id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15816	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
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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===== 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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX