![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#5798 closed defect (duplicate)
Crash setting StructureSeq chain_id
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-21.1.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 46000,
"procLaunch" : "2021-12-16 09:29:18.5966 -0800",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,4",
"procStartAbsTime" : 46929161100016,
"coalitionID" : 1063,
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"train" : "macOS 12.0.1",
"build" : "21A559",
"releaseType" : "User"
},
"captureTime" : "2021-12-16 09:29:48.4830 -0800",
"incident" : "9366BC98-4FE0-4397-BBE3-8AA2953FB9E8",
"bug_type" : "309",
"pid" : 8437,
"procExitAbsTime" : 46959042074314,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.1.1","CFBundleVersion":"1.1.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "191372BE-CC4D-8AE7-4E47-7B44646F1D9F",
"wakeTime" : 32073,
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"sleepWakeUUID" : "EDBF5E33-2178-41EC-B6FF-2C6130642651",
"sip" : "enabled",
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"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
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"faultingThread" : 0,
"threads" : 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Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/All_from_AF/Chimera_draft_1.cxs"
Log from Thu Dec 16 09:24:06 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to cryoem/210730_CryoEM map fits with
> crystal + alphafold/190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4" format ccp4
Opened 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4, grid size 190,190,190,
pixel 1.15, shown at level 4.8, step 1, values float32
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to cryoem/RealSpaceRefine_2/rsr2.pdb"
> format pdb
Chain information for rsr2.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
> show cartoons
> hide atoms
> volume #1 style mesh
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6N1.pdb"
Chain information for Af_Sc_Pex6N1.pdb #3
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6N1.pdb"
Chain information for Af_Sc_Pex6N1.pdb #4
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6N1.pdb"
Chain information for Af_Sc_Pex6N1.pdb #5
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6N2.pdb"
Chain information for Af_Sc_Pex6N2.pdb #6
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6N2.pdb"
Chain information for Af_Sc_Pex6N2.pdb #7
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6N2.pdb"
Chain information for Af_Sc_Pex6N2.pdb #8
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6D1.pdb"
Chain information for Af_Sc_Pex6D1.pdb #9
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6D1.pdb"
Chain information for Af_Sc_Pex6D1.pdb #10
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6D1.pdb"
Chain information for Af_Sc_Pex6D1.pdb #11
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6D2.pdb"
Chain information for Af_Sc_Pex6D2.pdb #12
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6D2.pdb"
Chain information for Af_Sc_Pex6D2.pdb #13
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6D2.pdb"
Chain information for Af_Sc_Pex6D2.pdb #14
---
Chain | Description
A | No description available
> align #3 toAtoms #2/B
Unequal number of atoms to pair, 1579 and 6802
> align #3 toAtoms #2/B matchNumbering true
Pairing dropped 198 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 2.360 angstroms
> select down
Nothing selected
> select down
Nothing selected
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> align #4 toAtoms #2/D matchNumbering true
Pairing dropped 198 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 2.376 angstroms
> align #5 toAtoms #2/F matchNumbering true
Pairing dropped 198 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 2.425 angstroms
> align #6 toAtoms #2/B matchNumbering true
Pairing dropped 396 atoms and 5405 reference atoms
RMSD between 1397 atom pairs is 3.924 angstroms
> align #7 toAtoms #2/D matchNumbering true
Pairing dropped 396 atoms and 5405 reference atoms
RMSD between 1397 atom pairs is 3.772 angstroms
> align #8 toAtoms #2/F matchNumbering true
Pairing dropped 396 atoms and 5405 reference atoms
RMSD between 1397 atom pairs is 3.825 angstroms
> align #9 toAtoms #2/B matchNumbering true
Pairing dropped 114 atoms and 4568 reference atoms
RMSD between 2234 atom pairs is 2.681 angstroms
> align #10 toAtoms #2/D matchNumbering true
Pairing dropped 114 atoms and 4568 reference atoms
RMSD between 2234 atom pairs is 2.581 angstroms
> align #11 toAtoms #2/F matchNumbering true
Pairing dropped 114 atoms and 4568 reference atoms
RMSD between 2234 atom pairs is 2.619 angstroms
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/Pex6 N1 - Xray data/Rapoport_model/Pex1Pex6 from
> Rapoport/pex16_asymm.pdb"
Chain information for pex16_asymm.pdb #15
---
Chain | Description
A C E | No description available
B D F | No description available
> hide cartoons
> show cartoons
> hide atoms
> align #15/B toAtoms #2/B matchNumbering true
Pairing dropped 9470 atoms and 16 reference atoms
RMSD between 6786 atom pairs is 5.859 angstroms
> fitmap #15 inMap #1 resolution 4
Fit map pex16_asymm.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 274106 points
correlation = 0.696, correlation about mean = 0.2101, overlap = 3.275e+05
steps = 52, shift = 0.447, angle = 0.379 degrees
Position of pex16_asymm.pdb map 4 (#16) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.62295878 0.09129507 -0.77690898 117.25556352
-0.78222016 0.06337379 -0.61977042 307.00838273
-0.00734632 0.99380530 0.11089211 -51.47211028
Axis 0.81096678 -0.38677438 -0.43901989
Axis point 0.00000000 210.38876180 176.75025278
Rotation angle (degrees) 95.81908385
Shift along axis -1.05533006
> align #12 toAtoms #15/B matchNubmering true
Expected a keyword
> align #15/B toAtoms #2/B matchNumbering true
Pairing dropped 9470 atoms and 16 reference atoms
RMSD between 6786 atom pairs is 5.859 angstroms
> align #15/B toAtoms #2/B matchNumbering true
Pairing dropped 9470 atoms and 16 reference atoms
RMSD between 6786 atom pairs is 5.859 angstroms
> fitmap #15 inMap #1 resolution 4
Fit map pex16_asymm.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 274106 points
correlation = 0.696, correlation about mean = 0.2101, overlap = 3.275e+05
steps = 52, shift = 0.447, angle = 0.379 degrees
Position of pex16_asymm.pdb map 4 (#16) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.62295878 0.09129507 -0.77690898 117.25556352
-0.78222016 0.06337379 -0.61977042 307.00838273
-0.00734632 0.99380530 0.11089211 -51.47211028
Axis 0.81096678 -0.38677438 -0.43901989
Axis point 0.00000000 210.38876180 176.75025278
Rotation angle (degrees) 95.81908385
Shift along axis -1.05533006
> align #12 toAtoms #15/B matchNumbering true
Pairing dropped 0 atoms and 13850 reference atoms
RMSD between 2406 atom pairs is 4.897 angstroms
> align #13 toAtoms #15/D matchNumbering true
Pairing dropped 0 atoms and 13850 reference atoms
RMSD between 2406 atom pairs is 4.383 angstroms
> align #14 toAtoms #15/F matchNumbering true
Pairing dropped 0 atoms and 13850 reference atoms
RMSD between 2406 atom pairs is 5.142 angstroms
> fitmap #3 inMap #1 resolution 4
Fit map Af_Sc_Pex6N1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 10335 points
correlation = 0.8225, correlation about mean = 0.3586, overlap = 1.215e+04
steps = 64, shift = 0.356, angle = 1.68 degrees
Position of Af_Sc_Pex6N1.pdb map 4 (#17) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.10874598 0.94412521 -0.31113004 149.15489049
-0.78492296 -0.27360520 -0.55591019 141.32905979
-0.60997562 0.18376011 0.77081902 105.59890209
Axis 0.38843878 0.15693913 -0.90801180
Axis point 154.90344048 17.44364851 0.00000000
Rotation angle (degrees) 107.80425895
Shift along axis -15.76744616
> fitmap #4 inMap #1 resolution 4
Fit map Af_Sc_Pex6N1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 10335 points
correlation = 0.8295, correlation about mean = 0.3624, overlap = 1.342e+04
steps = 52, shift = 0.148, angle = 1.25 degrees
Position of Af_Sc_Pex6N1.pdb map 4 (#17) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.64439923 -0.69899822 -0.31008242 115.91772670
0.47793868 -0.68469815 0.55023910 55.30608001
-0.59692901 0.20637327 0.77529725 106.78923960
Axis -0.27307240 0.22779200 0.93463483
Axis point 66.56231146 40.79296244 0.00000000
Rotation angle (degrees) 140.97761826
Shift along axis 80.75329438
> fitmap #5 inMap #1 resolution 4
Fit map Af_Sc_Pex6N1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 10335 points
correlation = 0.8266, correlation about mean = 0.3797, overlap = 1.368e+04
steps = 68, shift = 0.403, angle = 1.2 degrees
Position of Af_Sc_Pex6N1.pdb map 4 (#17) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.71645691 -0.23269927 0.65767814 58.18847086
0.31089429 0.95044148 -0.00239528 127.13267594
-0.62452721 0.20618449 0.75329524 107.72816366
Axis 0.14811715 0.91052264 0.38601792
Axis point 76.98945286 0.00000000 -17.90692023
Rotation angle (degrees) 44.75720683
Shift along axis 165.96089148
> fitmap #6 inMap #1 resolution 4
Fit map Af_Sc_Pex6N2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 11719 points
correlation = 0.822, correlation about mean = 0.4746, overlap = 1.654e+04
steps = 48, shift = 0.276, angle = 2.28 degrees
Position of Af_Sc_Pex6N2.pdb map 4 (#18) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.12020100 0.96664916 -0.22614401 147.89816457
-0.86756511 -0.21301434 -0.44939478 138.59086200
-0.48257900 0.14217695 0.86423563 108.79312728
Axis 0.30426933 0.13189491 -0.94341078
Axis point 151.50047093 10.17731984 0.00000000
Rotation angle (degrees) 103.56155320
Shift along axis -39.35630424
> fitmap #7 inMap #1 resolution 4
Fit map Af_Sc_Pex6N2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 11719 points
correlation = 0.8281, correlation about mean = 0.4633, overlap = 1.676e+04
steps = 64, shift = 0.446, angle = 1.7 degrees
Position of Af_Sc_Pex6N2.pdb map 4 (#18) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.69789326 -0.66886876 -0.25604605 114.35595226
0.53506614 -0.72457272 0.43439453 57.58554940
-0.47607691 0.16615945 0.86356344 109.65055792
Axis -0.21408698 0.17561365 0.96089886
Axis point 61.77121228 43.29042296 0.00000000
Rotation angle (degrees) 141.21036164
Shift along axis 90.99378393
> fitmap #8 inMap #1 resolution 4
Fit map Af_Sc_Pex6N2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 11719 points
correlation = 0.8251, correlation about mean = 0.4756, overlap = 1.737e+04
steps = 64, shift = 0.373, angle = 1.76 degrees
Position of Af_Sc_Pex6N2.pdb map 4 (#18) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.79606174 -0.29184567 0.53019978 61.10070593
0.33408735 0.94238661 0.01712052 127.21596888
-0.50464973 0.16350405 0.84769988 110.77886460
Axis 0.12015882 0.84945558 0.51379673
Axis point 60.08674965 0.00000000 -53.07523673
Rotation angle (degrees) 37.52627247
Shift along axis 172.32392170
> fitmap #9 inMap #1 resolution 4
Fit map Af_Sc_Pex6D1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 15043 points
correlation = 0.8133, correlation about mean = 0.5264, overlap = 2.389e+04
steps = 64, shift = 0.301, angle = 1.15 degrees
Position of Af_Sc_Pex6D1.pdb map 4 (#19) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.13841424 0.97069023 -0.19647384 147.42918352
-0.90401452 -0.20485426 -0.37522324 138.02454511
-0.40447403 0.12567896 0.90587281 108.39367256
Axis 0.25666427 0.10658012 -0.96060613
Axis point 148.00935808 8.06621099 0.00000000
Rotation angle (degrees) 102.63256243
Shift along axis -51.57314975
> fitmap #10 inMap #1 resolution 4
Fit map Af_Sc_Pex6D1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 15043 points
correlation = 0.823, correlation about mean = 0.5209, overlap = 2.436e+04
steps = 64, shift = 0.1, angle = 1.09 degrees
Position of Af_Sc_Pex6D1.pdb map 4 (#19) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.72201836 -0.66077409 -0.20510262 113.96719126
0.56471942 -0.73410338 0.37707320 58.27164992
-0.39972673 0.15642835 0.90318808 109.34524650
Axis -0.17507102 0.15442482 0.97236984
Axis point 58.88460855 44.28651620 0.00000000
Rotation angle (degrees) 140.93821019
Shift along axis 95.37025634
> fitmap #11 inMap #1 resolution 4
Fit map Af_Sc_Pex6D1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 15043 points
correlation = 0.8243, correlation about mean = 0.519, overlap = 2.57e+04
steps = 48, shift = 0.0941, angle = 0.851 degrees
Position of Af_Sc_Pex6D1.pdb map 4 (#19) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.83786280 -0.30237657 0.45448250 61.79130941
0.33762357 0.94127346 0.00382150 127.19372861
-0.42894784 0.15024211 0.89074747 110.39418934
Axis 0.13302785 0.80262502 0.58146081
Axis point 38.90327108 0.00000000 -71.00482602
Rotation angle (degrees) 33.39021490
Shift along axis 174.49872849
> fitmap #12 inMap #1 resolution 4
Fit map Af_Sc_Pex6D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 15543 points
correlation = 0.7336, correlation about mean = 0.08207, overlap = 1.397e+04
steps = 168, shift = 9.93, angle = 27.1 degrees
Position of Af_Sc_Pex6D2.pdb map 4 (#20) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.11922696 0.75381812 -0.64617581 140.66433985
-0.92657982 -0.31829211 -0.20034960 140.29201776
-0.35669982 0.57484639 0.73642166 106.20781635
Axis 0.41385967 -0.15454470 -0.89712658
Axis point 145.54190352 -2.76369516 0.00000000
Rotation angle (degrees) 110.52088013
Shift along axis -58.74794687
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #!15 models
> volume #1 level 3.926
> fitmap #13 inMap #1 resolution 4
Fit map Af_Sc_Pex6D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 15543 points
correlation = 0.7701, correlation about mean = 0.1615, overlap = 1.311e+04
steps = 80, shift = 7.45, angle = 10.3 degrees
Position of Af_Sc_Pex6D2.pdb map 4 (#20) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.66687081 -0.73447123 -0.12583850 109.67553031
0.60985415 -0.63497301 0.47422273 61.18554855
-0.42820700 0.23950216 0.87136529 108.85826134
Axis -0.16792631 0.21632372 0.96177170
Axis point 55.94061221 45.12224244 0.00000000
Rotation angle (degrees) 135.66281133
Shift along axis 99.51527375
> fitmap #14 inMap #1 resolution 4
Fit map Af_Sc_Pex6D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 15543 points
correlation = 0.8068, correlation about mean = 0.3138, overlap = 1.77e+04
steps = 88, shift = 7.56, angle = 2.87 degrees
Position of Af_Sc_Pex6D2.pdb map 4 (#20) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.82477586 -0.27155140 0.49598853 69.49671022
0.36590460 0.92504562 -0.10200205 129.96214312
-0.43111322 0.26561332 0.86231720 109.72931627
Axis 0.31057981 0.78326182 0.53855464
Axis point 31.30145708 0.00000000 -14.79718307
Rotation angle (degrees) 36.28634611
Shift along axis 182.47389242
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1N1.pdb"
Chain information for Af_Pex1N1.pdb #21
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1N1.pdb"
Chain information for Af_Pex1N1.pdb #22
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1N1.pdb"
Chain information for Af_Pex1N1.pdb #23
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1N2.pdb"
Chain information for Af_Pex1N2.pdb #24
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1N2.pdb"
Chain information for Af_Pex1N2.pdb #25
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1N2.pdb"
Chain information for Af_Pex1N2.pdb #26
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1D1.pdb"
Chain information for Af_Pex1D1.pdb #27
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1D1.pdb"
Chain information for Af_Pex1D1.pdb #28
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1D1.pdb"
Chain information for Af_Pex1D1.pdb #29
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1D2.pdb"
Chain information for Af_Pex1D2.pdb #30
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1D2.pdb"
Chain information for Af_Pex1D2.pdb #31
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Pex1D2.pdb"
Chain information for Af_Pex1D2.pdb #32
---
Chain | Description
A | No description available
> close #21
> close #22
> close #23
> align #24 toAtoms #2/A matchNumbering true
Pairing dropped 0 atoms and 3457 reference atoms
RMSD between 1731 atom pairs is 1.800 angstroms
> align #25 toAtoms #2/C matchNumbering true
Pairing dropped 0 atoms and 3457 reference atoms
RMSD between 1731 atom pairs is 2.298 angstroms
> align #26 toAtoms #2/E matchNumbering true
Pairing dropped 0 atoms and 3457 reference atoms
RMSD between 1731 atom pairs is 1.949 angstroms
> align #27 toAtoms #2/A matchNumbering true
Pairing dropped 213 atoms and 3319 reference atoms
RMSD between 1869 atom pairs is 2.775 angstroms
> align #28 toAtoms #2/B matchNumbering true
Pairing dropped 106 atoms and 4826 reference atoms
RMSD between 1976 atom pairs is 21.185 angstroms
> align #28 toAtoms #2/C matchNumbering true
Pairing dropped 213 atoms and 3319 reference atoms
RMSD between 1869 atom pairs is 2.778 angstroms
> align #29 toAtoms #2/E matchNumbering true
Pairing dropped 213 atoms and 3319 reference atoms
RMSD between 1869 atom pairs is 2.799 angstroms
> align #30 toAtoms #15/A matchNumbering true
Pairing dropped 609 atoms and 9547 reference atoms
RMSD between 2205 atom pairs is 5.287 angstroms
> align #31 toAtoms #15/C matchNumbering true
Pairing dropped 609 atoms and 9547 reference atoms
RMSD between 2205 atom pairs is 4.823 angstroms
> align #32 toAtoms #15/E matchNumbering true
Pairing dropped 609 atoms and 9547 reference atoms
RMSD between 2205 atom pairs is 5.577 angstroms
> fitmap #24 inMap #1 resolution 4
Fit map Af_Pex1N2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 11646 points
correlation = 0.7552, correlation about mean = 0.3217, overlap = 1.249e+04
steps = 100, shift = 0.39, angle = 2.17 degrees
Position of Af_Pex1N2.pdb map 4 (#21) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.34692050 -0.77644479 -0.52609853 109.07849020
0.73949189 -0.11857738 0.66263953 140.99525092
-0.57688639 -0.61892883 0.53303770 109.79109346
Axis -0.64539417 0.02557663 0.76342138
Axis point 19.28889898 138.41135252 -0.00000000
Rotation angle (degrees) 96.85225875
Shift along axis 17.02442951
> fitmap #25 inMap #1 resolution 4
Fit map Af_Pex1N2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 11646 points
correlation = 0.7509, correlation about mean = 0.3091, overlap = 1.215e+04
steps = 64, shift = 0.42, angle = 1.69 degrees
Position of Af_Pex1N2.pdb map 4 (#21) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.43222939 0.26868361 0.86080594 135.20207942
-0.68742128 0.71599190 0.12168642 90.68136016
-0.58363494 -0.64433277 0.49417157 109.47263130
Axis -0.40443981 0.76263024 -0.50480051
Axis point 172.94591340 0.00000000 -23.82970209
Rotation angle (degrees) 71.26470465
Shift along axis -40.78659686
> fitmap #26 inMap #1 resolution 4
Fit map Af_Pex1N2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 11646 points
correlation = 0.7481, correlation about mean = 0.298, overlap = 1.216e+04
steps = 48, shift = 0.344, angle = 1.42 degrees
Position of Af_Pex1N2.pdb map 4 (#21) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.82508183 0.47565771 -0.30494215 79.01994602
-0.05348796 -0.60303937 -0.79591617 92.26314647
-0.56247579 -0.64038524 0.52299879 110.33421972
Axis 0.25551573 0.42309201 -0.86931287
Axis point 65.38831891 65.05653869 0.00000000
Rotation angle (degrees) 162.28111281
Shift along axis -36.68831735
> fitmap #27 inMap #1 resolution 4
Fit map Af_Pex1D1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 13556 points
correlation = 0.786, correlation about mean = 0.5024, overlap = 2.065e+04
steps = 48, shift = 0.102, angle = 0.847 degrees
Position of Af_Pex1D1.pdb map 4 (#22) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.31397210 -0.85363047 -0.41561586 106.37013191
0.76798319 -0.02904115 0.63981125 141.60702414
-0.55823234 -0.52006888 0.64645574 106.58157201
Axis -0.58028164 0.07135024 0.81128439
Axis point 8.45370120 141.50355537 0.00000000
Rotation angle (degrees) 91.96601229
Shift along axis 34.84702501
> fitmap #28 inMap #1 resolution 4
Fit map Af_Pex1D1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 13556 points
correlation = 0.7896, correlation about mean = 0.4929, overlap = 2.019e+04
steps = 60, shift = 0.088, angle = 0.486 degrees
Position of Af_Pex1D1.pdb map 4 (#22) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.49018733 0.38252990 0.78319044 137.50828377
-0.67350038 0.73660239 0.06175882 92.01119262
-0.55327535 -0.55775245 0.61870719 106.24436195
Axis -0.34180043 0.73736282 -0.58263929
Axis point 177.71758054 0.00000000 -41.97235172
Rotation angle (degrees) 64.99176906
Shift along axis -41.05689650
> fitmap #289 inMap #1 resolution 4
No atoms or maps for #289
> fitmap #29 inMap #1 resolution 4
Fit map Af_Pex1D1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 13556 points
correlation = 0.8071, correlation about mean = 0.5004, overlap = 2.2e+04
steps = 64, shift = 0.119, angle = 0.774 degrees
Position of Af_Pex1D1.pdb map 4 (#22) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.84276164 0.43054639 -0.32308299 79.11288420
-0.09594494 -0.71074342 -0.69687758 89.90107344
-0.52966724 -0.55630352 0.64029604 107.46767945
Axis 0.24121338 0.35448134 -0.90341523
Axis point 62.66147529 58.59650524 0.00000000
Rotation angle (degrees) 163.05884140
Shift along axis -46.13659969
> fitmap #30 inMap #1 resolution 4
Fit map Af_Pex1D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 18648 points
correlation = 0.6809, correlation about mean = 0.1141, overlap = 1.427e+04
steps = 128, shift = 7.01, angle = 21.6 degrees
Position of Af_Pex1D2.pdb map 4 (#23) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.88219950 0.40373394 0.24232820 129.67317084
-0.47079421 0.74669417 0.46989428 100.95960206
0.00876721 -0.52862721 0.84880882 100.26852051
Axis -0.74088743 0.17329862 -0.64888629
Axis point 0.00000000 77.94441106 -225.81340841
Rotation angle (degrees) 42.36634955
Shift along axis -143.63992966
> fitmap #31 inMap #1 resolution 4
Fit map Af_Pex1D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 18648 points
correlation = 0.7163, correlation about mean = 0.2163, overlap = 1.734e+04
steps = 112, shift = 9.74, angle = 16.2 degrees
Position of Af_Pex1D2.pdb map 4 (#23) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.83223220 0.55084221 -0.06294774 83.10372256
-0.42544045 -0.70728773 -0.56457460 95.29534535
-0.35551369 -0.44307665 0.82297819 107.63776145
Axis 0.11837361 0.28504256 -0.95117739
Axis point 64.78936285 50.58784511 0.00000000
Rotation angle (degrees) 149.12298766
Shift along axis -65.38208724
> fitmap #32 inMap #1 resolution 4
Fit map Af_Pex1D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 18648 points
correlation = 0.7195, correlation about mean = 0.2101, overlap = 1.778e+04
steps = 80, shift = 4.57, angle = 5.08 degrees
Position of Af_Pex1D2.pdb map 4 (#23) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.01484925 -0.84358892 -0.53678415 108.09030111
0.98650989 -0.07516908 0.14542296 133.42944646
-0.16302677 -0.53170230 0.83109262 104.70597937
Axis -0.34080851 -0.18811836 0.92111945
Axis point 5.72280692 135.38954964 0.00000000
Rotation angle (degrees) 96.58133892
Shift along axis 34.50809085
> save "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/All_from_AF/Af_aligned_and_fit.cxs"
> open "/Users/ryanjudy/Documents/School/Lab/Structal analysis/Pex6 N1 - Xray
> data/Refine_179/pex6n1_refine_179.pdb"
Chain information for pex6n1_refine_179.pdb #33
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Structal analysis/Pex6 N1 - Xray
> data/Refine_179/pex6n1_refine_179.pdb"
Chain information for pex6n1_refine_179.pdb #34
---
Chain | Description
A | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Structal analysis/Pex6 N1 - Xray
> data/Refine_179/pex6n1_refine_179.pdb"
Chain information for pex6n1_refine_179.pdb #35
---
Chain | Description
A | No description available
> align #33 toAtoms #2/B matchNumbering true
Pairing dropped 7 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 1.592 angstroms
> align #34 toAtoms #2/D matchNumbering true
Pairing dropped 7 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 1.493 angstroms
> align #35 toAtoms #2/F matchNumbering true
Pairing dropped 7 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 1.478 angstroms
> fitmap #33 inMap #1 resolution 4
Fit map pex6n1_refine_179.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 8867 points
correlation = 0.8313, correlation about mean = 0.3582, overlap = 1.121e+04
steps = 64, shift = 0.405, angle = 1.58 degrees
Position of pex6n1_refine_179.pdb map 4 (#36) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.80308521 -0.19968384 -0.56140940 161.04495540
-0.59262131 -0.16949914 -0.78744525 172.14273708
0.06208168 0.96508881 -0.25445915 112.39826666
Axis 0.92180987 -0.32794811 -0.20667994
Axis point 0.00000000 64.90116595 150.85921327
Rotation angle (degrees) 108.08554049
Shift along axis 68.76847709
> fitmap #34 inMap #1 resolution 4
Fit map pex6n1_refine_179.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 8867 points
correlation = 0.8392, correlation about mean = 0.3674, overlap = 1.231e+04
steps = 56, shift = 0.335, angle = 0.823 degrees
Position of pex6n1_refine_179.pdb map 4 (#36) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.90877314 -0.01625665 -0.41697375 136.95242961
-0.40652560 0.25999342 0.87586549 29.84826150
0.09417179 0.96547353 -0.24288378 112.95508764
Axis 0.13800408 -0.78720805 -0.60104771
Axis point 63.73938721 0.00000000 60.65625576
Rotation angle (degrees) 161.05519170
Shift along axis -72.48819427
> fitmap #35 inMap #1 resolution 4
Fit map pex6n1_refine_179.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 8867 points
correlation = 0.839, correlation about mean = 0.388, overlap = 1.266e+04
steps = 60, shift = 0.157, angle = 0.066 degrees
Position of pex6n1_refine_179.pdb map 4 (#36) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.10924872 0.26498904 0.95804255 25.76310457
0.99068812 -0.10780897 -0.08315206 121.84826887
0.08125120 0.95820563 -0.27429948 115.04945569
Axis 0.67503632 0.56835995 0.47041784
Axis point 0.00000000 33.02998816 63.15636851
Rotation angle (degrees) 129.52611597
Shift along axis 140.76602317
> select #30/A:936
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
189 atoms, 192 bonds, 23 residues, 1 model selected
> select up
2814 atoms, 2855 bonds, 363 residues, 1 model selected
> select clear
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.07
> alphafold/multimer/ScP1D2_P6N12/ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb"
Chain information for ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb #37
---
Chain | Description
B | No description available
C | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.07
> alphafold/multimer/ScP1D2_P6N12/ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb"
Chain information for ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb #38
---
Chain | Description
B | No description available
C | No description available
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.07
> alphafold/multimer/ScP1D2_P6N12/ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb"
Chain information for ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb #39
---
Chain | Description
B | No description available
C | No description available
> align #37/C:1-200 toAtoms #2/B
Unequal number of atoms to pair, 1579 and 6802
> align #37/C:1-200 toAtoms #2/B matchNumbering true
Pairing dropped 198 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 2.150 angstroms
> hide #37 models
> show #37 models
> volume #1 level 3.384
> align #38/C:1-200 toAtoms #2/D matchNumbering true
Pairing dropped 198 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 2.056 angstroms
> align #39/C:1-200 toAtoms #2/F matchNumbering true
Pairing dropped 198 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 2.091 angstroms
> volume #1 level 1.801
> select #37/B:341
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:938
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #37/B:341
8 atoms, 7 bonds, 1 residue, 1 model selected
> hbonds sel
0 hydrogen bonds found
> close #40
> select #37/C
3506 atoms, 3583 bonds, 443 residues, 1 model selected
> delete #37/C
> delete #38/C
> delete #39/C
> resrenumber #37/B 603
Unknown command: resrenumber #37/B 603
> renumber_residues #37/B 603
Unknown command: renumber_residues #37/B 603
> ui tool show "Build Structure"
> delete #37/B:1-339
> delete #38/B:1-339
> delete #39/B:1-339
> delete #37/B:371:441
> delete #38/B:371:441
> delete #39/B:371:441
> fitmap #37 inMap #1 resolution 4
Fit map ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb map 4 in map
190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4 using 5124 points
correlation = 0.5556, correlation about mean = 0.1046, overlap = 4244
steps = 80, shift = 2.85, angle = 6.42 degrees
Position of ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb map 4 (#40) relative
to 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.64954946 -0.33907378 0.68052515 152.96781710
-0.52032035 0.85087209 -0.07268709 143.76195825
-0.55439357 -0.40130494 -0.72911049 121.63415498
Axis -0.25460759 0.95679428 -0.14042680
Axis point 121.05598086 0.00000000 38.15229507
Rotation angle (degrees) 139.80869128
Shift along axis 81.52315517
> fitmap #38 inMap #1 resolution 4
Fit map ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb map 4 in map
190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4 using 5124 points
correlation = 0.5688, correlation about mean = 0.1101, overlap = 4612
steps = 84, shift = 2.89, angle = 7.59 degrees
Position of ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb map 4 (#40) relative
to 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.12898501 0.89790547 -0.42086653 116.32243256
0.81710958 -0.14423615 -0.55814681 50.67658339
-0.56186724 -0.41588665 -0.71508286 122.47389206
Axis 0.65867449 0.65284313 -0.37409059
Axis point 0.00000000 -38.32507717 94.63798526
Rotation angle (degrees) 173.80055461
Shift along axis 63.88614748
> fitmap #39 inMap #1 resolution 4
Fit map ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb map 4 in map
190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4 using 5124 points
correlation = 0.5607, correlation about mean = 0.1152, overlap = 4563
steps = 100, shift = 3.38, angle = 7.46 degrees
Position of ScP1CP6N12_3dc33_unrelaxed_rank_1_model_2.pdb map 4 (#40) relative
to 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.75472123 -0.59118336 -0.28442590 54.38556352
-0.31588145 -0.70744619 0.63224900 129.48865367
-0.57499111 -0.38732688 -0.72066852 124.07263819
Axis -0.93083649 0.26527570 0.25134086
Axis point 0.00000000 91.76609041 49.27242439
Rotation angle (degrees) 146.79292998
Shift along axis 14.91064877
> delete #30:935-988
> hide #!30 models
> show #!30 models
> delete #31:935-988
> delete #32:935-988
> save "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/All_from_AF/Af_aligned_and_fit_p6n1_p1D2l.cxs"
> fitmap #30 inMap #1 resolution 4
Fit map Af_Pex1D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 15652 points
correlation = 0.7424, correlation about mean = 0.1507, overlap = 1.25e+04
steps = 68, shift = 0.802, angle = 3.3 degrees
Position of Af_Pex1D2.pdb map 4 (#23) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.87196631 0.44414540 0.20593597 128.56211460
-0.48730348 0.74701839 0.45221548 101.19541098
0.04701147 -0.49466998 0.86780847 99.40370643
Axis -0.70784495 0.11880413 -0.69630532
Axis point -0.00000000 54.41727647 -232.26761715
Rotation angle (degrees) 41.97843804
Shift along axis -148.19494077
> fitmap #31 inMap #1 resolution 4
Fit map Af_Pex1D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 15652 points
correlation = 0.7712, correlation about mean = 0.2779, overlap = 1.519e+04
steps = 80, shift = 0.29, angle = 1.72 degrees
Position of Af_Pex1D2.pdb map 4 (#23) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.82271804 0.56137420 -0.08940937 82.17010181
-0.42272505 -0.70935299 -0.56402293 95.01866767
-0.38005073 -0.42623626 0.82090444 107.69834840
Axis 0.13308475 0.28072331 -0.95051716
Axis point 65.23648548 50.08976895 0.00000000
Rotation angle (degrees) 148.82423447
Shift along axis -64.75958691
> fitmap #32 inMap #1 resolution 4
Fit map Af_Pex1D2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS Pex15.ccp4
using 15652 points
correlation = 0.7651, correlation about mean = 0.2702, overlap = 1.554e+04
steps = 56, shift = 0.144, angle = 3.43 degrees
Position of Af_Pex1D2.pdb map 4 (#23) relative to 190515_sharpened NTD_D1_D2
ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.04531101 -0.85652714 -0.51410910 108.44120217
0.99177341 -0.02310474 0.12590341 132.17583550
-0.11971805 -0.51558455 0.84843395 104.34008926
Axis -0.32141701 -0.19760931 0.92608945
Axis point 1.87513130 137.89511876 0.00000000
Rotation angle (degrees) 93.70847347
Shift along axis 35.65423409
> delete #3:1-175
> delete #4:1-175
> delete #5:1-175
> fitmap #3 inMap #1 resolution 4
Fit map Af_Sc_Pex6N1.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 1417 points
correlation = 0.7271, correlation about mean = 0.1216, overlap = 1540
steps = 192, shift = 6.15, angle = 26.9 degrees
Position of Af_Sc_Pex6N1.pdb map 4 (#17) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
0.21954502 0.80911134 -0.54510442 158.67279153
-0.87736635 -0.08060033 -0.47300305 130.97827242
-0.42664772 0.58210174 0.69219165 104.54936930
Axis 0.52944290 -0.05944060 -0.84626062
Axis point 182.75191280 -27.84604589 0.00000000
Rotation angle (degrees) 94.84335359
Shift along axis -12.25325826
> close #3
> open "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/Af_broken_into_domains/Af_Sc_Pex6N1.pdb"
Chain information for Af_Sc_Pex6N1.pdb #3
---
Chain | Description
A | No description available
> align #3 toAtoms #2/B matchNumbering true
Pairing dropped 198 atoms and 5421 reference atoms
RMSD between 1381 atom pairs is 2.360 angstroms
> fitmap #3 to_map #1 resolution 4
Expected a keyword
> hide #13 models
> show #13 models
> select #31/A:928
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #13/A:972
8 atoms, 7 bonds, 1 residue, 1 model selected
> save /Users/ryanjudy/Downloads/31_13.pdb, #13,31
No known data format for file suffix '.pdb,'
> save /Users/ryanjudy/Downloads/31_13.pdb format pdb models #13,31
> open /Users/ryanjudy/Downloads/31_13.pdb
Chain information for 31_13.pdb
---
Chain | Description
41.1/A | No description available
41.2/A | No description available
> hide #41.1 models
> show #41.1 models
> hide #!41.2 models
> show #!41.2 models
> help align
> select #30/A:932
5 atoms, 4 bonds, 1 residue, 1 model selected
> align #41 toAtoms #40 matchNumbering true
Pairing dropped 4793 atoms and 0 reference atoms
No atoms paired for alignment
> align #41 toAtoms #30 matchNumbering true
Pairing dropped 3096 atoms and 690 reference atoms
RMSD between 1697 atom pairs is 21.629 angstroms
> hide #41.1 models
> show #41.1 models
> hide #!41.2 models
> show #!41.2 models
> align #41.2 toAtoms #30 matchNumbering true
RMSD between 2387 atom pairs is 0.001 angstroms
> close #41
> open /Users/ryanjudy/Downloads/13_31_combined2.pdb
Chain information for 13_31_combined2.pdb #41
---
Chain | Description
A | No description available
B | No description available
> hide #!41 models
> show #!41 models
> align #41/A toAtoms #30 matchNumbering true
RMSD between 2387 atom pairs is 0.001 angstroms
> select #41/B
2406 atoms, 2449 bonds, 308 residues, 1 model selected
> hide #12 models
> fitmap #41/B inMap #1 resolution 4
Fit map 13_31_combined2.pdb map 4 in map 190515_sharpened NTD_D1_D2 ATPgS
Pex15.ccp4 using 15558 points
correlation = 0.7996, correlation about mean = 0.2483, overlap = 1.586e+04
steps = 116, shift = 8.75, angle = 23 degrees
Position of 13_31_combined2.pdb map 4 (#42) relative to 190515_sharpened
NTD_D1_D2 ATPgS Pex15.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.62927303 -0.74446552 -0.22312900 279.76144361
0.77619760 -0.61647834 -0.13218070 98.49067241
-0.03915022 -0.25636995 0.96578554 25.12528738
Axis -0.08081143 -0.11971719 0.98951367
Axis point 117.85932425 116.81631235 0.00000000
Rotation angle (degrees) 129.79054534
Shift along axis -9.53713270
> close #12
> delete #41/A
> select clear
> delete #3:1-175
> delete #4:1-175
> delete #5:1-175
> select #39/B:364
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete #39:372-440
> hide #!37 models
> show #!37 models
> delete #37:372-440
> delete #38:372-440
> hide #!2 models
> select clear
> save "/Users/ryanjudy/Documents/School/Lab/Book_3 Pex6N1
> crystallography/E3.08 sc16 combine to
> cryoem/All_from_AF/Chimera_draft_1.cxs"
opened ChimeraX session
OpenGL version: 4.1 INTEL-18.2.10
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,4
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10548.0.0,0)
OS Loader Version: 540.40.4~45
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 23:55
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash setting StructureSeq chain_id |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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