![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15816 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff84ed11fc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 58)
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{
"uptime" : 2000000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"coalitionID" : 1003,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-08-23 09:36:11.0987 -0500",
"codeSigningMonitor" : 0,
"incident" : "6F9AFA68-F094-468D-8C36-77CC7AA93EB1",
"pid" : 2953,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-21 13:45:27.9142 -0500",
"procStartAbsTime" : 1909650330602684,
"procExitAbsTime" : 2067488155339330,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"768DA260-76C1-5EB4-92DC-36F31D4684AE","thirdParty":true},
"parentProc" : "tcsh",
"parentPid" : 2047,
"coalitionName" : "com.apple.Terminal",
"crashReporterKey" : "D77CBDCE-560E-A76E-6409-11E87F8970FF",
"responsiblePid" : 2042,
"responsibleProc" : "Terminal",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4438192128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 108897000-10889b000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2953},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4438192128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 108897000-10889b000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=8.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG backing stores 20.6M 1 \nCG image 196K 19 \nColorSync 252K 30 \nCoreAnimation 820K 101 \nCoreGraphics 16K 3 \nCoreUI image data 5120K 36 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 7.6G 159 \nMALLOC guard page 48K 12 \nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 200K 50 \nStack 160.9M 51 \nStack Guard 56.0M 1 \nVM_ALLOCATE 536.1M 1033 \nVM_ALLOCATE (reserved) 224.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 45.0M 796 \n__DATA_CONST 64.2M 460 \n__DATA_DIRTY 1842K 230 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 211.5M 155 \n__OBJC_RO 71.8M 1 \n__OBJC_RW 2200K 2 \n__TEXT 1.0G 800 \ndyld private memory 292K 3 \nmapped file 511.3M 71 \nshared memory 3508K 30 \n=========== ======= ======= \nTOTAL 10.5G 4063 \nTOTAL, minus reserved VM space 10.3G 4063 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "9b32d37eed40f7db94dcf0c0e7f64901f98a5d9d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
},
"deploymentId" : 240000131
},
{
"rolloutId" : "65a8173205d942272410674b",
"factorPackIds" : {
"SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION" : "65d39fa4cb0e2417d11ce5f6"
},
"deploymentId" : 240000001
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
> color #1 gray(150)
> matchmaker #1.2-20 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 final.pdb, chain A (#1.1) with final.pdb, chain A (#1.2), sequence
alignment score = 1530.1
RMSD between 247 pruned atom pairs is 1.008 angstroms; (across all 302 pairs:
3.175)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.3), sequence
alignment score = 1521.7
RMSD between 244 pruned atom pairs is 1.036 angstroms; (across all 302 pairs:
2.417)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.4), sequence
alignment score = 1489.3
RMSD between 231 pruned atom pairs is 1.017 angstroms; (across all 302 pairs:
3.434)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.5), sequence
alignment score = 1510.3
RMSD between 161 pruned atom pairs is 0.887 angstroms; (across all 302 pairs:
3.956)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.6), sequence
alignment score = 1479.7
RMSD between 236 pruned atom pairs is 1.092 angstroms; (across all 302 pairs:
2.548)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.7), sequence
alignment score = 1513.9
RMSD between 214 pruned atom pairs is 1.011 angstroms; (across all 302 pairs:
2.504)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.8), sequence
alignment score = 1485.1
RMSD between 228 pruned atom pairs is 1.095 angstroms; (across all 302 pairs:
2.620)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.9), sequence
alignment score = 1470.1
RMSD between 256 pruned atom pairs is 0.908 angstroms; (across all 302 pairs:
2.226)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.10), sequence
alignment score = 1517.5
RMSD between 240 pruned atom pairs is 1.116 angstroms; (across all 302 pairs:
2.469)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.11), sequence
alignment score = 1513.3
RMSD between 180 pruned atom pairs is 1.074 angstroms; (across all 302 pairs:
2.523)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.12), sequence
alignment score = 1480.9
RMSD between 229 pruned atom pairs is 1.010 angstroms; (across all 302 pairs:
2.396)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.13), sequence
alignment score = 1517.5
RMSD between 185 pruned atom pairs is 1.275 angstroms; (across all 302 pairs:
3.446)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.14), sequence
alignment score = 1515.7
RMSD between 239 pruned atom pairs is 1.196 angstroms; (across all 302 pairs:
2.451)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.15), sequence
alignment score = 1513.9
RMSD between 162 pruned atom pairs is 0.920 angstroms; (across all 302 pairs:
3.261)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.16), sequence
alignment score = 1494.7
RMSD between 118 pruned atom pairs is 1.074 angstroms; (across all 302 pairs:
3.269)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.17), sequence
alignment score = 1501.3
RMSD between 238 pruned atom pairs is 0.907 angstroms; (across all 302 pairs:
3.101)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.18), sequence
alignment score = 1495.3
RMSD between 219 pruned atom pairs is 1.086 angstroms; (across all 302 pairs:
2.311)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.19), sequence
alignment score = 1473.1
RMSD between 205 pruned atom pairs is 1.197 angstroms; (across all 302 pairs:
3.212)
Matchmaker final.pdb, chain A (#1.1) with final.pdb, chain A (#1.20), sequence
alignment score = 1513.9
RMSD between 241 pruned atom pairs is 1.049 angstroms; (across all 302 pairs:
2.659)
> color #1:ile paleturquoise target a
> color #1:leu lightsalmon target a
> color #1:val khaki target a
> color #1:ala yellowgreen target a
> color #1:met thistle target a
> color #1:thr aquamarine target a
> color #1:phe plum target a
> color #1:tyr lightpink target a
> show #1:thr,met,ala,leu,val,ile,phe,tyr
> name meyfside #1:thr,met,ala,leu,val,ile,phe,tyr
> cartoon suppressBackboneDisplay false
> label #1.1 text {0.label_one_letter_code}{0.number}{0.insertion_code}
> label onTop false
> ui tool show "Side View"
> open pseudobonds/final_N_N.pb
Opened Pseudobonds final_N_N.pb, 254 bonds
> open pseudobonds/final_N_Methyl.pb
Opened Pseudobonds final_N_Methyl.pb, 391 bonds
> open pseudobonds/final_N_Aro.pb
Opened Pseudobonds final_N_Aro.pb, 10 bonds
> open pseudobonds/final_Methyl_Methyl.pb
Opened Pseudobonds final_Methyl_Methyl.pb, 372 bonds
> open pseudobonds/final_Methyl_Aro.pb
Opened Pseudobonds final_Methyl_Aro.pb, 93 bonds
> open pseudobonds/final_poor.pb
Opened Pseudobonds final_poor.pb, 56 bonds
> open pseudobonds/final_long.pb
Opened Pseudobonds final_long.pb, 110 bonds
> open pseudobonds/final_pdiff.pb
Opened Pseudobonds final_pdiff.pb, 48 bonds
> open pseudobonds/final_short.pb
Opened Pseudobonds final_short.pb, 2 bonds
> open pseudobonds/final_viol_upls.pb
Opened Pseudobonds final_viol_upls.pb, 178 bonds
> open pseudobonds/fgfr4_struc_cdn_model_v2.pb
Opened Pseudobonds fgfr4_struc_cdn_model_v2.pb, 396 bonds
> show #1:680,480,732,673,655,460,726,627,551,535
> hide H
> show #1.1@H,N target a
> open pseudobonds/hbond.pb
Opened Pseudobonds hbond.pb, 85 bonds
> name hbond
> #1.1:511,515,512,516,513,517,514,518,519,520,521,522,523,524,525,526,527,558,562,559,563,560,564,586,590,587,591,588,592,589,593,594,595,596,597,598,599,600,601,602,603,604,671,675,672,676,673,677,674,678,679,680,681,682,683,697,701,698,702,700,704,716,720,717,721,718,722,719,723,724,725,736,740,737,741,738,742,739,743,744,745,746,747,748,749,750,468,485,480,504,482,502,484,500,486,498,501,550,503,548,538,549,540,547,537,619,627,696,699,703,605@O,N
> show hbond target a
> open ../final.pdb maxModels 1
Chain information for final.pdb #14
---
Chain | Description
A | No description available
> rename #14 angle_restraints
> hide #14 target a
> color #14 gray(150)
> open ../final.pdb maxModels 1
Chain information for final.pdb #15
---
Chain | Description
A | No description available
> rename #15 rama_outliers
> hide #15 target a
> color #15 gray(150)
> name phipsi
> #14:459,460,461,462,463,464,465,466,467,468,469,470,471,477,478,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,530,532,536,537,538,539,540,541,542,543,545,546,547,548,549,550,551,552,553,554,555,562,563,564,565,566,575,585,586,587,588,589,590,591,605,606,607,608,609,610,613,614,615,621,622,623,624,625,627,628,629,631,632,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,671,672,673,674,675,676,686,688,691,692,693,699,700,701,702,703,704,705,706,707,708,709,710,717,718,719,720,721,722,726,727,728,729,730,731,732,733,735,736,737,738,741,742,743,744,745,746,747,748,749,750,633,634,668,669,670,685,687,689,690,694,712,716,725
> color phipsi purple target c
> name chi1chi2
> #14:481,500,521,524,590,618,627,628,626,631,677,678,680,682,683,685,690,693,708,726
> show chi1chi2 target a
> color chi1chi2 navy target a
> hide #14@H*,N,O target a
> color byhetero target a
> name viol_phipsi
> #14:468,469,470,485,487,489,492,493,494,495,496,505,506,540,541,542,548,555,564,606,613,631,632,652,653,657,660,664,665,666,693,717
> color viol_phipsi mediumpurple target c
> name chi1chi2 #14:521,631,726
> show chi1chi2 target a
> color chi1chi2 cornflowerblue target a
> hide #14@H*,N,O target a
> color byhetero target a
> name dissallowed_phipsi
> #15:454,456,457,474,479,488,506,534,559,568,569,573,582,611,612,618,633,634,636,638,639,641,648,649,651,696,714,752
> color dissallowed_phipsi mediumvioletred target c
> name dissallowed_chi1chi2
> #15:453,454,456,457,459,461,464,465,469,471,473,475,478,480,483,485,489,490,493,495,496,503,504,506,507,512,513,516,520,521,525,526,527,529,530,532,533,534,535,536,537,546,547,549,551,555,557,559,560,561,562,563,565,571,572,575,578,584,589,598,600,601,602,603,604,607,610,611,612,613,616,617,619,622,623,624,627,628,630,631,633,635,638,641,642,643,644,645,648,650,651,654,656,659,661,662,663,664,666,669,671,673,675,679,680,681,696,699,701,702,703,704,707,708,709,710,717,718,721,724,726,727,732,733,736,737,738,743,745,747,748
> show dissallowed_chi1chi2 target a
> color dissallowed_chi1chi2 medium violet red target a
> hide #15@H*,N,O target a
> color byhetero target a
> open ../final.pdb maxModels 1
Chain information for final.pdb #16
---
Chain | Description
A | No description available
> rename #16 noes
> hide #16 target a
> color #16 gray(150)
> color name c0 rgb(255,205,0)
Color 'c0' is opaque: rgb(100%, 80.4%, 0%) hex: #ffcd00
> color name c2 rgb(156,217,59)
Color 'c2' is opaque: rgb(61.2%, 85.1%, 23.1%) hex: #9cd93b
> color name c4 rgb(52,182,121)
Color 'c4' is opaque: rgb(20.4%, 71.4%, 47.5%) hex: #34b679
> color name c6 rgb(42,117,142)
Color 'c6' is opaque: rgb(16.5%, 45.9%, 55.7%) hex: #2a758e
> color name c8 rgb(59,81,139)
Color 'c8' is opaque: rgb(23.1%, 31.8%, 54.5%) hex: #3b518b
> color name c10 rgb(20,64,110)
Color 'c10' is opaque: rgb(7.84%, 25.1%, 43.1%) hex: #14406e
> color
> #16:452,453,456,457,461,490,559,560,569,571,592,595,598,599,601,602,604,612,616,617,627,636,637,638,639,641,643,644,645,647,648,649,650,654,656,669,670,676,681,688,713,714,723,724,725
> c0 target ac
> color
> #16:475,495,507,535,544,572,573,575,576,578,579,580,582,611,655,692,707,710,726,753,464,471,476,479,492,493,508,532,543,581,610,630,632,635,642,646,653,664,705,717,727
> c2 target ac
> color
> #16:459,488,510,511,531,556,566,605,606,607,608,657,663,680,690,700,720,731,733,752,460,496,506,530,557,565,640,659,668,684,686,687,696,706,709
> c4 target ac
> color
> #16:465,477,512,529,542,609,623,634,674,693,728,732,466,563,564,585,614,651,677,703,704,708,719,751
> c6 target ac
> color
> #16:513,528,622,624,625,665,671,697,737,474,478,522,594,600,666,667,699,738
> c8 target ac
> color
> #16:454,462,467,468,469,470,473,480,481,482,483,484,485,486,487,489,497,498,499,500,501,502,503,504,505,509,514,515,516,517,518,519,520,521,523,524,525,526,527,533,534,536,537,538,539,540,541,546,547,548
> c10 target ac
> color
> #16:549,550,551,552,553,554,555,558,561,562,584,586,588,589,590,591,593,596,597,603,613,615,618,619,620,621,626,628,629,631,633,660,661,662,672,673,675,678,679,682,683,685,695,698,701,702,718,721,722,729
> c10 target ac
> color #16:735,736,739,740,741,742,743,744,745,746,747,748,749,750 c10 target
> ac
> show #16:680,480,732,673,655,460,726,627,551,535
> show #16:thr,met,ala,leu,val,ile,phe,tyr
> hide #16@H*
> color byhetero
> key c0:0 c2:2 c4:4 c6:6 c8:8 c10:10 fontSize 14 colorTreatment distinct
> numericLabelSpacing equal
> key size 0.25000,0.03000
executed final_pra.cxc
> hide #1.2-20 target m
> hide #!1.1 models
> show #1.2 models
> hide #1.2 models
> show #!1.1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #10 models
> hide #11 models
> show #11 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide atoms
> show #1.2 models
> show #1.3-20 target m
> show :642
> hide cartoons
> hide #1.3-20 target m
> hide #!1.1 models
> show #!1.1 models
> hide #1.2 models
> show #1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show #1.3 models
> show #1.4 models
> hide #!1.1 models
> show #!1.1 models
> hide #1.2 models
> show #1.2 models
> show #1.5 models
> hide #1.5 models
> show #1.5 models
> hide #1.5 models
> hide #1.4 models
> show #1.1-20:640-645 cartoons
> hide #1.3 models
> hide #1.2 models
> show #1.1-20 cartoons
> show #1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.3 models
> show #1.4 models
> hide #1.3 models
> show #1.5 models
> hide #1.4 models
> show #1.6 models
> hide #1.6 models
> show #1.6 models
> hide #1.6 models
> show #1.7 models
> hide #1.7 models
> hide #1.5 models
> hide #!1 models
> show #!1.1 models
> hide #!1.1 models
> show #1.7 models
> show :642,660,641
> hide #1.7 models
> show #1.7 models
> hide #!1 models
> show :642,660,641,640
> show #!1.1 models
> hide #1.7 models
> hide #!1.1 models
> show #1.2 models
> hide #!1 models
> show #!1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #15 models
> hide #14 models
> show #14 models
> hide #14 models
> hide #16 models
> show #16 models
> hide #16 models
> hide #13 models
> hide #12 models
> hide #11 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #!1.1 models
> show #1.3 models
> hide #!1.1 models
> show #1.4 models
> hide #1.3 models
> hide : 641 atoms
> show :642,660,643,640
> hide #1.4 models
> show #!1.1 models
> show #1.2 models
> hide #!1.1 models
> hide #1.2 models
> show #1.3 models
> show #1.4 models
> hide #1.3 models
> show #1.5 models
> hide #1.4 models
> show #1.6 models
> hide #1.5 models
> open 6jpj
Summary of feedback from opening 6jpj fetched from pdb
---
note | Fetching compressed mmCIF 6jpj from http://files.rcsb.org/download/6jpj.cif
6jpj title:
Crystal structure of FGF401 in complex of FGFR4 [more info...]
Chain information for 6jpj #18
---
Chain | Description | UniProt
A | Fibroblast growth factor receptor 4 | FGFR4_HUMAN 445-753
Non-standard residues in 6jpj #18
---
FGF —
N-[5-cyano-4-(2-methoxyethylamino)pyridin-2-yl]-7-methanoyl-6-[(4-methyl-2-oxidanylidene-
piperazin-1-yl)methyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide
(Roblitinib; FGF-401)
SO4 — sulfate ion
> matchmaker #18 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 final.pdb, chain A (#1.1) with 6jpj, chain A (#18), sequence
alignment score = 1407.2
RMSD between 138 pruned atom pairs is 1.294 angstroms; (across all 299 pairs:
6.238)
> hide #1.6 models
> show #!1.1 models
> hide #!1.1 models
> show #1.2 models
> hide #1.2 models
> show #1.3 models
> show #1.2 models
> show #!1.1 models
> show #1.4 models
> hide #1.3 models
> hide #1.2 models
> hide #!1.1 models
> hide #1.4 models
> show #1.4 models
> show #1.5 models
> hide #1.4 models
> hide #1.5 models
> show #1.6 models
> show #1.2-20#!1.1 target m
> hide #1.2-20#!1.1 target m
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #1.2 models
> hide #1.2 models
> show #1.3 models
> hide #1.3 models
> show #1.4 models
> show #1.5 models
> hide #1.4 models
> hide #1.5 models
> show #1.6 models
> hide #1.6 models
> show #1.7 models
> show #1.8 models
> hide #1.7 models
> hide #1.8 models
> show #1.9 models
> hide #1.9 models
> show #1.10 models
> hide #1.10 models
> show #1.10 models
> hide #1.10 models
> show #1.11 models
> hide #1.11 models
> show #1.12 models
> hide #1.12 models
> show #1.13 models
> hide #18 models
> show #18 models
> hide #18 models
> show :642,660,643,640,702,673
> show :642,660,643,640,702,673,695,653
> distance #1.13/A:673@HE1 #1.13/A:702@HD12
> ~distance #1.13/A:673@HE1 #1.13/A:702@HD12
> distance #1.13/A:702@HD23 #1.13/A:673@HE1
> ~distance #1.13/A:702@HD23 #1.13/A:673@HE1
> show #1.14 models
> hide #1.14 models
> hide #1.13 models
> show #1.14 models
> show #18 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show #1.2 models
> show #1.3 models
> show #1.4 models
> hide #1.3 models
> show #1.3 models
> show #1.5 models
> hide #1.5 models
> show #1.5 models
> show #1.6 models
> show #1.7 models
> hide #1.7 models
> show #1.7 models
> show #1.8 models
> hide #1.8 models
> info residues #1:673 attribute chi1
residue id #1.1/A:673 chi1 -151.20882549391774 index 221
residue id #1.2/A:673 chi1 178.94210043674917 index 221
residue id #1.3/A:673 chi1 173.68716649126392 index 221
residue id #1.4/A:673 chi1 -148.0474097794322 index 221
residue id #1.5/A:673 chi1 -170.13068549223442 index 221
residue id #1.6/A:673 chi1 -172.75812864752575 index 221
residue id #1.7/A:673 chi1 175.35787644532144 index 221
residue id #1.8/A:673 chi1 153.89909149869288 index 221
residue id #1.9/A:673 chi1 177.7037594235731 index 221
residue id #1.10/A:673 chi1 169.46858646018734 index 221
residue id #1.11/A:673 chi1 -157.6362565086398 index 221
residue id #1.12/A:673 chi1 139.08654721339425 index 221
residue id #1.13/A:673 chi1 138.72436766746313 index 221
residue id #1.14/A:673 chi1 179.2186067385162 index 221
residue id #1.15/A:673 chi1 169.15324527698675 index 221
residue id #1.16/A:673 chi1 -179.92695001216632 index 221
residue id #1.17/A:673 chi1 151.17178450730464 index 221
residue id #1.18/A:673 chi1 -157.2465095151336 index 221
residue id #1.19/A:673 chi1 139.19937485185028 index 221
residue id #1.20/A:673 chi1 174.90275586591568 index 221
> info residues #1:673 attribute chi2
residue id #1.1/A:673 chi2 -64.07413528045949 index 221
residue id #1.2/A:673 chi2 94.47044905320391 index 221
residue id #1.3/A:673 chi2 91.7809164132326 index 221
residue id #1.4/A:673 chi2 -69.89129677553326 index 221
residue id #1.5/A:673 chi2 -59.45239194661469 index 221
residue id #1.6/A:673 chi2 -68.70324734630871 index 221
residue id #1.7/A:673 chi2 90.69349883324806 index 221
residue id #1.8/A:673 chi2 88.97938777179462 index 221
residue id #1.9/A:673 chi2 91.50001179829347 index 221
residue id #1.10/A:673 chi2 87.18304232807252 index 221
residue id #1.11/A:673 chi2 -63.324555603126946 index 221
residue id #1.12/A:673 chi2 87.76231353942892 index 221
residue id #1.13/A:673 chi2 87.24547958187883 index 221
residue id #1.14/A:673 chi2 95.9057224322636 index 221
residue id #1.15/A:673 chi2 90.48654598008078 index 221
residue id #1.16/A:673 chi2 91.88695734914216 index 221
residue id #1.17/A:673 chi2 85.1960740810465 index 221
residue id #1.18/A:673 chi2 -64.27218615317571 index 221
residue id #1.19/A:673 chi2 86.56532582467959 index 221
residue id #1.20/A:673 chi2 92.43315499993628 index 221
> hide #1.7 models
> hide #1.6 models
> hide #1.5 models
> info residues #18:673 attribute chi2
residue id #18/A:673 chi2 -74.3051664308634 index 230
> info residues #18:673 attribute chi1
residue id #18/A:673 chi1 176.78225050960714 index 230
> hide #1.2-5#!1.1 target m
> hide #1.14 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show #1.2 models
> hide #1.2 models
> show #1.4 models
> show #1.5 models
> show #1.6 models
> show #1.11 models
> show #1.18 models
> hide #18 models
> show #1.2 models
> hide #1.2 models
> show #18 models
> hide H
> show #1.2 models
> hide #1.2 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #1.11 models
> hide #1.18 models
> hide #18 models
> hide #17 models
> show #18 models
> hide #18 models
> hide #!1.1 models
> show #!1.1 models
> show #1.2 models
> hide #1.2 models
> show :642,660,643,640,702,673,695,653,726
> show #18 models
> hide #!1.1 models
> show #1.2 models
> hide #1.2 models
> show #1.3 models
> hide #1.3 models
> show #!1.1 models
> open /Users/ksinha01/Kinases_local/FGFR4/struc_calc/fgfr4_v88/final.pdb
Chain information for final.pdb
---
Chain | Description
19.1/A 19.2/A 19.3/A 19.4/A 19.5/A 19.6/A 19.7/A 19.8/A 19.9/A 19.10/A 19.11/A 19.12/A 19.13/A 19.14/A 19.15/A 19.16/A 19.17/A 19.18/A 19.19/A 19.20/A | No description available
> close #2-18#1
> show : 673
> hide #19.2-20 target m
> open 6jpj format mmcif fromDatabase pdb
6jpj title:
Crystal structure of FGF401 in complex of FGFR4 [more info...]
Chain information for 6jpj #1
---
Chain | Description | UniProt
A | Fibroblast growth factor receptor 4 | FGFR4_HUMAN 445-753
Non-standard residues in 6jpj #1
---
FGF —
N-[5-cyano-4-(2-methoxyethylamino)pyridin-2-yl]-7-methanoyl-6-[(4-methyl-2-oxidanylidene-
piperazin-1-yl)methyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide
(Roblitinib; FGF-401)
SO4 — sulfate ion
> matchmaker #1 to #19.1
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 final.pdb, chain A (#19.1) with 6jpj, chain A (#1), sequence
alignment score = 1458.8
RMSD between 142 pruned atom pairs is 1.241 angstroms; (across all 299 pairs:
6.260)
> show : 673
> show #19.2 models
> hide #19.1 models
> hide #19.2 models
> show #19.3 models
> hide #19.3 models
> show #19.4 models
> show #19.5 models
> show #19.6 models
> hide #19.5 models
> hide #19.4 models
> hide #19.6 models
> show #19.7 models
> show #19.8 models
> hide #19.7 models
> show #19.9 models
> hide #19.8 models
> show #19.10 models
> hide #19.9 models
> hide #19.10 models
> show #19.11 models
> hide #19.11 models
> show #19.12 models
> show #19.13 models
> hide #19.12 models
> show #19.14 models
> hide #19.13 models
> show #19.15 models
> hide #19.14 models
> show #19.16 models
> hide #19.15 models
> show #19.17 models
> show #19.18 models
> show #19.19 models
> show #19.20 models
> rename #19 id #2
> showmet2
Changed 95060 atom styles
> hide #1 models
> show #2.1-15 target m
> show: 673
Unknown command: show: 673
> show : 673
> color : 673 byelement
> show : 642
> color : 642 byelement
> show #1 models
> hide #!2 models
> showmet
Changed 2444 atom styles
> show #!2 models
> hide #1 models
> hide #2.2-20 target m
> show #2.2-20 target m
> info residues #1:734 attribute phi
residue id #1/A:734 phi -63.43595926912899 index 291
> info residues #1:734 attribute psi
residue id #1/A:734 psi 149.54240262076243 index 291
> info residues #2:734 attribute psi
residue id #2.1/A:734 psi 133.87597757355428 index 282
residue id #2.2/A:734 psi 104.209316282616 index 282
residue id #2.3/A:734 psi 112.49328960794324 index 282
residue id #2.4/A:734 psi 118.62469731969541 index 282
residue id #2.5/A:734 psi 135.25189334228818 index 282
residue id #2.6/A:734 psi 111.84909167936175 index 282
residue id #2.7/A:734 psi 140.36929938304527 index 282
residue id #2.8/A:734 psi 109.08005068497195 index 282
residue id #2.9/A:734 psi 116.18377731268987 index 282
residue id #2.10/A:734 psi 135.01577695048303 index 282
residue id #2.11/A:734 psi 160.30720568157125 index 282
residue id #2.12/A:734 psi 165.7305127753105 index 282
residue id #2.13/A:734 psi 118.62695657872638 index 282
residue id #2.14/A:734 psi 12.952523704063957 index 282
residue id #2.15/A:734 psi 19.676635342946934 index 282
residue id #2.16/A:734 psi 8.89013978573853 index 282
residue id #2.17/A:734 psi 12.443021936772196 index 282
residue id #2.18/A:734 psi 147.99625045326147 index 282
residue id #2.19/A:734 psi 126.34025348612812 index 282
residue id #2.20/A:734 psi -164.84753617987147 index 282
> hide #!2 models
> open /Users/ksinha01/Kinases_local/FGFR4/struc_calc/fgfr4_v89/fgfr4_v89.pdb
Chain information for fgfr4_v89.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A | No description available
> show #1 models
> hide #1 models
> 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 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.1), sequence
alignment score = 1429.4
RMSD between 138 pruned atom pairs is 1.275 angstroms; (across all 299 pairs:
6.615)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.2), sequence
alignment score = 1418
RMSD between 145 pruned atom pairs is 1.285 angstroms; (across all 299 pairs:
6.225)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.3), sequence
alignment score = 1422.2
RMSD between 163 pruned atom pairs is 1.229 angstroms; (across all 299 pairs:
6.782)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.4), sequence
alignment score = 1403.6
RMSD between 133 pruned atom pairs is 1.312 angstroms; (across all 299 pairs:
6.688)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.5), sequence
alignment score = 1412.6
RMSD between 148 pruned atom pairs is 1.308 angstroms; (across all 299 pairs:
6.670)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.6), sequence
alignment score = 1425.2
RMSD between 142 pruned atom pairs is 1.347 angstroms; (across all 299 pairs:
6.765)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.7), sequence
alignment score = 1418
RMSD between 122 pruned atom pairs is 1.306 angstroms; (across all 299 pairs:
5.678)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.8), sequence
alignment score = 1427
RMSD between 136 pruned atom pairs is 1.191 angstroms; (across all 299 pairs:
6.507)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.9), sequence
alignment score = 1404.8
RMSD between 137 pruned atom pairs is 1.221 angstroms; (across all 299 pairs:
6.948)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.10), sequence
alignment score = 1411.4
RMSD between 141 pruned atom pairs is 1.266 angstroms; (across all 299 pairs:
6.332)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.11), sequence
alignment score = 1416.8
RMSD between 156 pruned atom pairs is 1.258 angstroms; (across all 299 pairs:
5.885)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.12), sequence
alignment score = 1436
RMSD between 135 pruned atom pairs is 1.199 angstroms; (across all 299 pairs:
6.336)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.13), sequence
alignment score = 1427.6
RMSD between 152 pruned atom pairs is 1.284 angstroms; (across all 299 pairs:
5.936)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.14), sequence
alignment score = 1402.4
RMSD between 147 pruned atom pairs is 1.231 angstroms; (across all 299 pairs:
6.255)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.15), sequence
alignment score = 1424.6
RMSD between 141 pruned atom pairs is 1.232 angstroms; (across all 299 pairs:
6.879)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.16), sequence
alignment score = 1407.2
RMSD between 118 pruned atom pairs is 1.250 angstroms; (across all 299 pairs:
6.790)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.17), sequence
alignment score = 1428.2
RMSD between 134 pruned atom pairs is 1.232 angstroms; (across all 299 pairs:
6.364)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.18), sequence
alignment score = 1426.4
RMSD between 132 pruned atom pairs is 1.301 angstroms; (across all 299 pairs:
6.713)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.19), sequence
alignment score = 1435.4
RMSD between 133 pruned atom pairs is 1.241 angstroms; (across all 299 pairs:
6.760)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#3.20), sequence
alignment score = 1413.2
RMSD between 138 pruned atom pairs is 1.297 angstroms; (across all 299 pairs:
6.589)
> show #1 models
> show #!2 models
> hide #!2 models
> info residues #1:730 attribute phi
residue id #1/A:730 phi -55.65214415614515 index 287
> info residues #1:730 attribute psi
residue id #1/A:730 psi -27.17088641714837 index 287
> info residues #1:730 attribute phi,psi
> info residues #1:730 attribute phi psi
Expected a keyword
> info residues #1:730 attribute (phi,psi)
> info residues #1:730 attribute phi
residue id #1/A:730 phi -55.65214415614515 index 287
> info residues #1:730 attribute psi
residue id #1/A:730 psi -27.17088641714837 index 287
> info residues #1:729 attribute p?i
> info residues #1:729 attribute phi
residue id #1/A:729 phi -77.18756141621154 index 286
> info residues #1:729 attribute psi
residue id #1/A:729 psi 117.51575921389855 index 286
> info residues #3:729 attribute phi
residue id #3.1/A:729 phi -63.612640128372576 index 277
residue id #3.2/A:729 phi -65.09716472274266 index 277
residue id #3.3/A:729 phi -97.13344738777396 index 277
residue id #3.4/A:729 phi -88.83641272848477 index 277
residue id #3.5/A:729 phi -96.0376216269169 index 277
residue id #3.6/A:729 phi -95.65191574542078 index 277
residue id #3.7/A:729 phi -98.32007277804483 index 277
residue id #3.8/A:729 phi -64.72890868901406 index 277
residue id #3.9/A:729 phi -65.55281962176595 index 277
residue id #3.10/A:729 phi -65.77076272883116 index 277
residue id #3.11/A:729 phi -65.1447741892744 index 277
residue id #3.12/A:729 phi -79.0560515564643 index 277
residue id #3.13/A:729 phi -94.63549388878606 index 277
residue id #3.14/A:729 phi -96.03995398864369 index 277
residue id #3.15/A:729 phi -95.43530071375444 index 277
residue id #3.16/A:729 phi -69.36355685000109 index 277
residue id #3.17/A:729 phi -96.5984498381828 index 277
residue id #3.18/A:729 phi -64.31764942705627 index 277
residue id #3.19/A:729 phi -96.80303957889068 index 277
residue id #3.20/A:729 phi -94.08937243581568 index 277
> info residues #3:729 attribute psi
residue id #3.1/A:729 psi 113.22519053335412 index 277
residue id #3.2/A:729 psi 118.65789578066145 index 277
residue id #3.3/A:729 psi 144.96331468858065 index 277
residue id #3.4/A:729 psi 114.0614341654581 index 277
residue id #3.5/A:729 psi 107.95461416630769 index 277
residue id #3.6/A:729 psi 113.37507388691961 index 277
residue id #3.7/A:729 psi 109.15427574246641 index 277
residue id #3.8/A:729 psi 113.40980113144776 index 277
residue id #3.9/A:729 psi 125.715398146825 index 277
residue id #3.10/A:729 psi 124.12408069630997 index 277
residue id #3.11/A:729 psi 114.66212063719394 index 277
residue id #3.12/A:729 psi 113.58670327674415 index 277
residue id #3.13/A:729 psi 107.3033612839929 index 277
residue id #3.14/A:729 psi 107.01443140556289 index 277
residue id #3.15/A:729 psi 108.00174029365994 index 277
residue id #3.16/A:729 psi 113.277620909845 index 277
residue id #3.17/A:729 psi 109.38477030906463 index 277
residue id #3.18/A:729 psi 114.50012795174656 index 277
residue id #3.19/A:729 psi 106.40816353352687 index 277
residue id #3.20/A:729 psi 111.27735151561298 index 277
> info residues #3:730 attribute psi
residue id #3.1/A:730 psi -25.685986810995505 index 278
residue id #3.2/A:730 psi -11.977652831021413 index 278
residue id #3.3/A:730 psi -15.373332759687772 index 278
residue id #3.4/A:730 psi -17.217911815934528 index 278
residue id #3.5/A:730 psi -14.174233532247007 index 278
residue id #3.6/A:730 psi -8.55267057693416 index 278
residue id #3.7/A:730 psi -11.605964547417692 index 278
residue id #3.8/A:730 psi -30.415952183762037 index 278
residue id #3.9/A:730 psi -13.120542498643395 index 278
residue id #3.10/A:730 psi -14.518832535182757 index 278
residue id #3.11/A:730 psi -43.96395411070749 index 278
residue id #3.12/A:730 psi -11.798397027726317 index 278
residue id #3.13/A:730 psi -26.45393795114328 index 278
residue id #3.14/A:730 psi -21.098075307671472 index 278
residue id #3.15/A:730 psi -13.337254407132752 index 278
residue id #3.16/A:730 psi -40.471924570340164 index 278
residue id #3.17/A:730 psi -27.212462328982166 index 278
residue id #3.18/A:730 psi -39.11135005081553 index 278
residue id #3.19/A:730 psi -17.1374767999934 index 278
residue id #3.20/A:730 psi -10.936720318092284 index 278
> close #2
> rename #3 id #2
> hide #!2 models
> open /Users/ksinha01/Kinases_local/FGFR4/pdbs/fgfr4_alphafold_C477A.pdb
> format pdb
Chain information for fgfr4_alphafold_C477A.pdb #3
---
Chain | Description
A | No description available
> 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 6jpj, chain A (#1) with fgfr4_alphafold_C477A.pdb, chain A (#3),
sequence alignment score = 1541.5
RMSD between 247 pruned atom pairs is 0.812 angstroms; (across all 299 pairs:
5.307)
> distance #1/A:729@CB #1/A:728@CB
> ~distance #1/A:729@CB #1/A:728@CB
> show #!2 models
> hide #2.2-20 target m
> hide #2.1 models
> hide #1 models
> ui tool show H-Bonds
> hbonds saveFile
> /Users/ksinha01/Kinases_local/FGFR4/struc_calc/fgfr4_v89/hbond_file.txt
> twoColors true reveal true
11761 hydrogen bonds found
4446 strict hydrogen bonds found
> close #2
> close #4
> close #3
> ui tool show H-Bonds
> hbonds saveFile
> /Users/ksinha01/Kinases_local/FGFR4/struc_calc/fgfr4_v89/hbond_file.txt
> twoColors true reveal true
363 hydrogen bonds found
196 strict hydrogen bonds found
> show #!1 models
> hide #1.1 models
> show #1.1 models
> open /Users/ksinha01/Kinases_local/FGFR4/struc_calc/fgfr4_v89/fgfr4_v89.pdb
Chain information for fgfr4_v89.pdb
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | No description available
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.1), sequence
alignment score = 1429.4
RMSD between 138 pruned atom pairs is 1.275 angstroms; (across all 299 pairs:
6.615)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.2), sequence
alignment score = 1418
RMSD between 145 pruned atom pairs is 1.285 angstroms; (across all 299 pairs:
6.225)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.3), sequence
alignment score = 1422.2
RMSD between 163 pruned atom pairs is 1.229 angstroms; (across all 299 pairs:
6.782)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.4), sequence
alignment score = 1403.6
RMSD between 133 pruned atom pairs is 1.312 angstroms; (across all 299 pairs:
6.688)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.5), sequence
alignment score = 1412.6
RMSD between 148 pruned atom pairs is 1.308 angstroms; (across all 299 pairs:
6.670)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.6), sequence
alignment score = 1425.2
RMSD between 142 pruned atom pairs is 1.347 angstroms; (across all 299 pairs:
6.765)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.7), sequence
alignment score = 1418
RMSD between 122 pruned atom pairs is 1.306 angstroms; (across all 299 pairs:
5.678)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.8), sequence
alignment score = 1427
RMSD between 136 pruned atom pairs is 1.191 angstroms; (across all 299 pairs:
6.507)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.9), sequence
alignment score = 1404.8
RMSD between 137 pruned atom pairs is 1.221 angstroms; (across all 299 pairs:
6.948)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.10), sequence
alignment score = 1411.4
RMSD between 141 pruned atom pairs is 1.266 angstroms; (across all 299 pairs:
6.332)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.11), sequence
alignment score = 1416.8
RMSD between 156 pruned atom pairs is 1.258 angstroms; (across all 299 pairs:
5.885)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.12), sequence
alignment score = 1436
RMSD between 135 pruned atom pairs is 1.199 angstroms; (across all 299 pairs:
6.336)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.13), sequence
alignment score = 1427.6
RMSD between 152 pruned atom pairs is 1.284 angstroms; (across all 299 pairs:
5.936)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.14), sequence
alignment score = 1402.4
RMSD between 147 pruned atom pairs is 1.231 angstroms; (across all 299 pairs:
6.255)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.15), sequence
alignment score = 1424.6
RMSD between 141 pruned atom pairs is 1.232 angstroms; (across all 299 pairs:
6.879)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.16), sequence
alignment score = 1407.2
RMSD between 118 pruned atom pairs is 1.250 angstroms; (across all 299 pairs:
6.790)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.17), sequence
alignment score = 1428.2
RMSD between 134 pruned atom pairs is 1.232 angstroms; (across all 299 pairs:
6.364)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.18), sequence
alignment score = 1426.4
RMSD between 132 pruned atom pairs is 1.301 angstroms; (across all 299 pairs:
6.713)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.19), sequence
alignment score = 1435.4
RMSD between 133 pruned atom pairs is 1.241 angstroms; (across all 299 pairs:
6.760)
Matchmaker 6jpj, chain A (#1) with fgfr4_v89.pdb, chain A (#2.20), sequence
alignment score = 1413.2
RMSD between 138 pruned atom pairs is 1.297 angstroms; (across all 299 pairs:
6.589)
> hide #2.2-20 target m
> hide #!2 models
> ui tool show "Add Hydrogens"
> ui tool show H-Bonds
> label #1 : 729
> hide #!1 models
> show #!2 models
> show #2.1: 672,669
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> show #1: 672,669
> label #1 : 729,669,672
> hide #!2 models
> distance #1/A:672@CG1 #1/A:669@NE2
> ~distance #1/A:672@CG1 #1/A:669@NE2
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #2.2-20 target m
> show #2: 672,669
> hide #2.2-20 target m
> open /Users/ksinha01/Kinases_local/FGFR4/struc_calc/fgfr4_v90/fgfr4_v90.pdb
Chain information for fgfr4_v90.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A | No description available
> 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 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.1), sequence
alignment score = 1425.2
RMSD between 126 pruned atom pairs is 1.256 angstroms; (across all 299 pairs:
6.556)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.2), sequence
alignment score = 1421
RMSD between 147 pruned atom pairs is 1.278 angstroms; (across all 299 pairs:
6.633)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.3), sequence
alignment score = 1410.2
RMSD between 125 pruned atom pairs is 1.359 angstroms; (across all 299 pairs:
6.917)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.4), sequence
alignment score = 1409
RMSD between 149 pruned atom pairs is 1.268 angstroms; (across all 299 pairs:
6.565)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.5), sequence
alignment score = 1399.4
RMSD between 133 pruned atom pairs is 1.276 angstroms; (across all 299 pairs:
6.285)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.6), sequence
alignment score = 1419.2
RMSD between 123 pruned atom pairs is 1.268 angstroms; (across all 299 pairs:
6.524)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.7), sequence
alignment score = 1425.8
RMSD between 111 pruned atom pairs is 1.014 angstroms; (across all 299 pairs:
7.242)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.8), sequence
alignment score = 1438.4
RMSD between 116 pruned atom pairs is 1.328 angstroms; (across all 299 pairs:
5.888)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.9), sequence
alignment score = 1419.2
RMSD between 139 pruned atom pairs is 1.269 angstroms; (across all 299 pairs:
6.586)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.10), sequence
alignment score = 1403
RMSD between 119 pruned atom pairs is 1.180 angstroms; (across all 299 pairs:
6.212)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.11), sequence
alignment score = 1415.6
RMSD between 124 pruned atom pairs is 1.286 angstroms; (across all 299 pairs:
6.814)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.12), sequence
alignment score = 1419.8
RMSD between 122 pruned atom pairs is 1.166 angstroms; (across all 299 pairs:
6.298)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.13), sequence
alignment score = 1441.4
RMSD between 126 pruned atom pairs is 1.250 angstroms; (across all 299 pairs:
6.724)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.14), sequence
alignment score = 1430.6
RMSD between 120 pruned atom pairs is 1.269 angstroms; (across all 299 pairs:
6.521)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.15), sequence
alignment score = 1423.4
RMSD between 135 pruned atom pairs is 1.236 angstroms; (across all 299 pairs:
6.584)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.16), sequence
alignment score = 1415
RMSD between 131 pruned atom pairs is 1.286 angstroms; (across all 299 pairs:
6.812)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.17), sequence
alignment score = 1432.4
RMSD between 126 pruned atom pairs is 1.357 angstroms; (across all 299 pairs:
7.569)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.18), sequence
alignment score = 1427.6
RMSD between 129 pruned atom pairs is 1.204 angstroms; (across all 299 pairs:
6.238)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.19), sequence
alignment score = 1413.8
RMSD between 116 pruned atom pairs is 1.369 angstroms; (across all 299 pairs:
7.105)
Matchmaker 6jpj, chain A (#1) with fgfr4_v90.pdb, chain A (#3.20), sequence
alignment score = 1446.2
RMSD between 124 pruned atom pairs is 1.198 angstroms; (across all 299 pairs:
6.141)
> hide #!2 models
> show #3: 672,669
> show #3: 672,669 atoms
> info residues #1:669 attribute phi
residue id #1/A:669 phi -78.70425429895909 index 226
> info residues #1:669 attribute psi
residue id #1/A:669 psi -17.76488357604416 index 226
> hide #3.1 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.1-20 target m
> show #3.16 models
> distance #3.16/A:669@NE2 #3.16/A:672@CG2
> show #3.1 models
> show #3.2 models
> hide #3.1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide atoms
> open /Users/ksinha01/Kinases_local/FGFR4/struc_calc/fgfr4_v91/fgfr4_v91.pdb
Chain information for fgfr4_v91.pdb
---
Chain | Description
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A 5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A | No description available
> matchmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.1), sequence
alignment score = 1437.8
RMSD between 143 pruned atom pairs is 1.315 angstroms; (across all 299 pairs:
6.168)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.2), sequence
alignment score = 1420.4
RMSD between 140 pruned atom pairs is 1.279 angstroms; (across all 299 pairs:
7.083)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.3), sequence
alignment score = 1418
RMSD between 145 pruned atom pairs is 1.247 angstroms; (across all 299 pairs:
6.832)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.4), sequence
alignment score = 1425.2
RMSD between 138 pruned atom pairs is 1.285 angstroms; (across all 299 pairs:
6.457)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.5), sequence
alignment score = 1438.4
RMSD between 126 pruned atom pairs is 1.295 angstroms; (across all 299 pairs:
6.568)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.6), sequence
alignment score = 1418
RMSD between 126 pruned atom pairs is 1.272 angstroms; (across all 299 pairs:
6.265)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.7), sequence
alignment score = 1438.4
RMSD between 144 pruned atom pairs is 1.294 angstroms; (across all 299 pairs:
6.536)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.8), sequence
alignment score = 1430.6
RMSD between 134 pruned atom pairs is 1.299 angstroms; (across all 299 pairs:
6.936)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.9), sequence
alignment score = 1415
RMSD between 135 pruned atom pairs is 1.329 angstroms; (across all 299 pairs:
7.234)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.10), sequence
alignment score = 1431.2
RMSD between 141 pruned atom pairs is 1.220 angstroms; (across all 299 pairs:
7.179)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.11), sequence
alignment score = 1433.6
RMSD between 130 pruned atom pairs is 1.279 angstroms; (across all 299 pairs:
6.798)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.12), sequence
alignment score = 1445.6
RMSD between 150 pruned atom pairs is 1.197 angstroms; (across all 299 pairs:
6.641)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.13), sequence
alignment score = 1426.4
RMSD between 103 pruned atom pairs is 1.177 angstroms; (across all 299 pairs:
7.280)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.14), sequence
alignment score = 1413.8
RMSD between 130 pruned atom pairs is 1.267 angstroms; (across all 299 pairs:
6.834)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.15), sequence
alignment score = 1417.4
RMSD between 108 pruned atom pairs is 0.989 angstroms; (across all 299 pairs:
7.151)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.16), sequence
alignment score = 1419.8
RMSD between 138 pruned atom pairs is 1.145 angstroms; (across all 299 pairs:
6.941)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.17), sequence
alignment score = 1446.2
RMSD between 123 pruned atom pairs is 1.398 angstroms; (across all 299 pairs:
6.520)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.18), sequence
alignment score = 1439
RMSD between 134 pruned atom pairs is 1.254 angstroms; (across all 299 pairs:
6.866)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.19), sequence
alignment score = 1407.2
RMSD between 141 pruned atom pairs is 1.325 angstroms; (across all 299 pairs:
6.464)
Matchmaker 6jpj, chain A (#1) with fgfr4_v91.pdb, chain A (#5.20), sequence
alignment score = 1438.4
RMSD between 132 pruned atom pairs is 1.278 angstroms; (across all 299 pairs:
6.693)
> hide #!3 models
> hide #!1 models
> show #!1 models
===== Log before crash end =====
Log:
> alias dd distance delete
> alias rd ui mousemode right distance
> alias rs ui mousemode right select
> alias nmr1 hide #1.2-20 models
> alias slall label sel text
> "{0.label_one_letter_code}{0.number}{0.insertion_code}"
> alias lmearo label #1:thr,met,ala,leu,val,ile,phe,tyr text
> "{0.label_one_letter_code}{0.number}{0.insertion_code}"
> alias showbb show #1@N,C,CA,O,H; cartoon #1 suppress false; transparency #1
> 50 target c; hide #1:hoh
> alias hidebb hide #1@N,C,CA,O,H target a; transparency $1 0 target c
> alias sdist ui tool show Distances
> alias showmet show #1:ile,leu,val,met,ala,thr target a; hide H; color #1:ile
> paleturquoise target a; color #1:leu lightsalmon target a; color #1:val
> khaki target a; color #1:met thistle target a; color #1:ala yellowgreen
> target ab; color #1:thr aquamarine target a;color byhetero target a ; style
> #1 ball
> alias showmet2 show #2:ile,leu,val,met,ala,thr target a; hide H; color
> #2:ile paleturquoise target a; color #2:leu lightsalmon target a; color
> #2:val khaki target a; color #2:met thistle target a; color #2:ala
> yellowgreen target ab; color #2:thr aquamarine target a;color byhetero
> target a ; style #2 ball
> alias showmet3 show #3:ile,leu,val,met,ala,thr target a; hide H; color
> #3:ile paleturquoise target a; color #3:leu lightsalmon target a; color
> #3:val khaki target a; color #3:met thistle target a; color #3:ala
> yellowgreen target ab; color #3:thr aquamarine target a;color byhetero
> target a ; style #3 ball
> alias showaro show #1:phe,tyr,his,trp target ab; hide H; color #1:phe plum
> target a; color #1:tyr lightpink target a; color byhetero target a
> ui mousemode right distance
> alias fgfr1_brake show #1: 546,562,638
> alias fgfr2_brake show #1: 549,565,641
> alias fgfr3_brake show #1: 540,556,632
> alias fgfr4_brake show #1: 535,551,627
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open fgfr4_v92.pdb
Chain information for fgfr4_v92.pdb
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | No description available
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 10-Core Intel Core i9
Processor Speed: 3.6 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache (per Core): 256 KB
L3 Cache: 20 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 23 days, 22 hours, 34 minutes
Graphics/Displays:
AMD Radeon Pro 5300:
Chipset Model: AMD Radeon Pro 5300
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0047
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XL-012
Option ROM Version: 113-D322A1XL-012
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG Ultra HD:
Resolution: 6720 x 3780
UI Looks like: 3360 x 1890 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Crash connecting or disconnecting an external display or waking from sleep on Mac with AMD graphics. Crashed in displayConfigFinalizedProc. Has been reported dozens of times. Bug in Qt 6.6, possibly fixed in Qt 6.7 used by ChimeraX daily builds.