angles: -69.2 172.7) to pdb7wcn (1).ent #!3/R LEU 65
> undo
Undo failed, probably because structures have been modified.
> show sel surfaces
> hide sel surfaces
> select #3/R:6-36,38-66,74-116,118-143,163-210,222-250,255-280,283-300
1914 atoms, 1947 bonds, 250 residues, 1 model selected
> select #3/R:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/R:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel surfaces
> show #!1 models
> hide #!3 models
> select #1/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!3 models
> hide #!1 models
> hide #!3 surfaces
> hide #!3 models
> show #!1 models
> show sel atoms
> color sel byelement
> select #1/R:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for apo69-230410-oleamide.pdb_R SES surface #1.3: minimum,
-13.84, mean 1.37, maximum 20.16
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> hide sel surfaces
> color (#!1 & sel) byelement
> select #1/R:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:93-94
15 atoms, 14 bonds, 2 residues, 1 model selected
> select
> #1/R:6-35,39-65,75-108,110-116,119-142,163-209,222-235,239-250,254-281,284-299
1833 atoms, 1863 bonds, 239 residues, 1 model selected
> select #1/R:93-94
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/R:93-94
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/R:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byelement
> select #1/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byelement
> lighting soft
> set bgColor white
Mismatch between Cocoa '\x0' and Carbon 'n' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'N' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'n' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'N' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02dc' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02dc' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '~' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02dc' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select clear
> hide #!1 cartoons
> show #!1 cartoons
> hide #!1 atoms
> color /N #c1bcbf
> color /A #ffccc3
> color /B #b1d0a9
> color /C #99bdbd
> color /B #509579
> color /A #cf9198
> color /A #d86967
> color /A #eebabb
> color /R #eebabb
> color /A #58539f
> color /A #b3a2c7
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> lighting simple
> lighting flat
> view
[Repeated 1 time(s)]
> lighting soft
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color /A #92c2dd
> color /A #cedfef
> color /A #6eb1de
> color /A #bccbe5
> lighting flat
> color /C #94bbab
> lighting soft
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> show sel & #!1 surfaces
> color ligand #639ccf
> select clear
> lighting flat
> view
[Repeated 1 time(s)]
> lighting soft
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide-overall.tif" width 1208 height 723 supersample 3
> transparentBackground true
> color B #b2d3b7
> color C #a5ccbe
> color /C #a5ccbe
> color /C #9aae8f
> color /B #a8c3b5
> color /B #bad077
> view
> lighting flat
> lighting soft
> cartoon style #1 xsection oval modeHelix default
> cartoon style #1 modeHelix tube sides 20
> cartoon style (#1 & coil) xsection oval
> cartoon style #1 xsection barbell modeHelix default
> undo
[Repeated 1 time(s)]
> cartoon style #1 xsection oval modeHelix default
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> undo
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> show tool
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~hide tool
Unknown command: ~hide tool
> ~hide tool bar
Unknown command: ~hide tool bar
> cartoon style #1 xsection oval modeHelix default
> ui tool show Toolbar
> view
> lighting flat
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> show #!1 surfaces
> style #!1 sphere
Changed 8196 atom styles
> hide #!1 surfaces
> show #!1 atoms
> style #!1 sphere
Changed 8196 atom styles
> style #!1 stick
Changed 8196 atom styles
> style #!1 sphere
Changed 8196 atom styles
> style #!1 ball
Changed 8196 atom styles
> hide #!1 cartoons
> style #!1 stick
Changed 8196 atom styles
> hide #!1 atoms
> show #!1 surfaces
> show #!1 cartoons
> hide #!1 surfaces
> view
> view orient
[Repeated 1 time(s)]
> ui tool show "Side View"
> lighting soft
> view
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lightning soft 100
Unknown command: lightning soft 100
> lightning 100
Unknown command: lightning 100
> lightning soft 10
Unknown command: lightning soft 10
> show ligand
> show surfaces ligand
Expected ',' or a keyword
> show ligand surfaces
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> view
> color /R ad9cc2
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /R #ad9cc2
> color ligand #e1a08b
> set bgColor white
> view
[Repeated 1 time(s)]
> lighting soft
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide-overall.tif" width 828 height 723 supersample 3
> color /C #a5ccbe
> color /C #94bbab
> help help:user/preferences.html#startup
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> hide sel & #!1 surfaces
> style sel & #!1 sphere
Changed 20 atom styles
> undo
> style sel & #!1 ball
Changed 20 atom styles
> show sel & #!1 surfaces
> style sel & #!1 sphere
Changed 20 atom styles
> hide sel & #!1 surfaces
> show sel & #!1 surfaces
> style sel & #!1 sphere
Changed 20 atom styles
> style sel & #!1 stick
Changed 20 atom styles
> style sel & #!1 ball
Changed 20 atom styles
> hide sel & #!1 surfaces
> style sel & #!1 sphere
Changed 20 atom styles
> hide sel & #!1 surfaces
> show sel & #!1 surfaces
> hide sel & #!1 atoms
> show sel & #!1 atoms
> style sel & #!1 stick
Changed 20 atom styles
> style sel & #!1 sphere
Changed 20 atom styles
> hide sel & #!1 surfaces
> show sel & #!1 surfaces
> select clear
> view
> lighting soft
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide-overall.positions"
Must specify models when saving positions file /Users/scarlettzhang/杂事/Ye
Lab/GPCR interaction/写文章/GPR119 AS+oleamide/作图/oleamide-overall.positions.
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overall.tif" width 2000 height 1746 supersample 3
> view
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overall.tif" width 828 height 723 supersample 3
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overall.positions"
Must specify models when saving positions file /Users/scarlettzhang/杂事/Ye
Lab/GPCR interaction/写文章/GPR119 AS+oleamide/作图/oleamide overall.positions.
> hide /A
> hide ribbons /A
Expected ',' or a keyword
> hide cartoons /A
Expected ',' or a keyword
> hide atoms /A
Expected ',' or a keyword
> hide atoms /A
Expected ',' or a keyword
> ui windowfill toggle
[Repeated 1 time(s)]
> hide /A atoms
> hide /A
> hide /B
> select /B
5194 atoms, 5288 bonds, 678 residues, 2 models selected
> hide sel & #!1 cartoons
> select /A
3894 atoms, 3966 bonds, 4 pseudobonds, 470 residues, 4 models selected
> hide sel & #!1 cartoons
> select /C
872 atoms, 884 bonds, 113 residues, 2 models selected
> hide sel & #!1 cartoons
> select /N
1953 atoms, 1995 bonds, 257 residues, 2 models selected
> hide sel & #!1 surfaces
[Repeated 1 time(s)]
> hide sel & #!1 cartoons
> select /R
4534 atoms, 4645 bonds, 2 pseudobonds, 580 residues, 4 models selected
> show sel & #!1 surfaces
> hide sel & #!1 surfaces
> style sel & #!1 stick
Changed 2260 atom styles
> show sel & #!1 surfaces
> select LIGAND
Expected an objects specifier or a keyword
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> hide sel & #!1 surfaces
> style sel & #!1 ball
Changed 20 atom styles
> select clear
> show #!1 cartoons
> undo
> hide #!1 surfaces
> undo
> show #!1 surfaces
> mlp #!1
Map values for surface "apo69-230410-oleamide.pdb_A SES surface": minimum
-31.11, mean -4.751, maximum 24.95
Map values for surface "apo69-230410-oleamide.pdb_B SES surface": minimum
-28.36, mean -5.482, maximum 22.35
Map values for surface "apo69-230410-oleamide.pdb_C SES surface": minimum
-27.02, mean -3.591, maximum 22.72
Map values for surface "apo69-230410-oleamide.pdb_N SES surface": minimum
-28.42, mean -6.856, maximum 22.41
Map values for surface "apo69-230410-oleamide.pdb_R SES surface": minimum
-28.75, mean 0.6277, maximum 26.33
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!1
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
apo69-230410-oleamide.pdb #1/B ARG 140
apo69-230410-oleamide.pdb #1/B GLU 141
apo69-230410-oleamide.pdb #1/B GLU 183
apo69-230410-oleamide.pdb #1/B GLU 226
apo69-230410-oleamide.pdb #1/C ILE 9
apo69-230410-oleamide.pdb #1/N ASP 106
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for apo69-230410-oleamide.pdb_A SES surface #1.4: minimum,
-15.87, mean 0.15, maximum 13.78
Coulombic values for apo69-230410-oleamide.pdb_B SES surface #1.5: minimum,
-18.01, mean -1.42, maximum 9.77
Coulombic values for apo69-230410-oleamide.pdb_C SES surface #1.6: minimum,
-12.27, mean -0.61, maximum 12.44
Coulombic values for apo69-230410-oleamide.pdb_N SES surface #1.7: minimum,
-8.15, mean 1.27, maximum 9.97
Coulombic values for apo69-230410-oleamide.pdb_R SES surface #1.3: minimum,
-13.84, mean 1.37, maximum 20.16
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp #!1
Map values for surface "apo69-230410-oleamide.pdb_A SES surface": minimum
-31.11, mean -4.751, maximum 24.95
Map values for surface "apo69-230410-oleamide.pdb_B SES surface": minimum
-28.36, mean -5.482, maximum 22.35
Map values for surface "apo69-230410-oleamide.pdb_C SES surface": minimum
-27.02, mean -3.591, maximum 22.72
Map values for surface "apo69-230410-oleamide.pdb_N SES surface": minimum
-28.42, mean -6.856, maximum 22.41
Map values for surface "apo69-230410-oleamide.pdb_R SES surface": minimum
-28.75, mean 0.6277, maximum 26.33
To also show corresponding color key, enter the above mlp command and add key
true
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> style sel & #!1 stick
Changed 20 atom styles
> hide sel & #!1 surfaces
> undo
[Repeated 6 time(s)]
> view
> show #!1 cartoons
> hide #!1 atoms
> hide #!1 surfaces
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> style sel & #!1 sphere
Changed 20 atom styles
> select clear
> view
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide-overall.tif" width 2100 height 1834 supersample 3
> transparentBackground true
> hide all
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> style sel & #!1 stick
Changed 20 atom styles
> style sel & #!1 ball
Changed 20 atom styles
> style sel & #!1 stick
Changed 20 atom styles
> select /R
4534 atoms, 4645 bonds, 2 pseudobonds, 580 residues, 4 models selected
> select /A, /B
Expected an objects specifier or a keyword
> select /A&/B
Nothing selected
> select /A
3894 atoms, 3966 bonds, 4 pseudobonds, 470 residues, 4 models selected
> hide sel & #!1 cartoons
> select /B
5194 atoms, 5288 bonds, 678 residues, 2 models selected
> hide sel & #!1 cartoons
> select /C
872 atoms, 884 bonds, 113 residues, 2 models selected
> hide sel & #!1 cartoons
> select /N
1953 atoms, 1995 bonds, 257 residues, 2 models selected
> hide sel & #!1 cartoons
> transparency 75
> select clear
> transparency 75
> transparency ribbon 75
Missing or invalid "percent" argument: Expected a number
> transparency 75 ribbons
> transparency 780 ribbons
> transparency 80 ribbons
> transparency 50 ribbons
> transparency 60 ribbons
> transparency 70 ribbons
> transparency 00 atoms
> transparency 0 atoms
> transparency 75 ribbons
> select clear
> transparency 75 ribbons
> transparency 85 ribbons
> transparency 80 ribbons
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> color (#!1 & sel) byelement
> select N
2860 atoms, 2098 residues, 2 models selected
> select #1/R:401@N03
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select clear
> color sel byelement
> select #1/R:401@O01
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select clear
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> contacts sel select true makePseudobonds false
433 contacts
> show sel & #!1 atoms
> select clear
[Repeated 1 time(s)]
> undo
[Repeated 4 time(s)]
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> contacts sel select true makePseudobonds false
433 contacts
> hide sel & #!1 atoms
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select #3/R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/R:60-61
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/R:60-61
12 atoms, 11 bonds, 2 residues, 1 model selected
> select clear
> select #3/R:6-36,38-66,74-116,118-143,163-210,222-250,255-280,283-300
1914 atoms, 1947 bonds, 250 residues, 1 model selected
> select #3/R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #!1 atoms
> undo
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> contacts sel select true makePseudobonds false
433 contacts
> select /R:61
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:82
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:885
Nothing selected
> select /R:85
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:86
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:89
10 atoms, 8 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:93
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:94
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:90
10 atoms, 8 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select /R:157
22 atoms, 22 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:169
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:173
8 atoms, 6 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
[Repeated 3 time(s)]
> select /R:238
28 atoms, 30 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:261
18 atoms, 16 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:265
28 atoms, 30 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:156
12 atoms, 10 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> transparency 80 ribbons
> transparency 90 ribbons
> transparency 88 ribbons
> transparency 85 ribbons
> select clear
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> hbonds sel & #!1 reveal true
1 hydrogen bonds found
> select clear
> select /R:7,61
38 atoms, 36 bonds, 4 residues, 2 models selected
> select /R:7,61,85,82,86,89,93,94,157,169,173,238,261,265,82,90,156
264 atoms, 252 bonds, 32 residues, 2 models selected
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> name frozen "oleamide pocker" sel
Not registering illegal selector name "oleamide pocker"
> select oleamide pocket
Expected an objects specifier or a keyword
> select oleamide pocker
Expected an objects specifier or a keyword
> select “oleamide pocker”
Expected an objects specifier or a keyword
> select /R:7,61,85,82,86,89,93,94,157,169,173,238,261,265,82,90,156
264 atoms, 252 bonds, 32 residues, 2 models selected
> sym sel
apo69-230410-oleamide.pdb mmCIF Assemblies
---
pdb7wcn (1).ent mmCIF Assemblies
---
> sym sel copies
Missing "copies" keyword's argument
> copy sel
Unknown command: copy sel
> save sel
Cannot determine format for 'sel'
> name sel “olpocket”
"sel" is reserved and cannot be redefined
> unfrozen sel
Unknown command: unfrozen sel
> name sel pocket
"sel" is reserved and cannot be redefined
> name unfrozen sel
> name sel olpocket
"sel" is reserved and cannot be redefined
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label (#!1 & sel) attribute label_specifier
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> label (#!1 & sel) text "{0.label_one_letter_code} {0.number}
Invalid "text" argument: Expected 'default' or a text string
> label (#!1 & sel) text "{0.label_one_letter_code} {0.number}"
> select #1/R:261@OE2
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select #1/R:156@OG
1 atom, 1 residue, 1 model selected
> color sel by element
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel byelement
> select #1/R:261@OE1
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #1/R:82@SD
1 atom, 1 residue, 1 model selected
> color sel byelement
> view
> select #1/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byelement
> view
> ui tool show "Side View"
> view
> view sel
> ui tool show "Side View"
> view
> select clear
> view
> ui tool show "Side View"
> view
[Repeated 1 time(s)]
> select #1/R:86@OG1
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #1/R:173
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select clear
> select #1/R:173@O
1 atom, 1 residue, 1 model selected
> color sel byelement
> select clear
> mlp #!1
Map values for surface "apo69-230410-oleamide.pdb_A SES surface": minimum
-31.11, mean -4.751, maximum 24.95
Map values for surface "apo69-230410-oleamide.pdb_B SES surface": minimum
-28.36, mean -5.482, maximum 22.35
Map values for surface "apo69-230410-oleamide.pdb_C SES surface": minimum
-27.02, mean -3.591, maximum 22.72
Map values for surface "apo69-230410-oleamide.pdb_N SES surface": minimum
-28.42, mean -6.856, maximum 22.41
Map values for surface "apo69-230410-oleamide.pdb_R SES surface": minimum
-28.75, mean 0.6277, maximum 26.33
To also show corresponding color key, enter the above mlp command and add key
true
> mlp #!1
Map values for surface "apo69-230410-oleamide.pdb_A SES surface": minimum
-31.11, mean -4.751, maximum 24.95
Map values for surface "apo69-230410-oleamide.pdb_B SES surface": minimum
-28.36, mean -5.482, maximum 22.35
Map values for surface "apo69-230410-oleamide.pdb_C SES surface": minimum
-27.02, mean -3.591, maximum 22.72
Map values for surface "apo69-230410-oleamide.pdb_N SES surface": minimum
-28.42, mean -6.856, maximum 22.41
Map values for surface "apo69-230410-oleamide.pdb_R SES surface": minimum
-28.75, mean 0.6277, maximum 26.33
To also show corresponding color key, enter the above mlp command and add key
true
> undo
[Repeated 2 time(s)]
> hide sel surfaces
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> undo
> select /R
4534 atoms, 4645 bonds, 3 pseudobonds, 580 residues, 5 models selected
> hide sel & #!1 surfaces
> select clear
> hide surfaces
> color sel byelement
> view
> select clear
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select /R：262
Expected an objects specifier or a keyword
> select /R:262
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> undo
> select /R:265
28 atoms, 30 bonds, 2 residues, 2 models selected
> select /R:65
17 atoms, 15 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> show sel & #!1 surfaces
> hide sel & #!1 surfaces
> mlp sel & #!1
Map values for surface "apo69-230410-oleamide.pdb_R SES surface": minimum
-28.75, mean 0.6277, maximum 26.33
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel & #!1 surfaces
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> undo
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> hbonds sel & #!1 reveal true
0 hydrogen bonds found
> hbonds sel & #!1 reveal true
0 hydrogen bonds found
> select clear
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> hbonds sel & #!1 reveal true
1 hydrogen bonds found
> ~hbonds
> hbonds sel & #!1 reveal true
1 hydrogen bonds found
> select #1/R:65@NE2
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select #1/R:65@OE1
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select clear
> select /R:262
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select clear
> select #1/R:262@NH2
1 atom, 1 residue, 1 model selected
> select /R:262
22 atoms, 20 bonds, 2 residues, 2 models selected
> color (#!1 & sel) byelement
> undo
> select clear
> select #1/R:262@NH2
1 atom, 1 residue, 1 model selected
> select #1/R:262@NH1
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select #1/R:262@NH2
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select #1/R:262@NE
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select clear
> select /R:257
24 atoms, 24 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select clear
> select #1/R:257@OH
1 atom, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select clear
> label #1,4 text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> undo
> redo
> undo
[Repeated 1 time(s)]
> ~label #1,4 text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label delete #1,4 text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> ~label #1,4
> hide sel atoms
[Repeated 1 time(s)]
> select /R:257
24 atoms, 24 bonds, 2 residues, 2 models selected
> hide sel & #!1 atoms
> select /R:165
22 atoms, 22 bonds, 2 residues, 2 models selected
> select /R:158
22 atoms, 22 bonds, 2 residues, 2 models selected
> select /R:156
12 atoms, 10 bonds, 2 residues, 2 models selected
> select /R:157
22 atoms, 22 bonds, 2 residues, 2 models selected
> select /R:158
22 atoms, 22 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:174
22 atoms, 22 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:146
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/R:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /R:85
14 atoms, 12 bonds, 2 residues, 2 models selected
> select /R:89
10 atoms, 8 bonds, 2 residues, 2 models selected
> select /R:262
22 atoms, 20 bonds, 2 residues, 2 models selected
> select /R:256
16 atoms, 14 bonds, 2 residues, 2 models selected
> select /R:156
12 atoms, 10 bonds, 2 residues, 2 models selected
> select /R:158
22 atoms, 22 bonds, 2 residues, 2 models selected
> select /R:157
22 atoms, 22 bonds, 2 residues, 2 models selected
> select /R:65
17 atoms, 15 bonds, 2 residues, 2 models selected
> select catoons
Expected an objects specifier or a keyword
> select sticks
Expected an objects specifier or a keyword
> select stick
Expected an objects specifier or a keyword
> select ligand
55 atoms, 57 bonds, 2 residues, 2 models selected
> style sel & #!1 ball
Changed 20 atom styles
> style sel & #!1 stick
Changed 20 atom styles
> select clear
[Repeated 2 time(s)]
> select #1/R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/R:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/R:61
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #1/R:83
22 atoms, 19 bonds, 3 residues, 2 models selected
> select #1/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:64
16 atoms, 14 bonds, 2 residues, 2 models selected
> select clear
> select #1/R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:83
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #1/R:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:137
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/R:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:90
5 atoms, 4 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
[Repeated 1 time(s)]
> select #1/R:174
11 atoms, 11 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:169
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:158
11 atoms, 11 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:261
9 atoms, 8 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:157@CG
1 atom, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:79
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:86
7 atoms, 6 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:238
14 atoms, 15 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:265
14 atoms, 15 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:262
11 atoms, 10 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/R:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
> select #1/R:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> ui mousemode right "mark surface"
> ui mousemode right "mark center"
> select #1/R:164
10 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right "mark center"
> ui mousemode right "mark point"
> ui mousemode right "mark center"
> marker #5 position 124.5,114.4,159.2 color yellow radius 1
> undo
[Repeated 1 time(s)]
> ui mousemode right "mark maximum"
> ui mousemode right "mark plane"
> ui mousemode right "mark surface"
> ui mousemode right "mark center"
> ui mousemode right "mark point"
> ui mousemode right "link markers"
> ui mousemode right "move markers"
> ui mousemode right "resize markers"
> ui mousemode right "move markers"
> ui mousemode right "delete markers"
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 8193 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> undo
[Repeated 1 time(s)]
> redo
[Repeated 1 time(s)]
> show sel cartoons
> select #1/B:58@C
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
[Repeated 1 time(s)]
> show sel surfaces
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select lab
Expected an objects specifier or a keyword
> select label
Expected an objects specifier or a keyword
> ～label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
Unknown command: ～label (#!1 & sel) text "{0.label_one_letter_code}
{0.number}{0.insertion_code}"
> select add #1
8196 atoms, 8359 bonds, 4 pseudobonds, 1048 residues, 6 models selected
> select subtract #1
6 models selected
> hide #!1 models
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #1.7 models
> hide #1.8 models
> show #1.8 models
> hide #1.8 models
> show #1.8 models
> hide #1.8 models
> show #1.8 models
> show #1.2 models
> hide #1.2 models
> show #1.1 models
> hide #1.1 models
> select add #1.8
1 model selected
> show #5#!1 atoms
> undo
> select subtract #1.8
Nothing selected
> select add #1.7
980 atoms, 129 residues, 1 model selected
> select subtract #1.7
1 model selected
> select add #1.1
3 pseudobonds, 1 model selected
> select subtract #1.1
Nothing selected
> select add #1.1
3 pseudobonds, 1 model selected
> select subtract #1.1
Nothing selected
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> view
[Repeated 1 time(s)]
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select /R:7
22 atoms, 22 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select /R:82
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select /A
3894 atoms, 3966 bonds, 4 pseudobonds, 470 residues, 4 models selected
> select /R
4534 atoms, 4645 bonds, 3 pseudobonds, 580 residues, 5 models selected
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/119-oleamide receptor only.pdb"
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/119-oleamide receptor only.pdb"
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/作图/119-oleamide receptor only.pdb
---
warnings | End residue of secondary structure not found: HELIX 19 19 VAL R 39
GLN R 65 1 27
Start residue of secondary structure not found: HELIX 1 1 GLU A 10 ALA A 39 1
30
Start residue of secondary structure not found: HELIX 2 2 LYS A 53 GLN A 59 1
7
Start residue of secondary structure not found: HELIX 3 3 TRP A 234 PHE A 238
1 5
Start residue of secondary structure not found: HELIX 4 4 ARG A 265 ASN A 278
1 14
Start residue of secondary structure not found: HELIX 5 5 LYS A 280 LEU A 282
1 3
65 messages similar to the above omitted
Chain information for 119-oleamide receptor only.pdb
---
Chain | Description
6.1/A 6.2/A | No description available
6.1/B 6.2/B | No description available
6.1/C | No description available
6.2/C | No description available
6.1/N | No description available
6.2/N | No description available
6.1/R | No description available
6.2/R | No description available
> hide sel & #!1 atoms
> delete /A
> delete /B
> delete /N
> delete /C
> select add #2
4534 atoms, 4645 bonds, 3 pseudobonds, 580 residues, 11 models selected
> select subtract #2
4534 atoms, 4645 bonds, 3 pseudobonds, 580 residues, 9 models selected
> show #!2 models
> hide #!2 models
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/119-oleamide receptor.pdb"
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/119-oleamide receptor only.pdb"
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/作图/119-oleamide receptor only.pdb
---
warnings | End residue of secondary structure not found: HELIX 19 19 VAL R 39
GLN R 65 1 27
Start residue of secondary structure not found: HELIX 1 1 GLU A 10 ALA A 39 1
30
Start residue of secondary structure not found: HELIX 2 2 LYS A 53 GLN A 59 1
7
Start residue of secondary structure not found: HELIX 3 3 TRP A 234 PHE A 238
1 5
Start residue of secondary structure not found: HELIX 4 4 ARG A 265 ASN A 278
1 14
Start residue of secondary structure not found: HELIX 5 5 LYS A 280 LEU A 282
1 3
65 messages similar to the above omitted
Chain information for 119-oleamide receptor only.pdb
---
Chain | Description
7.1/A 7.2/A | No description available
7.1/B 7.2/B | No description available
7.1/C | No description available
7.2/C | No description available
7.1/N | No description available
7.2/N | No description available
7.1/R | No description available
7.2/R | No description available
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/119-oleamide receptor.pdb"
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/作图/119-oleamide receptor.pdb
---
warnings | End residue of secondary structure not found: HELIX 2 2 VAL R 39
GLN R 65 1 27
Start residue of secondary structure not found: HELIX 1 1 SER R 6 LYS R 35 1
30
Start residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1
27
Start residue of secondary structure not found: HELIX 3 3 LYS R 75 LYS R 108 1
34
Start residue of secondary structure not found: HELIX 4 4 PRO R 110 ILE R 116
1 7
Start residue of secondary structure not found: HELIX 5 5 GLY R 119 GLY R 142
1 24
5 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1 27
Start residue of secondary structure not found: HELIX 1 1 SER R 6 LYS R 35 1
30
Start residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1
27
Start residue of secondary structure not found: HELIX 3 3 LYS R 75 LYS R 108 1
34
Start residue of secondary structure not found: HELIX 4 4 PRO R 110 ILE R 116
1 7
Start residue of secondary structure not found: HELIX 5 5 GLY R 119 GLY R 142
1 24
5 messages similar to the above omitted
Chain information for 119-oleamide receptor.pdb
---
Chain | Description
8.1/R 8.4/R | No description available
8.2/R 8.5/R | No description available
> close #7
> close #3
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!8 models
> hide #!1 models
> show #!8 models
> hide #5 models
> hide #4 models
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!8 models
> select /R
15862 atoms, 16248 bonds, 8 pseudobonds, 2030 residues, 15 models selected
> select #8.1/R
2260 atoms, 2313 bonds, 1 pseudobond, 290 residues, 2 models selected
> hide (#!8.1 & sel) target a
> hide sel cartoons
> close #8
> show #5 models
> hide #5 models
> show #!6 models
> hide #6.3#!6.1-2 surfaces
> hide #6.3#!6.1-2 atoms
> show #6.3#!6.1-2 cartoons
> close #6
> show #!1 models
> select /R
2260 atoms, 2313 bonds, 2 pseudobonds, 290 residues, 3 models selected
> select /A
Nothing selected
> show #!1 cartoons
[Repeated 1 time(s)]
> hide #!1 cartoons
> show #!1 cartoons
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/apo69-230410-oleamide.pdb"
Chain information for apo69-230410-oleamide.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
R | No description available
> hide #!3 models
> select add #1
2260 atoms, 2313 bonds, 2 pseudobonds, 290 residues, 4 models selected
> select /R
4520 atoms, 4626 bonds, 3 pseudobonds, 580 residues, 5 models selected
> select /R
4520 atoms, 4626 bonds, 3 pseudobonds, 580 residues, 5 models selected
> select add #3
10456 atoms, 10672 bonds, 5 pseudobonds, 1338 residues, 7 models selected
> select subtract #3
2260 atoms, 2313 bonds, 2 pseudobonds, 290 residues, 5 models selected
> select subtract #4
2260 atoms, 2313 bonds, 1 pseudobond, 290 residues, 4 models selected
> select ligand
40 atoms, 38 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> select add #3
8216 atoms, 8378 bonds, 3 pseudobonds, 1049 residues, 4 models selected
> select subtract #3
20 atoms, 19 bonds, 1 residue, 2 models selected
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/119-oleamide receptor.pdb"
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/119-oleamide receptor.pdb"
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/119-oleamide receptor.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER R 6
LYS R 35 1 30
Start residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1
27
Start residue of secondary structure not found: HELIX 3 3 LYS R 75 LYS R 108 1
34
Start residue of secondary structure not found: HELIX 4 4 PRO R 110 ILE R 116
1 7
Start residue of secondary structure not found: HELIX 5 5 GLY R 119 GLY R 142
1 24
5 messages similar to the above omitted
Chain information for 119-oleamide receptor.pdb
---
Chain | Description
6.3/A | No description available
6.3/B | No description available
6.3/C | No description available
6.3/N | No description available
6.1/R 6.3/R | No description available
> hide #!1 models
> hide #!6 models
> show #!6 models
> hide #!6.3 models
> hide #6.2 models
> show #6.2 models
> hide #6.2 models
> show #6.2 models
> hide #6.2 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> color #1 #ad9cc2ff
> color #1 #fdf7f2ff
> color #1 #f0f0f0ff
> undo
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> view
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #6.3.1 models
> close #6.3
> show #6.2 models
> hide #6.2 models
> hide #!6.1 models
> show #!6.1 models
> show #6.2 models
> hide #6.2 models
> close #6.2
> color #6.1 #ad9cc2ff
> hide #!6 models
> show #!1 models
> hide #!6.1 models
> undo
[Repeated 3 time(s)]
> show #!1 models
> hide #!1 models
> hide #!6.1 models
> show #!1 models
> ui tool show "Side View"
> view sel
> select /R:7,65
60 atoms, 57 bonds, 6 residues, 3 models selected
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> view
> hide #!1 models
> show #5 models
> hide #5 models
> show #!6.1 models
> select add #1
2300 atoms, 2351 bonds, 2 pseudobonds, 294 residues, 7 models selected
> select subtract #1
40 atoms, 38 bonds, 4 residues, 4 models selected
> select add #3
8216 atoms, 8378 bonds, 3 pseudobonds, 1050 residues, 3 models selected
> select subtract #3
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #6
2260 atoms, 2313 bonds, 1 pseudobond, 290 residues, 3 models selected
> select ligand
60 atoms, 57 bonds, 3 residues, 3 models selected
> select add #1
2300 atoms, 2351 bonds, 2 pseudobonds, 292 residues, 7 models selected
> select subtract #1
40 atoms, 38 bonds, 2 residues, 4 models selected
> select add #3
8216 atoms, 8378 bonds, 3 pseudobonds, 1049 residues, 3 models selected
> select subtract #3
20 atoms, 19 bonds, 1 residue, 1 model selected
> select /R:7,65,61,82,85,86,89,90,93,94,174,169,238,265,
Expected an objects specifier or a keyword
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265
366 atoms, 351 bonds, 42 residues, 3 models selected
> hide #!6 models
> hide #!6.1 models
> show #!1 models
> close #1
> show #!3 models
> show #4 models
> close #3
> hide #4 models
> select subtract #4
122 atoms, 117 bonds, 14 residues, 1 model selected
> show #!6 models
> show #!6.1 models
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> contacts sel select true makePseudobonds false
48 contacts
> show sel atoms
> undo
[Repeated 1 time(s)]
> close #2
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265
122 atoms, 117 bonds, 14 residues, 1 model selected
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
144 atoms, 140 bonds, 16 residues, 1 model selected
> show sel atoms
> color cartoon cyan
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color cartoons cyan
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color cyan cartoons
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/apo69-230410-oleamide.pdb"
Chain information for apo69-230410-oleamide.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
R | No description available
> hide #!6 models
> hide #!6.1 models
> hide #!1 models
> show #!1 models
> close #1
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/119-oleamide receptor.pdb"
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/119-oleamide receptor.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER R 6
LYS R 35 1 30
Start residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1
27
Start residue of secondary structure not found: HELIX 3 3 LYS R 75 LYS R 108 1
34
Start residue of secondary structure not found: HELIX 4 4 PRO R 110 ILE R 116
1 7
Start residue of secondary structure not found: HELIX 5 5 GLY R 119 GLY R 142
1 24
5 messages similar to the above omitted
Chain information for 119-oleamide receptor.pdb
---
Chain | Description
1.3/A | No description available
1.3/B | No description available
1.3/C | No description available
1.3/N | No description available
1.1/R 1.3/R | No description available
> close #1
> show #4 models
> show #5 models
> show #!6 models
> show #!6.1 models
> color #6 #c7b7e0ff models
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> ui tool show Log
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
144 atoms, 140 bonds, 16 residues, 1 model selected
> save /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
Cannot determine format for '/R:'
> save pdb /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
Cannot determine format for 'pdb'
> save /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158 pdb
Cannot determine format for '/R:'
> save "/R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158" pdb
Cannot determine format for '/R:
7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158'
> save "/R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158" pdb
Cannot determine format for '/R:
7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158'
> save pdb "/R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158"
Cannot determine format for 'pdb'
> save sel pdb
Cannot determine format for 'sel'
> color #5 #f4bba4ff
> color ligand #f4bba4
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select /R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /R:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /R:7
11 atoms, 11 bonds, 1 residue, 1 model selected
> select/R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
Unknown command: select/R:
7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
144 atoms, 140 bonds, 16 residues, 1 model selected
> select subtract #4
144 atoms, 140 bonds, 16 residues, 1 model selected
> hide #4 models
> hide #5 models
> select clear
> transparency ribbons 75
Missing or invalid "percent" argument: Expected a number
> transparency 75 ribbons
> view
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> view
> view sel
> select clear
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting soft
> undo
[Repeated 2 time(s)]
> lighting soft
> select clear
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> undo
[Repeated 5 time(s)]
> select #6.1/R:223
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> view
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> graphics silhouettes false
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> select ions
Nothing selected
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> view sel
> select clear
> select #6.1/R:401@O01
1 atom, 1 residue, 1 model selected
> select #6.1/R:156
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6.1/R:401@N03
1 atom, 1 residue, 1 model selected
> select #6.1/R:401@O01
1 atom, 1 residue, 1 model selected
> select #6.1/R:401@N03
1 atom, 1 residue, 1 model selected
> color byattribute element
No known/registered numeric attribute element
> color byelement
> ui tool show "Color Actions"
> color sel byelement
[Repeated 2 time(s)]
> select #6.1/R:401@O01
1 atom, 1 residue, 1 model selected
> color byelement
> color sel byelement
> color byelement
> select #6.1/R:65@OE1
1 atom, 1 residue, 1 model selected
> select clear
> select #6.1/R:65@OE1
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #6.1/R:65@NE2
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #6.1/R:155@SG
1 atom, 1 residue, 1 model selected
> color sel byelement
> select clear
> color byelement
> select #6.1/R:156
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #6.1/R:156@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #6.1/R:156@OG
1 atom, 1 residue, 1 model selected
> select add #6.1/R:261@OE2
2 atoms, 2 residues, 1 model selected
> select add #6.1/R:261@OE1
3 atoms, 2 residues, 1 model selected
> color sel byelement
> color byelement
> select #6.1/R:82@SD
1 atom, 1 residue, 1 model selected
> select #6.1/R:265@NE1
1 atom, 1 residue, 1 model selected
> select add #6.1/R:82@SD
2 atoms, 2 residues, 1 model selected
> color sel byelement
> color byelement
> undo
> select add #6.1/R:86@OG1
3 atoms, 3 residues, 1 model selected
> select add #6.1/R:238@NE1
4 atoms, 4 residues, 1 model selected
> color sel byelement
> select #6.1/R:23
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select #6.1/R:65@NE2
1 atom, 1 residue, 1 model selected
> select add #6.1/R:401@O01
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> select clear
[Repeated 2 time(s)]
> select #6.1/R:65@NE2
1 atom, 1 residue, 1 model selected
> select #6.1/R:401@O01
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #6.1/R:65@NE2
1 atom, 1 residue, 1 model selected
> select add #6.1/R:401@O01
2 atoms, 2 residues, 1 model selected
> distance #6.1/R:65@NE2 #6.1/R:401@O01
Distance between 119-oleamide receptor.pdb #6.1/R GLN 65 NE2 and LIG 401 O01:
3.412Å
> undo
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> ~distance #6.1/R:65@NE2 #6.1/R:401@O01
> select #6.1/R:155@SG
1 atom, 1 residue, 1 model selected
> select #6.1/R:65@OE1
1 atom, 1 residue, 1 model selected
> select add #6.1/R:155@SG
2 atoms, 2 residues, 1 model selected
> distance #6.1/R:65@OE1 #6.1/R:155@SG
Distance between 119-oleamide receptor.pdb #6.1/R GLN 65 OE1 and CYS 155 SG:
6.668Å
> undo
> ~distance #6.1/R:65@OE1 #6.1/R:155@SG
> select clear
> transparency 0 sticks
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 0 atoms
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/119-oleamide receptor.pdb"
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/119-oleamide receptor.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER R 6
LYS R 35 1 30
Start residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1
27
Start residue of secondary structure not found: HELIX 3 3 LYS R 75 LYS R 108 1
34
Start residue of secondary structure not found: HELIX 4 4 PRO R 110 ILE R 116
1 7
Start residue of secondary structure not found: HELIX 5 5 GLY R 119 GLY R 142
1 24
5 messages similar to the above omitted
Chain information for 119-oleamide receptor.pdb
---
Chain | Description
1.3/A | No description available
1.3/B | No description available
1.3/C | No description available
1.3/N | No description available
1.1/R 1.3/R | No description available
> close #1
> select clear
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting simple
> graphics silhouettes true
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> lighting full
> lighting shadows false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> close
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/119-oleamide receptor.pdb" format pdb
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/119-oleamide receptor.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER R 6
LYS R 35 1 30
Start residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1
27
Start residue of secondary structure not found: HELIX 3 3 LYS R 75 LYS R 108 1
34
Start residue of secondary structure not found: HELIX 4 4 PRO R 110 ILE R 116
1 7
Start residue of secondary structure not found: HELIX 5 5 GLY R 119 GLY R 142
1 24
5 messages similar to the above omitted
Chain information for 119-oleamide receptor.pdb
---
Chain | Description
1.3/A | No description available
1.3/B | No description available
1.3/C | No description available
1.3/N | No description available
1.1/R 1.3/R | No description available
> close
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/119-oleamide receptor.pdb" format pdb
No such file/path: /Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
AS+oleamide/作图/119-oleamide receptor.pdb
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide overal.pdb" format pdb
No such file/path: /Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
AS+oleamide/作图/oleamide overal.pdb
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/119-oleamide receptor only.pdb" format pdb
No such file/path: /Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
AS+oleamide/作图/119-oleamide receptor only.pdb
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/119-oleamide receptor.pdb" format pdb
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/119-oleamide receptor.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER R 6
LYS R 35 1 30
Start residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1
27
Start residue of secondary structure not found: HELIX 3 3 LYS R 75 LYS R 108 1
34
Start residue of secondary structure not found: HELIX 4 4 PRO R 110 ILE R 116
1 7
Start residue of secondary structure not found: HELIX 5 5 GLY R 119 GLY R 142
1 24
5 messages similar to the above omitted
Chain information for 119-oleamide receptor.pdb
---
Chain | Description
1.3/A | No description available
1.3/B | No description available
1.3/C | No description available
1.3/N | No description available
1.1/R 1.3/R | No description available
> delete /A
> delete /B
> delete /C
> delete /N
> hide #!1.1 models
> hide #1.2 models
> hide #!1.3 models
> show #!1.3 models
> hide #1.1.1 models
> hide #!1.3 models
> show #!1.3 models
> show #1.2 models
> show #1.1.1 models
> hide #!1.1 models
> hide #1.1.1 models
> hide #1.2 models
> hide #!1.3 surfaces
> hide #!1.3 atoms
> show #!1.3 cartoons
> color /R #ad9cc2
> color ligand #e1a086
> show ligand sphere
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show ligand atoms
> select ligand
40 atoms, 38 bonds, 2 residues, 2 models selected
> style sel & #!1.3 sphere
Changed 20 atom styles
> transparency 75 cartoons
> view sel
> style sel & #!1.3 ball
Changed 20 atom styles
> style sel & #!1.3 stick
Changed 20 atom styles
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
288 atoms, 280 bonds, 32 residues, 2 models selected
> show sel & #!1.3 atoms
> style sel & #!1.3 stick
Changed 144 atom styles
> color byelement
> select clear
> select #1.3/R:65@OE1
1 atom, 1 residue, 1 model selected
> select #1.3/R:65@NE2
1 atom, 1 residue, 1 model selected
> select add #1.3/R:65@OE1
2 atoms, 1 residue, 1 model selected
> undo
[Repeated 7 time(s)]
> label (#!1.3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> close #1.1
> close #1.2
> select clear
> select add /R:65@OE1
1 atom, 1 residue, 1 model selected
> select add /R:65@NE2
2 atoms, 1 residue, 1 model selected
> select add /R:265@NE1
3 atoms, 2 bonds, 2 residues, 1 model selected
> select add /R:238@NE1
4 atoms, 2 bonds, 3 residues, 1 model selected
> select add /R:238@NE1
4 atoms, 2 bonds, 3 residues, 1 model selected
> color sel byelement
> select clear
> undo
[Repeated 9 time(s)]
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
144 atoms, 140 bonds, 16 residues, 1 model selected
> hide sel atoms
> show sel atoms
> close
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/119-oleamide receptor.pdb" format pdb
Summary of feedback from opening /Users/scarlettzhang/杂事/Ye Lab/GPCR
interaction/写文章/GPR119 AS+oleamide/119-oleamide receptor.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER R 6
LYS R 35 1 30
Start residue of secondary structure not found: HELIX 2 2 VAL R 39 GLN R 65 1
27
Start residue of secondary structure not found: HELIX 3 3 LYS R 75 LYS R 108 1
34
Start residue of secondary structure not found: HELIX 4 4 PRO R 110 ILE R 116
1 7
Start residue of secondary structure not found: HELIX 5 5 GLY R 119 GLY R 142
1 24
5 messages similar to the above omitted
Chain information for 119-oleamide receptor.pdb
---
Chain | Description
1.3/A | No description available
1.3/B | No description available
1.3/C | No description available
1.3/N | No description available
1.1/R 1.3/R | No description available
> delete /A
> delete /B
> delete /C
> delete /N
> show ligand
> color ligand #e1a086
> color /R #ad9cc2
> hide cartoons
> hide atoms
> hide cartoons
> show cartoons
> show ligand
> color ligand #e1a086
> select ligand
40 atoms, 38 bonds, 2 residues, 2 models selected
> view sel
> transparency 75 cartoons
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158
288 atoms, 280 bonds, 32 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 288 atom styles
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select clear
> select #1.1/R:65@OE1
1 atom, 1 residue, 1 model selected
> select #1.1/R:65@NE2
1 atom, 1 residue, 1 model selected
> select add #1.1/R:65@OE1
2 atoms, 1 residue, 1 model selected
> select add #1.1/R:401@O01
3 atoms, 2 residues, 1 model selected
> select add #1.1/R:401@N03
4 atoms, 2 residues, 1 model selected
> color sel byelement
> select clear
> select #1.1/R:65@OE1
1 atom, 1 residue, 1 model selected
> color sel byelement
[Repeated 1 time(s)]
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 119-oleamide receptor.pdb_R SES surface #1.1.3: minimum,
-13.84, mean 1.37, maximum 20.16
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> hide sel surfaces
> color sel byhetero
> color byelement
> color sel byelement
> color byelement
> select add #1.1/R:86@OG1
2 atoms, 1 bond, 2 residues, 2 models selected
> color sel red
> undo
> select clear
> select #1.1/R:401@O01
1 atom, 1 residue, 1 model selected
> color sel red
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #1.1.1 models
> hide #1.1.2 models
> hide #1.1.3 models
> hide #1.2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #1.1.1 models
> hide #!1.1 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.1 models
> close #1.3
> close #1.2
> show #1.1.2 models
> hide #1.1.2 models
> show #1.1.2 models
> hide #1.1.2 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> show #1.1.3 models
> hide #1.1.3 models
> color byelement
> undo
> select clear
> select /R:82@SD
1 atom, 1 residue, 1 model selected
> select clear
> select /R:82@SD
1 atom, 1 residue, 1 model selected
> select clear
> select /R:82@SD
1 atom, 1 residue, 1 model selected
> select /R:82@SD
1 atom, 1 residue, 1 model selected
> color sel byelement
> select /R:93@CG2
1 atom, 1 residue, 1 model selected
> color sel byelement
> select /R:86@OG1
1 atom, 1 residue, 1 model selected
> color sel byelement
> color byelement
> select /R:265@NE1
1 atom, 1 residue, 1 model selected
> select add /R:238@NE1
2 atoms, 2 residues, 2 models selected
> color sel byelement
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> show #1.1.2 models
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158,261
153 atoms, 148 bonds, 17 residues, 1 model selected
> label (#!1.1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select clear
[Repeated 1 time(s)]
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.pdb"
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.pdb"
Chain information for oleamide pocket.pdb #2
---
Chain | Description
R | No description available
> hide #!1 models
> hide #!2 models
> show #!1 models
> close #2
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.cxs"
——— End of log from Fri May 5 17:18:04 2023 ———
opened ChimeraX session
> transparency 70 cartoons
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.tif" width 864 height 670 supersample 3
> ui tool show "Side View"
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> view sel
> select clear
> select /R:261@OE2
1 atom, 1 residue, 1 model selected
> color sel byelement
> select clear
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.tif" width 1200 height 1036 supersample 3
> transparentBackground true
> transparency 75 cartoons
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.tif" width 1200 height 1036 supersample 3
> transparentBackground true
> transparency 50 cartoons
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.tif" width 776 height 670 supersample 3
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.tif" width 1200 height 1036 supersample 3
> transparentBackground true
> transparency 75 cartoons
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.tif" width 1200 height 1036 supersample 3
> transparentBackground true
> graphics silhouettes true
> undo
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> lighting full
> graphics silhouettes true
> lighting full
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
[Repeated 2 time(s)]
> lighting full
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> transparency 70 cartoons
> select atoms
Expected an objects specifier or a keyword
> select sticks
Expected an objects specifier or a keyword
> select cartoons
Expected an objects specifier or a keyword
> select labels
Expected an objects specifier or a keyword
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158,261
153 atoms, 148 bonds, 17 residues, 1 model selected
> graphics silhouettes true
> undo
> lighting soft
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting soft
[Repeated 1 time(s)]
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting soft
[Repeated 1 time(s)]
> lighting simple
[Repeated 1 time(s)]
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> select clear
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.tif" width 1200 height 1036 supersample 3
> transparentBackground true
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide-pocket.tif" width 12000 height 10361 supersample 3
> transparency 70 cartoons
> transparency 50 cartoons
> select ligand
20 atoms, 19 bonds, 1 residue, 1 model selected
> view sel
> transparency 75 cartoons
> select /R: 7,65,61,82,85,86,89,90,93,94,174,169,238,265,157,158,261
153 atoms, 148 bonds, 17 residues, 1 model selected
> color sel #a07da0
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> select clear
> undo
[Repeated 2 time(s)]
> select clear
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket .tif" width 1200 height 1036 supersample 3
> transparentBackground true
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide-pocket.tif" width 1200 height 1036 supersample 3
> transparentBackground true
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.tif" width 1200 height 1036 supersample 3
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/oleamide pocket.cxs"
——— End of log from Fri May 5 17:54:14 2023 ———
opened ChimeraX session
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel MET rotLib Dunbrack
/R MET 82: phi -62.0, psi -42.4 trans
Changed 135 bond radii
> swapaa #!1.1/R:82 MET criteria 9 rotLib Dunbrack retain false
Using Dunbrack library
119-oleamide receptor.pdb #!1.1/R MET 82: phi -62.0, psi -42.4 trans
Applying MET rotamer (chi angles: -67.4 -64.0 172.2) to 119-oleamide
receptor.pdb #!1.1/R MET 82
> select /R:82@SD
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 1 residue, 1 model selected
> contacts sel distanceOnly 4.0 select true makePseudobonds false
56 distances
> select up
127 atoms, 122 bonds, 13 residues, 2 models selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /R:156@OG
1 atom, 1 residue, 1 model selected
> color (#!1.1 & sel) byelement
> select clear
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting soft
> cartoon style width 1.2
> select /R:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
172 atoms, 177 bonds, 24 residues, 2 models selected
> hide sel
> hide sel cartoons
> select clear
> hide #1.1.2 models
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/pocket/oleamide pocket.tif" width 1200 height 1003
> supersample 3 transparentBackground true
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/pocket/oleamide pocket.tif" width 1200 height 1003
> supersample 3
> select /R:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
165 atoms, 171 bonds, 20 residues, 2 models selected
> select down
5 atoms, 4 bonds, 1 residue, 2 models selected
> select /R:160
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /R:159
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add /R:158
23 atoms, 21 bonds, 3 residues, 2 models selected
> select add /R:161
34 atoms, 32 bonds, 4 residues, 2 models selected
> hide sel cartoons
> undo
> select clear
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/pocket/oleamide pocket.cxs"
[Repeated 1 time(s)]
——— End of log from Fri Jun 9 15:40:14 2023 ———
opened ChimeraX session
> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/结构/pdb7xz5.ent"
pdb7xz5.ent title:
GPR119-GS-LPC complex [more info...]
Chain information for pdb7xz5.ent #2
---
Chain | Description | UniProt
A | guanine nucleotide-binding protein G(S) subunit α isoforms short |
B | transducin β chain 1 | GBB1_HUMAN 2-340
G | G γ-I | GBG2_HUMAN 1-71
N | NANOBODY35 |
R | soluble cytochrome B562,glucose-dependent insulinotropic receptor |
C562_ECOLX -121--17, GP119_HUMAN 1-335
Non-standard residues in pdb7xz5.ent #2
---
LSC —
(4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium
4-oxide
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> matchmaker #!2 to #1.1
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 119-oleamide receptor.pdb, chain R (#1.1) with pdb7xz5.ent, chain R
(#2), sequence alignment score = 1453.9
RMSD between 272 pruned atom pairs is 0.802 angstroms; (across all 287 pairs:
1.184)
> select add #2
16508 atoms, 16673 bonds, 3 pseudobonds, 1053 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select ligand
107 atoms, 105 bonds, 2 residues, 2 models selected
> show sel atoms
> select H
8241 atoms, 1053 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> delete sel
> select clear
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select proteins
Expected an objects specifier or a keyword
> select cartoon proteins
Expected an objects specifier or a keyword
> select cartoon
Expected an objects specifier or a keyword
> hide cartoons
> select add #1
2260 atoms, 2313 bonds, 2 pseudobonds, 290 residues, 5 models selected
> hide sel atoms
> select ligand
55 atoms, 53 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> select add #1.1/R:401@C02
1 atom, 1 bond, 1 residue, 2 models selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
3 atoms, 1 bond, 2 residues, 2 models selected
> select up
55 atoms, 53 bonds, 2 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 1 residue, 2 models selected
> color sel #f095bc
> select clear
> select #2/R:401@C35
1 atom, 1 residue, 1 model selected
> select #2/R:401@C35
1 atom, 1 residue, 1 model selected
> select #2/R:401@N32
1 atom, 1 residue, 1 model selected
> select #2/R:401@N32
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #2/R:401@O33
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #2/R:401@C21
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #2/R:401@O25
1 atom, 1 residue, 1 model selected
> select add #2/R:401@O34
2 atoms, 1 residue, 2 models selected
> select add #2/R:401@P24
3 atoms, 1 residue, 2 models selected
> color sel byelement
> select add #2/R:401@O23
4 atoms, 1 residue, 2 models selected
> select add #2/R:401@O35
5 atoms, 1 residue, 2 models selected
> color sel byelement
> select #2/R:401@O32
1 atom, 1 residue, 1 model selected
> select add #2/R:401@O19
2 atoms, 1 residue, 2 models selected
> color sel byelement
> select C2
1521 atoms, 2 bonds, 1342 residues, 2 models selected
> show sel atoms
> hide sel atoms
> undo
[Repeated 1 time(s)]
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 1521 atom styles
> style sel sphere
Changed 1521 atom styles
> undo
No visible atoms selected
> select #1.1/R:401@C12
1 atom, 1 residue, 1 model selected
> label (#!1.1 & sel) atoms attribute idatm_type
> select clear
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
4 atoms, 2 bonds, 2 residues, 2 models selected
> select up
55 atoms, 53 bonds, 2 residues, 4 models selected
> select C2
1521 atoms, 2 bonds, 1342 residues, 2 models selected
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color sel yellow
> select add #2/R:401@C10
1 atom, 2 bonds, 1 residue, 2 models selected
> select add #2/R:401@C9
2 atoms, 2 bonds, 1 residue, 3 models selected
> select add #1.1/R:401@C12
3 atoms, 2 bonds, 2 residues, 3 models selected
> select add #1.1/R:401@C11
4 atoms, 2 bonds, 2 residues, 4 models selected
> select subtract #2/R:401@C10
3 atoms, 1 bond, 2 residues, 4 models selected
> select clear
> select add #2/R:401@C10
1 atom, 1 residue, 1 model selected
> select add #1.1/R:401@C11
2 atoms, 2 residues, 3 models selected
> select add #1.1/R:401@C12
3 atoms, 2 residues, 4 models selected
> select add #2/R:401@C9
4 atoms, 2 residues, 4 models selected
> color sel yellow
> select clear
[Repeated 1 time(s)]
> show cartoons
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> transparency 70 cartoons
> transparency 80 cartoons
> select #2/R:163
7 atoms, 7 bonds, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
87 atoms, 90 bonds, 11 residues, 1 model selected
> select up
1595 atoms, 1632 bonds, 210 residues, 1 model selected
> color sel #71afe0
> select clear
> select #2/R:255
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 4 residues, 1 model selected
> select up
664 atoms, 682 bonds, 82 residues, 1 model selected
> color sel #71afe0
> select clear
> transparency 90 cartoons
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> lighting soft
> select #1.1/R:157
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
165 atoms, 171 bonds, 20 residues, 2 models selected
> select up
1582 atoms, 1619 bonds, 208 residues, 2 models selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
165 atoms, 171 bonds, 20 residues, 2 models selected
> hide cartoons sel
Expected ',' or a keyword
> hide sel cartoons
> select #2/R:157
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
147 atoms, 152 bonds, 18 residues, 1 model selected
> hide sel cartoons
> select #2/R:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1.1/R:86
14 atoms, 12 bonds, 2 residues, 2 models selected
> select up
532 atoms, 536 bonds, 70 residues, 3 models selected
> hide sel cartoons
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/Fig1. overall structure of oleamide-bingding
> complex/配体结构比较.tif" width 1200 height 931 supersample 3
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> save "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/Fig1. overall structure of oleamide-bingding
> complex/配体结构比较.cxs"
——— End of log from Sun Sep 3 14:30:22 2023 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Time since boot: 10 days 4:27
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202304202331
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.5.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.2.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash handling text input |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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