The following bug report has been submitted:
Platform: macOS-12.5.1-x86_64-i386-64bit
ChimeraX Version: 1.7rc202311070653 (2023-11-07 06:53:13 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000114d0000 (most recent call first):
File "/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000011bf1b600 (most recent call first):
File "/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree (total: 62)
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{
"uptime" : 290000,
"procLaunch" : "2023-11-15 20:21:57.2319 +0800",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"procStartAbsTime" : 291660886013755,
"coalitionID" : 22365,
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"build" : "21G83",
"releaseType" : "User"
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"captureTime" : "2023-11-15 21:35:54.9120 +0800",
"incident" : "47F6D9E4-22A7-4FCC-AFEF-6BA0A89A618F",
"bug_type" : "309",
"pid" : 5600,
"procExitAbsTime" : 296098512021206,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7-rc2023.11.07.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"B6E3514E-1567-56DF-AA93-3DDA0EAB8D1C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "6C7F2DF1-31E8-5057-CB2F-9BF9DA978A28",
"wakeTime" : 32900,
"bridgeVersion" : {"build":"19P6066","train":"6.6"},
"sleepWakeUUID" : "4229BDB0-D5CE-4CD8-BE4D-4EEEBFF288D1",
"sip" : "enabled",
"vmRegionInfo" : "0x40 is not in any region. Bytes before following region: 140737487335360\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff07000-7ffffff08000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
"vmregioninfo" : "0x40 is not in any region. Bytes before following region: 140737487335360\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff07000-7ffffff08000 [ 4K] r-x\/r-x SM=ALI ",
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"path" : "\/Applications\/ChimeraX-1.7-rc2023.11.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
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"size" : 19331678208,
"uuid" : "4d3a144c-02bb-31f1-bca9-83a5cb058c59"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=4.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 9488K 91 \nColorSync 232K 28 \nCoreAnimation 28.9M 156 \nCoreGraphics 12K 2 \nCoreImage 60K 3 \nCoreServices 624K 2 \nCoreUI image data 5096K 37 \nFoundation 44K 2 \nKernel Alloc Once 8K 1 \nMALLOC 3.4G 3372 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 112K 28 \nStack 172.7M 29 \nStack Guard 56.0M 1 \nVM_ALLOCATE 286.3M 307 \n__CTF 756 1 \n__DATA 47.0M 692 \n__DATA_CONST 32.9M 352 \n__DATA_DIRTY 1659K 218 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 678.5M 159 \n__TEXT 820.5M 693 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 566.9M 96 \nshared memory 3108K 31 \n=========== ======= ======= \nTOTAL 6.1G 6332 \nTOTAL, minus reserved VM space 6.0G 6332 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
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{
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"factorPackIds" : {
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}
],
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7rc202311070653 (2023-11-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/T491P_Model/ALPK1-coot-
> AYUAGS.pdb"
Summary of feedback from opening /Users/zhouhualin/Library/Mobile
Documents/com~apple~CloudDocs/Downloads/ALPK1/T491P_Model/ALPK1-coot-
AYUAGS.pdb
---
warning | Cannot find LINK/SSBOND residue ZN (1501 )
Chain information for ALPK1-coot-AYUAGS.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue TPO (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpvppnv38z/ante.in.mol2 -fi
mol2 -o
/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpvppnv38z/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(TPO) ``
(TPO) `Welcome to antechamber 20.0: molecular input file processor.`
(TPO) ``
(TPO) `Info: Finished reading file
(/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpvppnv38z/ante.in.mol2);
atoms read (29), bonds read (28).`
(TPO) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(TPO) ``
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(TPO) `Info: Total number of electrons: 128; net charge: -3`
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(TPO) ``
Charges for residue TPO determined
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpa47bz4bq/ante.in.mol2 -fi
mol2 -o
/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpa47bz4bq/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpa47bz4bq/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(HIS)
`/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/antechamber
-i /var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpa47bz4bq/ante.in.mol2
-fi mol2 -o
/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpa47bz4bq/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpa47bz4bq/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HIS) ``
Charges for residue HIS determined
Coulombic values for ALPK1-coot-AYUAGS.pdb_A SES surface #1.3: minimum,
-26.22, mean -1.02, maximum 21.07
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.3 models
> log metadata #1
No models had metadata
> log chains #1
Chain information for ALPK1-coot-AYUAGS.pdb #1
---
Chain | Description
A | No description available
> sequence chain #1/A
Alignment identifier is 1/A
> select /A:1238
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:966-1238
2268 atoms, 2328 bonds, 273 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!1 & sel) #72e7e8ff
> color (#!1 & sel) #9ae2e7ff
> select /A:497
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:2-497
3858 atoms, 3922 bonds, 496 residues, 1 model selected
> color sel light pink
> select clear
> select ::name="AGS"
31 atoms, 33 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel navy
> color sel byhetero
> select ::name="AYU"
40 atoms, 43 bonds, 1 residue, 1 model selected
> color sel yellow green
> color sel byhetero
> select clear
> select /A:1601@ZN
1 atom, 1 residue, 1 model selected
> color sel medium slate blue
> select clear
Drag select of 290 atoms, 769 residues, 5 pseudobonds, 268 bonds
> hide sel atoms
> select clear
> select ::name="AGS"
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel navy
> color sel byhetero
> show sel atoms
> select clear
> select ::name="AYU"
40 atoms, 43 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow green
> color sel byhetero
Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color sel yellow green
> color sel byhetero
> style sel sphere
Changed 40 atom styles
> select /A:1701@N9
1 atom, 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
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 31 atom styles
> show #1.3 models
> select clear
> coulombic
Coulombic values for ALPK1-coot-AYUAGS.pdb_A SES surface #1.3: minimum,
-26.22, mean -1.02, maximum 21.07
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> select /A:1301@O32
1 atom, 1 residue, 1 model selected
> select up
40 atoms, 43 bonds, 1 residue, 1 model selected
> style sel stick
Changed 40 atom styles
> show #1.3 models
> select clear
> hide #1.3 models
> lighting soft
> select /A:1301@N10
1 atom, 1 residue, 1 model selected
> select up
40 atoms, 43 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 40 atom styles
> select clear
> show #1.3 models
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> graphics silhouettes false
> hide #1.3 models
> hide #!1 models
> show #!1 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #!1 models
> show #!1 models
> hide #1.3 models
> show #1.3 models
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> hide #!1 models
> show #!1 models
> hide #1.3 models
> lighting soft
> show #1.3 models
> lighting simple
> hide #1.3 models
> lighting simple
> show #1.3 models
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/e.cxs"
Mismatch between Cocoa '\x0' and Carbon 'r' for virtual key 15 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'R' for virtual key 15 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'r' for virtual key 15 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'R' for virtual key 15 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ae' for virtual key 15 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2030' for virtual key 15 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ae' for virtual key 15 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2030' for virtual key 15 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> turn y 180
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> turn y 180
> show #1.3 models
> hide #1.3 models
> turn x 180
> show #1.3 models
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/e-2.bmp"
> width 965 height 723 supersample 3
> turn x 180
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/e-1.bmp"
> width 965 height 723 supersample 3
> turn y 90
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU
> AGS/e-]3.bmp" width 965 height 723 supersample 3
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/e-4.bmp"
> width 965 height 723 supersample 3
> transparency 80
> transparency 50
> hide #1.3 models
> select /A:1701@O2B
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel stick
Changed 31 atom styles
> select /A:1301@C04
1 atom, 1 residue, 1 model selected
> select up
40 atoms, 43 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 40 atom styles
> style sel stick
Changed 40 atom styles
> select clear
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> transparency 50
> transparency 60
> transparency 70
> transparency 60
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/e-5.bmp"
> width 965 height 723 supersample 3
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> clip
Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> ui mousemode right clip
> ui mousemode right "clip rotate"
> hide #!1.3 models
> show #1.3 models
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> hide #!1.3 models
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> show #1.3 models
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> coulombic protein surfaces #1.1.1 offset 0
> coulombic protein surfaces #1.3 offset 0
Coulombic values for ALPK1-coot-AYUAGS.pdb_A SES surface #1.3: minimum,
-60.73, mean -1.79, maximum 34.23
Coulombic values for cap front #1.3.1: minimum, -1170.23, mean 0.34, maximum
3241.47
> coulombic protein surfaces #1.3 offset 0
Coulombic values for ALPK1-coot-AYUAGS.pdb_A SES surface #1.3: minimum,
-60.73, mean -1.79, maximum 34.23
Coulombic values for cap front #1.3.1: minimum, -1170.23, mean 0.34, maximum
3241.47
> hide #!1.3 models
> show #1.3 models
> coulombic protein surfaces #1.1.1 offset 0
> coulombic protein surfaces #1.3 offset 0
Coulombic values for ALPK1-coot-AYUAGS.pdb_A SES surface #1.3: minimum,
-60.73, mean -1.79, maximum 34.23
Coulombic values for cap front #1.3.1: minimum, -1170.23, mean 0.34, maximum
3241.47
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/e
> clip.bmp" width 545 height 612 supersample 3
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/AGS
> E-1.bmp" width 545 height 612 supersample 3
> save "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/AGS
> E-2.bmp" width 545 height 612 supersample 3
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
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 31 atom styles
> style sel stick
Changed 31 atom styles
> style sel sphere
Changed 31 atom styles
> style sel ball
Changed 31 atom styles
> select clear
> select /A:1701@C1'
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel stick
Changed 31 atom styles
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel ball
Changed 31 atom styles
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel stick
Changed 31 atom styles
> select clear
> close session
> open "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/T491P_Model/K233A_mutant_model-
> coot.pdb"
Summary of feedback from opening /Users/zhouhualin/Library/Mobile
Documents/com~apple~CloudDocs/Downloads/ALPK1/T491P_Model/K233A_mutant_model-
coot.pdb
---
warning | Cannot find LINK/SSBOND residue ZN (1401 )
Chain information for K233A_mutant_model-coot.pdb #1
---
Chain | Description
A | No description available
> close session
> open "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/e.cxs"
> format session
opened ChimeraX session
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> ui mousemode right clip
> hide #!1.3 models
> select /A:1701@C5'
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel stick
Changed 31 atom styles
> select /A:1301@C37
1 atom, 1 residue, 1 model selected
> select up
40 atoms, 43 bonds, 1 residue, 1 model selected
> style sel stick
Changed 40 atom styles
> select clear
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> show #1.3 models
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> clip
> ui mousemode right zone
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> hide #!1 models
> show #!1 models
> hide #1.2 models
> show #1.2 models
> hide #!1.3 models
> ui mousemode right "clip rotate"
> show #1.3 models
> ui mousemode right clip
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> coulombic protein surfaces #1.3 offset 0
Coulombic values for ALPK1-coot-AYUAGS.pdb_A SES surface #1.3: minimum,
-60.73, mean -1.79, maximum 34.23
Coulombic values for cap front #1.3.1: minimum, -2037.67, mean 0.78, maximum
6531.90
> transparency 60
> transparency 30
> transparency 0
> transparency 30
> close session
> open "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/T491P_Model/ALPK1-coot-
> AYU.pdb"
Summary of feedback from opening /Users/zhouhualin/Library/Mobile
Documents/com~apple~CloudDocs/Downloads/ALPK1/T491P_Model/ALPK1-coot-AYU.pdb
---
warning | Cannot find LINK/SSBOND residue ZN (1501 )
Chain information for ALPK1-coot-AYU.pdb #1
---
Chain | Description
A | No description available
> close session
> open "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/chimera x pic/AYU AGS/e.cxs"
> format session
opened ChimeraX session
> close session
> open "/Users/zhouhualin/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/ALPK1/T491P_Model/ALPK1-coot-
> AYU.pdb" format pdb
Summary of feedback from opening /Users/zhouhualin/Library/Mobile
Documents/com~apple~CloudDocs/Downloads/ALPK1/T491P_Model/ALPK1-coot-AYU.pdb
---
warning | Cannot find LINK/SSBOND residue ZN (1501 )
Chain information for ALPK1-coot-AYU.pdb #1
---
Chain | Description
A | No description available
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue TPO (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpzv_4u3yp/ante.in.mol2 -fi
mol2 -o
/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpzv_4u3yp/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(TPO) ``
(TPO) `Welcome to antechamber 20.0: molecular input file processor.`
(TPO) ``
(TPO) `Info: Finished reading file
(/var/folders/1d/lrg9h42532sd_qssr1sks6j80000gn/T/tmpzv_4u3yp/ante.in.mol2);
atoms read (29), bonds read (28).`
(TPO) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(TPO) ``
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(TPO) `Info: Total number of electrons: 128; net charge: -3`
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(TPO) ``
Charges for residue TPO determined
Coulombic values for ALPK1-coot-AYU.pdb_A SES surface #1.3: minimum, -20.02,
mean -0.95, maximum 15.99
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.3 models
Drag select of 11 residues
Drag select of 165 atoms, 770 residues, 4 pseudobonds, 153 bonds
> hide sel atoms
> select clear
> select ::name="AYU"
40 atoms, 43 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:1301@C27
1 atom, 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
40 atoms, 43 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel yellow green
> color sel byhetero
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7rc202311070653 (2023-11-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0)
OS Loader Version: 540.120.3~19
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 66 days 5:27
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
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: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.12
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
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: 1.5.4
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7rc202311070653
ChimeraX-CoreFormats: 1.2
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: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.1
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
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: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.44.0
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
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: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.11.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
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: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.7
wcwidth: 0.2.9
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
