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Opened 8 weeks ago
Closed 8 weeks ago
#18613 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020abb20c0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 117)
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{
"uptime" : 1000000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 41716,
"osVersion" : {
"train" : "macOS 15.6",
"build" : "24G84",
"releaseType" : "User"
},
"captureTime" : "2025-08-25 15:29:27.3298 +0800",
"codeSigningMonitor" : 1,
"incident" : "21D36728-ED0B-4DC5-B181-82491FE93563",
"pid" : 60693,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-23 22:18:21.3058 +0800",
"procStartAbsTime" : 21784873426870,
"procExitAbsTime" : 24116134244403,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4B764D4A-44DA-587C-B5DB-F4B21D0B739E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "72006326-E93A-79ED-CE4E-652FF4F2A5CE",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["regionIneligible","countryBillingIneligible","countryLocationIneligible"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "34370387-1AAD-46A8-8686-95F45E5D3615",
"wakeTime" : 4,
"sleepWakeUUID" : "75C99E60-85D6-4762-A7F2-F8916F34E80A",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4311678616\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100ff0000-100ff4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":60693},
"ktriageinfo" : "CL - (arg = 0x0) cluster_pagein past EOF\nAPFS - (arg = 0x3bcc001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\n",
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4311678616\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100ff0000-100ff4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/chenxi/Desktop/0817_lipf/7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb
> format pdb
Chain information for 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1
---
Chain | Description
A B C | No description available
> open /Users/chenxi/Desktop/PDB/7wlt.pdb format pdb
7wlt.pdb title:
The curved structure of MPIEZO1 In lipid bilayer [more info...]
Chain information for 7wlt.pdb #2
---
Chain | Description | UniProt
A C E | protein FAM38A | PIEZ1_MOUSE 1-2547
Non-standard residues in 7wlt.pdb #2
---
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol
> open
> /Users/chenxi/Desktop/0817_lipf/rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb
> format pdb
Chain information for rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb #3
---
Chain | Description
A B C | No description available
> open
> /Users/chenxi/Desktop/0808rhlip_all/rhlipc0808/rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb
> format pdb
Chain information for
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb #4
---
Chain | Description
A B C | No description available
> open /Users/chenxi/Desktop/PDB/8ixo.pdb format pdb
8ixo.pdb title:
Intermediate structure of MPIEZO1-S2472E [more info...]
Chain information for 8ixo.pdb #5
---
Chain | Description | UniProt
A B F | protein FAM38A | PIEZ1_MOUSE 1-2547
Non-standard residues in 8ixo.pdb #5
---
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> select #1-8: 2501-2547
6207 atoms, 6297 bonds, 705 residues, 5 models selected
> ui tool show Matchmaker
> matchmaker #!2-5 & sel to #1 & sel
Computing secondary structure
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 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
7wlt.pdb, chain A (#2), sequence alignment score = 233.4
RMSD between 44 pruned atom pairs is 0.675 angstroms; (across all 47 pairs:
0.953)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence
alignment score = 215.4
RMSD between 45 pruned atom pairs is 1.182 angstroms; (across all 47 pairs:
1.253)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4),
sequence alignment score = 232.8
RMSD between 44 pruned atom pairs is 0.736 angstroms; (across all 47 pairs:
1.064)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
8ixo.pdb, chain A (#5), sequence alignment score = 230.4
RMSD between 44 pruned atom pairs is 0.727 angstroms; (across all 47 pairs:
1.079)
> cartoon style sel modeHelix tube sides 20
> set bgColor white
> color #1 #ffb48cff
> color #1 #ffca8cff
> color #1 #ffca80ff
> color #2 #90ceebff
> color #2 #90b3ebff
> color #2 #90b3ffff
> select add #1
39729 atoms, 40584 bonds, 39 pseudobonds, 5061 residues, 6 models selected
> select subtract #1
4968 atoms, 5040 bonds, 564 residues, 4 models selected
> select add #2
37632 atoms, 38481 bonds, 33 pseudobonds, 4509 residues, 6 models selected
> select subtract #2
3720 atoms, 3774 bonds, 423 residues, 3 models selected
> select add #3
36756 atoms, 37572 bonds, 45 pseudobonds, 4728 residues, 4 models selected
> select subtract #3
2481 atoms, 2517 bonds, 282 residues, 2 models selected
> select add #4
38838 atoms, 39771 bonds, 36 pseudobonds, 4680 residues, 3 models selected
> select subtract #4
1233 atoms, 1251 bonds, 141 residues, 1 model selected
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> select subtract #5
Nothing selected
> color #2 #29b3ffff
> color #2 #299dffff
> color #2 #299d8fff
> color #2 #29728fff
> color #2 #297270ff
> color #2 #299d70ff
> color #2 #299d8fff
> color #2 #309d8fff
> color #2 #3a9d8fff
> color #2 #759d8fff
> color #2 #209d8fff
> color #2 #20918fff
> color #2 #20919cff
> color #2 #209182ff
> color #3 #90a0ddff
> color #3 #90b3ddff
> color #3 #90b3ffff
> color #4 #20ee90ff
> color #4 #209190ff
> color #4 #209182ff
> color #2 #9e9a9aff
> color #2 #c6c2c1ff
> color #2 #b6b1b1ff
> color #2 #ada9a8ff
> color #5 #f28072ff
> color #5 #f2a772ff
> color #5 #f2a7bcff
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> view orient
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5.1 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> select #3: 2116-2492
8721 atoms, 8946 bonds, 9 pseudobonds, 1089 residues, 2 models selected
> select ~sel & ##selected
25554 atoms, 26109 bonds, 36 pseudobonds, 3357 residues, 2 models selected
> hide sel cartoons
> show #!1 models
> hide #!3 models
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> select subtract #3
Nothing selected
> select #1: 2116-2492
8724 atoms, 8949 bonds, 6 pseudobonds, 1089 residues, 2 models selected
> select ~sel & ##selected
26037 atoms, 26595 bonds, 33 pseudobonds, 3408 residues, 2 models selected
> hide sel cartoons
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!3 models
> select #1: 2476
21 atoms, 18 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indian red
> select #3: 2476
21 atoms, 18 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indian red
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> select subtract #3
Nothing selected
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> hide #!1,3 atoms
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting soft
> view orient
> turn z 50
> turn y 50
> view orient
> turn y 90
> turn z 90
> turn x 5
> turn x -5
> turn y 5
> select #1 and #3 2185-2213
Expected a keyword
> select #1, #3: 2185-2213
Expected an objects specifier or a keyword
> select #1 and #3: 2185-2213
Expected a keyword
> select #1: 2185-2213
702 atoms, 720 bonds, 87 residues, 1 model selected
> transparency 50
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> turn y 5
> ui tool show "Side View"
> ui dockable false "Side View"
> save /Users/chenxi/Desktop/RH-figure/change/rhlf-wtlf.png width 2000 height
> 1468 supersample 3 transparentBackground true
> hide #!1 models
> show #!5 models
> select #5: 2116-2492
8814 atoms, 9045 bonds, 3 pseudobonds, 1101 residues, 2 models selected
> select ~sel & ##selected
23298 atoms, 23754 bonds, 36 pseudobonds, 3099 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #5: 2476
21 atoms, 18 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indian red
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> select subtract #5
Nothing selected
> save /Users/chenxi/Desktop/RH-figure/change/rhlf-se.png width 2000 height
> 1468 supersample 3 transparentBackground true
> turn z 90
> turn z -90
> turn x 90
> ui tool show "Side View"
> save /Users/chenxi/Desktop/RH-figure/change/rhlf-se-cap.png width 2000
> height 1468 supersample 3 transparentBackground true
> hide #!5 models
> show #!1 models
> save /Users/chenxi/Desktop/RH-figure/change/rhlf-wtlf-cap.png width 2000
> height 1468 supersample 3 transparentBackground true
> ui tool show "Side View"
> turn x -90
> ui tool show "Side View"
> show #!5 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!5 models
> ui mousemode right select
Drag select of 1155 residues, 6 pseudobonds
> select ~sel & ##selected
26037 atoms, 26595 bonds, 33 pseudobonds, 3408 residues, 2 models selected
> select ~sel & ##selected
8724 atoms, 8949 bonds, 6 pseudobonds, 1089 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select ~sel & ##selected
26037 atoms, 26595 bonds, 33 pseudobonds, 3408 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> ui tool show "Side View"
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!5 models
> ui tool show "Side View"
> view orient
> turn x -90
> turn y 5
> turn y -5
> turn y 5
> show #!2 models
> hide #!2 models
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting simple
> lighting soft
> save "/Users/chenxi/Desktop/RH-figure/model align/sehole+rhlf.png" width
> 2000 height 1468 supersample 3 transparentBackground true
> log metadata #5
Metadata for 8ixo.pdb #5
---
Title | Intermediate structure of MPIEZO1-S2472E
Citation | AN intermediate open structure reveals the gating transitionof the mechanically activated PIEZO1 channel. PMID: 39719701
Non-standard residues | P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine)
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol
Gene source | Mus musculus (house mouse)
Experimental method | Electron microscopy
Resolution | 4.00Å
> log chains #5
Chain information for 8ixo.pdb #5
---
Chain | Description | UniProt
A B F | protein FAM38A | PIEZ1_MOUSE 1-2547
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!5 models
> hide #!2.1 models
> hide #!2 atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #1.1 models
> hide #3.1 models
> hide #4.1 models
> hide #!1 models
> save "/Users/chenxi/Desktop/RH-figure/model align/7wlt.png" width 894 height
> 656 supersample 3
> save "/Users/chenxi/Desktop/RH-figure/model align/7wlt.png" width 2000
> height 1468 supersample 3 transparentBackground true
> open /Users/chenxi/Desktop/PDB/8yfg_hp1_RH_mdfic.pdb
8yfg_hp1_RH_mdfic.pdb title:
Human PIEZO1-R2456H_mdfic [more info...]
Chain information for 8yfg_hp1_RH_mdfic.pdb #6
---
Chain | Description | UniProt
A B D | piezo-type mechanosensitive ion channel component 1 | PIEZ1_HUMAN 1-2521
C E F | myod family inhibitor domain-containing protein | MDFIC_HUMAN 2-247
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> hide sel surfaces
> hide (#!6 & sel) target a
> show sel cartoons
> hide sel atoms
> cartoon style (#!6 & sel) modeHelix tube sides 20
> select #1-6: 2116-2492
52605 atoms, 53946 bonds, 27 pseudobonds, 6609 residues, 12 models selected
> ui tool show Matchmaker
> matchmaker #!2-6 & sel to #1 & sel
Computing secondary structure
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 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
7wlt.pdb, chain A (#2), sequence alignment score = 1801.5
RMSD between 254 pruned atom pairs is 0.701 angstroms; (across all 363 pairs:
2.467)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence
alignment score = 1756.8
RMSD between 203 pruned atom pairs is 0.938 angstroms; (across all 363 pairs:
15.989)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain C (#4),
sequence alignment score = 1798.8
RMSD between 239 pruned atom pairs is 1.053 angstroms; (across all 363 pairs:
2.319)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
8ixo.pdb, chain B (#5), sequence alignment score = 1754.3
RMSD between 220 pruned atom pairs is 0.715 angstroms; (across all 361 pairs:
9.420)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 1473.7
RMSD between 164 pruned atom pairs is 1.284 angstroms; (across all 340 pairs:
11.113)
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1-6: 2501-2547
6762 atoms, 6864 bonds, 768 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!1,3-6 & sel to #2 & sel
Computing secondary structure
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 7wlt.pdb, chain A (#2) with
7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1), sequence alignment
score = 233.4
RMSD between 44 pruned atom pairs is 0.675 angstroms; (across all 47 pairs:
0.953)
Matchmaker 7wlt.pdb, chain A (#2) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence
alignment score = 229.8
RMSD between 42 pruned atom pairs is 0.993 angstroms; (across all 47 pairs:
1.286)
Matchmaker 7wlt.pdb, chain A (#2) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4),
sequence alignment score = 240.6
RMSD between 47 pruned atom pairs is 0.343 angstroms; (across all 47 pairs:
0.343)
Matchmaker 7wlt.pdb, chain A (#2) with 8ixo.pdb, chain A (#5), sequence
alignment score = 244.8
RMSD between 47 pruned atom pairs is 0.506 angstroms; (across all 47 pairs:
0.506)
Matchmaker 7wlt.pdb, chain A (#2) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6),
sequence alignment score = 101.9
RMSD between 20 pruned atom pairs is 0.385 angstroms; (across all 21 pairs:
1.216)
> select add #1
40284 atoms, 41151 bonds, 39 pseudobonds, 5124 residues, 7 models selected
> select add #2
72948 atoms, 74592 bonds, 72 pseudobonds, 9069 residues, 9 models selected
> select subtract #1
38187 atoms, 39048 bonds, 33 pseudobonds, 4572 residues, 7 models selected
> select subtract #2
4275 atoms, 4341 bonds, 486 residues, 4 models selected
> select add #2
38187 atoms, 39048 bonds, 33 pseudobonds, 4572 residues, 7 models selected
> select subtract #2
4275 atoms, 4341 bonds, 486 residues, 4 models selected
> select add #3
37311 atoms, 38139 bonds, 45 pseudobonds, 4791 residues, 5 models selected
> select subtract #3
3036 atoms, 3084 bonds, 345 residues, 3 models selected
> select add #4
39393 atoms, 40338 bonds, 36 pseudobonds, 4743 residues, 4 models selected
> select subtract #4
1788 atoms, 1818 bonds, 204 residues, 2 models selected
> select add #5
32667 atoms, 33366 bonds, 39 pseudobonds, 4263 residues, 4 models selected
> select subtract #5
555 atoms, 567 bonds, 63 residues, 1 model selected
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> color #6 #ffdbcaff
> color #6 #fcd9c8ff
> show #!5 models
> hide #!2 models
> color #6 #fcbca1ff
> color #6 #fc6f9aff
> color #6 #fc7e6dff
> color #6 #d76b5dff
> color #6 #c76356ff
> color #6 #c75851ff
> color #6 #c74d47ff
> color #6 #c7708eff
> color #6 #c75655ff
> color #6 #c74743ff
> color #6 #c74f5cff
> color #6 #c74641ff
> color #6 #853ac7ff
> color #6 #6f41c7ff
> color #6 #ac76c7ff
> color #6 #c7605dff
> color #6 #c75956ff
> color #6 #c7565bff
> color #6 #52c7b0ff
> show #!4 models
> hide #!4 models
> color #6 #72c7bdff
> show #!4 models
> hide #!4 models
> color #6 #c75e59ff
> color #6 #c74142ff
> color #6 #c74e58ff
> color #6 #c74738ff
> show #!4 models
> hide #!4 models
> color #6 #c7c5c1ff
> color #6 #bfc7c1ff
> show #!2 models
> hide #!2 models
> color #6 #c4c7c2ff
> color #6 #cdd0cbff
> color #6 #fcfff9ff
> show #!2 models
> hide #!2 models
> color #6 #73ff77ff
> color #6 #b5ffbeff
> color #6 #c7ffb3ff
> color #6 #c1ffc0ff
> color #6 #acffa3ff
> color #6 #fa6956ff
> color #6 #faf3acff
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> ui tool show "Color Actions"
> color sel indian red
> color sel dim gray
> color sel dark goldenrod
> color sel rosy brown
> color sel burly wood
> color sel blue violet
> color sel yellow green
> color sel olive
> color sel chartreuse
> color sel yellow green
> color sel dark khaki
> color sel indian red
> color sel saddle brown
> color sel sienna
> color sel coral
> color sel cornflower blue
> color sel peru
> color sel yellow green
> color sel dark goldenrod
> color sel salmon
> color sel indian red
> color sel salmon
> color sel indian red
> color sel sea green
> color sel dark sea green
> show #!4 models
> color sel gainsboro
> show #!2 models
> color #2 #7b7a7aff
> color #2 #939292ff
> hide #!5 models
> hide #!4 models
> select subtract #6
Nothing selected
> color #6 #fdffffff
> hide #6.1 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> color #2 #b1b1b1ff
> show #!6 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> show #!2 models
> show #!4 models
> show #!5 models
> hide #!5 models
> color #4 #54ada4ff
> hide #!4 models
> hide #!2 models
> show #!3 models
> hide #!6 models
> show #!6 models
> view orient
> turn z 90
> turn x 90
> turn x 180
> turn y 5
> hide #!6 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> turn y -5
> hide #!1 models
> show #!2 models
> hide #!5 models
> save "/Users/chenxi/Desktop/RH-figure/model align/7wlt.png" width 2000
> height 1468 supersample 3 transparentBackground true
> show #!6 models
> color #6 #bfffbaff
> color #6 #64ffa6ff
> color #6 #cfff46ff
> color #6 #ecff78ff
> color #6 #ff7e75ff
> color #6 #ff847eff
> color #6 #ff7c7bff
> show #!5 models
> hide #!5 models
> color #6 #e87070ff
> color #6 #df6c6cff
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> ui tool show "Color Actions"
> color sel indian red
> select subtract #6
Nothing selected
> color #2 #ccccccff
> color #2 silver
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!6 models
> show #!5 models
> show #!1 models
> save "/Users/chenxi/Desktop/RH-figure/model align/sehole+wtlf.png" width
> 2000 height 1468 supersample 3 transparentBackground true
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!5 models
Drag select of 1140 residues
> undo
> hide #!5 models
> hide #!3 models
> show #!5 models
> show #!1 models
> select #1-6: 2476
138 atoms, 120 bonds, 18 residues, 6 models selected
> color (#!1,5 & sel) red
> select add #1
34878 atoms, 35646 bonds, 39 pseudobonds, 4512 residues, 7 models selected
> select subtract #1
117 atoms, 102 bonds, 15 residues, 5 models selected
> select clear
> save "/Users/chenxi/Desktop/RH-figure/model align/sehole+wtlf.png" width
> 2000 height 1468 supersample 3 transparentBackground true
> hide #!1 models
> hide #!5 models
> show #!3 models
Drag select of 1155 residues
> hide sel cartoons
> select ~sel & ##selected
25554 atoms, 26109 bonds, 36 pseudobonds, 3357 residues, 2 models selected
> show sel cartoons
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!5 models
> save "/Users/chenxi/Desktop/RH-figure/model align/sehole+rhlf.png" width
> 2000 height 1468 supersample 3 transparentBackground true
> hide #!3 models
> hide #!5 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
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> select #1-6: 2476
138 atoms, 120 bonds, 18 residues, 6 models selected
> color sel red
> select clear
> hide #!1 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!6 models
> show #!2 models
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!6 models
> save "/Users/chenxi/Desktop/RH-figure/model align/8yfg+7wlt.png" width 2000
> height 1468 supersample 3 transparentBackground true
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> show #!1 models
> show sel cartoons
> select subtract #1
Nothing selected
> save "/Users/chenxi/Desktop/RH-figure/model align/7wlu.png" width 2000
> height 1468 supersample 3 transparentBackground true
> hide #!1 models
> show #!3 models
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> show sel cartoons
> select subtract #3
Nothing selected
> hide #!3 models
> show #!3 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf.png" width 2000
> height 1468 supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 atoms
> show #!5 models
> hide #!5 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlc.png" width 894 height
> 656 supersample 3
> hide #!4 models
> show #!4 models
> show #!2 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlc+7wlt.png" width 2000
> height 1468 supersample 3 transparentBackground true
> hide #!4 models
> hide #!2 models
> show #!1 models
> show #!3 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf+7wlu.png" width 2000
> height 1468 supersample 3 transparentBackground true
> hide #!1 models
> show #!5 models
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> show sel cartoons
> select subtract #5
Nothing selected
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf+8ixo.png" width 2000
> height 1468 supersample 3 transparentBackground true
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!6 models
> hide #!3 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> open /Users/chenxi/Desktop/mP1-RH-detergent/RH-full-
> length/RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb
> format pdb
Chain information for
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb #7
---
Chain | Description
A B C | No description available
> hide #!7 models
> show #!7 models
> hide #!3 models
> hide #!5 models
> hide #!7 surfaces
> hide #7 target a
> show #!7 cartoons
> cartoon style #7 modeHelix tube sides 20
> hide #7.1 models
> hide #!7 models
> show #!7 models
> select add #7
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle
> color sel plum
> color sel gainsboro
> color sel medium purple
> color sel purple
> color sel thistle
> color #7 #cfb1deff
> color #7 #c69fdeff
> color #7 #c5afdeff
> color #7 #c1abdaff
> color #7 #b399daff
> color #7 #b4a0daff
> color #7 #ad96daff
> color #7 #ad98daff
> select subtract #7
Nothing selected
> hide #!7 models
> select #1-7: 2501-2547
8010 atoms, 8130 bonds, 909 residues, 7 models selected
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> view orient
> ui tool show Matchmaker
> matchmaker #!1,3-7 & sel to #2 & sel
Computing secondary structure
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 7wlt.pdb, chain A (#2) with
7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1), sequence alignment
score = 233.4
RMSD between 44 pruned atom pairs is 0.675 angstroms; (across all 47 pairs:
0.953)
Matchmaker 7wlt.pdb, chain A (#2) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence
alignment score = 229.8
RMSD between 42 pruned atom pairs is 0.993 angstroms; (across all 47 pairs:
1.286)
Matchmaker 7wlt.pdb, chain A (#2) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4),
sequence alignment score = 240.6
RMSD between 47 pruned atom pairs is 0.343 angstroms; (across all 47 pairs:
0.343)
Matchmaker 7wlt.pdb, chain A (#2) with 8ixo.pdb, chain A (#5), sequence
alignment score = 244.8
RMSD between 47 pruned atom pairs is 0.506 angstroms; (across all 47 pairs:
0.506)
Matchmaker 7wlt.pdb, chain A (#2) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6),
sequence alignment score = 101.9
RMSD between 20 pruned atom pairs is 0.385 angstroms; (across all 21 pairs:
1.216)
Matchmaker 7wlt.pdb, chain A (#2) with
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb,
chain A (#7), sequence alignment score = 233.4
RMSD between 47 pruned atom pairs is 0.329 angstroms; (across all 47 pairs:
0.329)
> select clear
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!6 models
> hide #!7 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> view orient
> turn x 90
> turn x 180
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> turn y -20
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!3 models
> show #!3 models
> turn y 5
> show #!2 models
> hide #!3 models
> show #!3 models
> turn y -5
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> show #!5 models
> hide #!2 models
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> select clear
> ui mousemode right "rotate selected models"
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> view matrix models
> #5,0.6268,-0.77847,0.033399,220.59,-0.77721,-0.62768,-0.044291,490.46,0.055443,0.0018034,-0.99846,424.49
> select subtract #5
Nothing selected
> select #1-7: 2490-2547
9909 atoms, 10086 bonds, 1140 residues, 7 models selected
> ui tool show Matchmaker
> matchmaker #!2-7 & sel to #1 & sel ssFraction false
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
7wlt.pdb, chain A (#2), sequence alignment score = 301
RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs:
1.091)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence
alignment score = 301
RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs:
1.301)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4),
sequence alignment score = 301
RMSD between 54 pruned atom pairs is 0.933 angstroms; (across all 58 pairs:
1.170)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
8ixo.pdb, chain A (#5), sequence alignment score = 301
RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs:
1.216)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 161
RMSD between 29 pruned atom pairs is 0.658 angstroms; (across all 32 pairs:
1.523)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb,
chain A (#7), sequence alignment score = 301
RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs:
1.062)
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!2-7 & sel to #1 & sel alg Smith-Waterman ssFraction false
> showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with 7wlt.pdb
(#2), sequence alignment score = 301
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, 7wlt.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs:
1.091)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb (#3), sequence alignment
score = 301
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A,
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs:
1.301)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb (#4), sequence
alignment score = 301
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3:
7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A,
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 54 pruned atom pairs is 0.933 angstroms; (across all 58 pairs:
1.170)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with 8ixo.pdb
(#5), sequence alignment score = 301
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4:
7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, 8ixo.pdb #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs:
1.216)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with
8yfg_hp1_RH_mdfic.pdb (#6), sequence alignment score = 161
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5:
7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, 8yfg_hp1_RH_mdfic.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 29 pruned atom pairs is 0.658 angstroms; (across all 32 pairs:
1.523)
Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb
(#7), sequence alignment score = 301
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6:
7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A,
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs:
1.062)
> select #1/A:2541 #7/A:2541
18 atoms, 16 bonds, 2 residues, 2 models selected
> show #!1 models
> show #!2 models
> show #!4 models
> show #!6 models
> show #!7 models
> select add #1
34770 atoms, 35552 bonds, 39 pseudobonds, 4498 residues, 3 models selected
> select subtract #1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!5 models
> show #!6 models
> show #!7 models
> select #1-7: 2490-2547
9909 atoms, 10086 bonds, 1140 residues, 7 models selected
> ui tool show "Similar Structures"
> ui tool show Matchmaker
> select add #1
43164 atoms, 44097 bonds, 39 pseudobonds, 5463 residues, 8 models selected
> select add #2
75561 atoms, 77262 bonds, 72 pseudobonds, 9375 residues, 10 models selected
> select add #3
108330 atoms, 110784 bonds, 117 pseudobonds, 13647 residues, 11 models
selected
> select subtract #3
74055 atoms, 75729 bonds, 72 pseudobonds, 9201 residues, 9 models selected
> select clear
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> rename chain C to B #1
Missing or invalid "models" argument: invalid models specifier
> rename #1 chain C to B
Expected a keyword
> rename #1 chainC to B
Expected a keyword
> rename #1 chainC B
Expected a keyword
> ui tool show "Change Chain IDs"
> changechains #* B
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (B/576/)
> rename #1 chainC
> ui tool show "Change Chain IDs"
> select #1/C
11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected
> changechains sel B
Proposed chainID change conflicts with existing residue chainC #1/B GLU 576
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> select #1/B
11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected
> show #!2 models
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> changechains C D
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (D/576/)
> select #1/ B
11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel D
Chain IDs of 1499 residues changed
> select #1/ C
11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 1499 residues changed
> select #1/ D
11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 1499 residues changed
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!3 models
> select #3/ B
11425 atoms, 11685 bonds, 15 pseudobonds, 1482 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel D
Chain IDs of 1482 residues changed
> select #3/ C
11425 atoms, 11685 bonds, 15 pseudobonds, 1482 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 1482 residues changed
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 0 residues changed
> select #3/ D
11425 atoms, 11685 bonds, 15 pseudobonds, 1482 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 1482 residues changed
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select #5/ F
10704 atoms, 10933 bonds, 13 pseudobonds, 1400 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 1400 residues changed
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> hide #!5 models
> select subtract #5
Nothing selected
> show #!6 models
> select #6/ D
10394 atoms, 10647 bonds, 15 pseudobonds, 1280 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 1280 residues changed
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> hide #!6 models
> show #!7 models
> select #7/ B
14702 atoms, 15091 bonds, 17 pseudobonds, 1848 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel D
Chain IDs of 1848 residues changed
> select #7/ B
Nothing selected
> select #7/ C
14702 atoms, 15091 bonds, 17 pseudobonds, 1848 residues, 2 models selected
> ui tool show "Renumber Residues"
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 1848 residues changed
> select #7/ D
14702 atoms, 15091 bonds, 17 pseudobonds, 1848 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 1848 residues changed
> select add #7
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!7 models
> show #!1 models
> rename #1 7wlu-rechain
> matchmaker #2-7 to #1 :2490-2547
Computing secondary structure
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 7wlu-rechain, chain A (#1) with 7wlt.pdb, chain A (#2), sequence
alignment score = 280.3
RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs:
1.091)
Matchmaker 7wlu-rechain, chain A (#1) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence
alignment score = 268.3
RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs:
1.301)
Matchmaker 7wlu-rechain, chain A (#1) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain C (#4),
sequence alignment score = 288.7
RMSD between 55 pruned atom pairs is 0.970 angstroms; (across all 58 pairs:
1.172)
Matchmaker 7wlu-rechain, chain A (#1) with 8ixo.pdb, chain A (#5), sequence
alignment score = 277.3
RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs:
1.216)
Matchmaker 7wlu-rechain, chain A (#1) with 8yfg_hp1_RH_mdfic.pdb, chain A
(#6), sequence alignment score = 273.4
RMSD between 50 pruned atom pairs is 0.747 angstroms; (across all 58 pairs:
1.460)
Matchmaker 7wlu-rechain, chain A (#1) with
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb,
chain A (#7), sequence alignment score = 272.5
RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs:
1.062)
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!3 models
> select #1: 2490-2547
1506 atoms, 1533 bonds, 174 residues, 1 model selected
> select #1-7: 2490-2547
9909 atoms, 10086 bonds, 1140 residues, 7 models selected
> ui tool show Matchmaker
> matchmaker #!2-7 & sel to #1 & sel ssFraction false showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlu-rechain, chain A (#1) with 7wlt.pdb, chain A (#2), sequence
alignment score = 301
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7wlu-rechain #1/A, 7wlt.pdb
#2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs:
1.091)
Matchmaker 7wlu-rechain, chain A (#1) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence
alignment score = 301
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5: 7wlu-rechain #1/A,
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs:
1.301)
Matchmaker 7wlu-rechain, chain A (#1) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4),
sequence alignment score = 301
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6: 7wlu-rechain #1/A,
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 54 pruned atom pairs is 0.933 angstroms; (across all 58 pairs:
1.170)
Matchmaker 7wlu-rechain, chain A (#1) with 8ixo.pdb, chain A (#5), sequence
alignment score = 301
Alignment identifier is 7
Showing conservation header ("seq_conservation" residue attribute) for
alignment 7
Hiding conservation header for alignment 7
Chains used in RMSD evaluation for alignment 7: 7wlu-rechain #1/A, 8ixo.pdb
#5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7
RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs:
1.216)
Matchmaker 7wlu-rechain, chain A (#1) with 8yfg_hp1_RH_mdfic.pdb, chain A
(#6), sequence alignment score = 161
Alignment identifier is 8
Showing conservation header ("seq_conservation" residue attribute) for
alignment 8
Hiding conservation header for alignment 8
Chains used in RMSD evaluation for alignment 8: 7wlu-rechain #1/A,
8yfg_hp1_RH_mdfic.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 8
RMSD between 29 pruned atom pairs is 0.658 angstroms; (across all 32 pairs:
1.523)
Matchmaker 7wlu-rechain, chain A (#1) with
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb,
chain A (#7), sequence alignment score = 301
Alignment identifier is 9
Showing conservation header ("seq_conservation" residue attribute) for
alignment 9
Hiding conservation header for alignment 9
Chains used in RMSD evaluation for alignment 9: 7wlu-rechain #1/A,
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 9
RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs:
1.062)
> matchmaker #2-7/A,B,C:50-100 to #1/A,B,C:50-100
No 'to' model specified
> matchmaker #2-7 /A,B,C: 2490-2547 to #1/ A,B,C: 2490-2547
Computing secondary structure
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 7wlu-rechain, chain A (#1) with 7wlt.pdb, chain A (#2), sequence
alignment score = 280.3
RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs:
1.091)
Matchmaker 7wlu-rechain, chain A (#1) with
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence
alignment score = 268.3
RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs:
1.301)
Matchmaker 7wlu-rechain, chain A (#1) with
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain C (#4),
sequence alignment score = 288.7
RMSD between 55 pruned atom pairs is 0.970 angstroms; (across all 58 pairs:
1.172)
Matchmaker 7wlu-rechain, chain A (#1) with 8ixo.pdb, chain A (#5), sequence
alignment score = 277.3
RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs:
1.216)
Matchmaker 7wlu-rechain, chain A (#1) with 8yfg_hp1_RH_mdfic.pdb, chain A
(#6), sequence alignment score = 140.3
RMSD between 29 pruned atom pairs is 0.658 angstroms; (across all 32 pairs:
1.523)
Matchmaker 7wlu-rechain, chain A (#1) with
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb,
chain A (#7), sequence alignment score = 272.5
RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs:
1.062)
> show #!4 models
> hide #!3 models
> select #1-7: 2490-2547
9909 atoms, 10086 bonds, 1140 residues, 7 models selected
> select ~sel
239871 atoms, 245531 bonds, 288 pseudobonds, 30102 residues, 16 models
selected
> hide sel & #!1,4 cartoons
> view orient
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!5 models
> show #!6 models
> show #!7 models
> select #1-7: 2490-2547
9909 atoms, 10086 bonds, 1140 residues, 7 models selected
> select ~sel
239871 atoms, 245531 bonds, 288 pseudobonds, 30102 residues, 16 models
selected
> hide sel cartoons
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!3 models
> show #!1 models
> view orient
> select add #1
241377 atoms, 247067 bonds, 288 pseudobonds, 30276 residues, 16 models
selected
> select add #2
242892 atoms, 248612 bonds, 288 pseudobonds, 30450 residues, 16 models
selected
> select subtract #2
208980 atoms, 213905 bonds, 255 pseudobonds, 26364 residues, 13 models
selected
> select clear
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> ui tool show Matchmaker
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!4 models
> hide #!4 models
> select #1/C
11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Proposed chainID change conflicts with existing residue 7wlu-rechain #1/B GLU
576
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> select #2/C
11304 atoms, 11569 bonds, 11 pseudobonds, 1362 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 1362 residues changed
> select #2/E
11304 atoms, 11569 bonds, 11 pseudobonds, 1362 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 1362 residues changed
> select add #2
33912 atoms, 34707 bonds, 33 pseudobonds, 4086 residues, 3 models selected
> select subtract #2
Nothing selected
> rename #3 rhlf-0814
> rename #4 rhlc
> rename #7 rhdc
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #1/A#1/B#1/C to #2/A#2/B#2/C pairing ss ssFraction false
> showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlt.pdb, chain A (#2) with 7wlu-rechain, chain A (#1), sequence
alignment score = 7177
Alignment identifier is 10
Showing conservation header ("seq_conservation" residue attribute) for
alignment 10
Hiding conservation header for alignment 10
Chains used in RMSD evaluation for alignment 10: 7wlu-rechain #1/A, 7wlt.pdb
#2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 10
Matchmaker 7wlt.pdb, chain B (#2) with 7wlu-rechain, chain B (#1), sequence
alignment score = 7177
Alignment identifier is 11
Showing conservation header ("seq_conservation" residue attribute) for
alignment 11
Hiding conservation header for alignment 11
Chains used in RMSD evaluation for alignment 11: 7wlu-rechain #1/B, 7wlt.pdb
#2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 11
Matchmaker 7wlt.pdb, chain C (#2) with 7wlu-rechain, chain C (#1), sequence
alignment score = 7177
Alignment identifier is 12
Showing conservation header ("seq_conservation" residue attribute) for
alignment 12
Hiding conservation header for alignment 12
Chains used in RMSD evaluation for alignment 12: 7wlu-rechain #1/C, 7wlt.pdb
#2/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 12
RMSD between 750 pruned atom pairs is 0.634 angstroms; (across all 3822 pairs:
24.058)
> select clear
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!1 models
> ui tool show Matchmaker
> matchmaker #3/A#3/B#3/C to #2/A#2/B#2/C pairing ss ssFraction false
> showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlt.pdb, chain A (#2) with rhlf-0814, chain A (#3), sequence
alignment score = 7066
Alignment identifier is 10
Showing conservation header ("seq_conservation" residue attribute) for
alignment 10
Hiding conservation header for alignment 10
Chains used in RMSD evaluation for alignment 10: 7wlt.pdb #2/A, rhlf-0814 #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 10
Matchmaker 7wlt.pdb, chain B (#2) with rhlf-0814, chain B (#3), sequence
alignment score = 7066
Alignment identifier is 11
Showing conservation header ("seq_conservation" residue attribute) for
alignment 11
Hiding conservation header for alignment 11
Chains used in RMSD evaluation for alignment 11: 7wlt.pdb #2/B, rhlf-0814 #3/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 11
Matchmaker 7wlt.pdb, chain C (#2) with rhlf-0814, chain C (#3), sequence
alignment score = 7066
Alignment identifier is 12
Showing conservation header ("seq_conservation" residue attribute) for
alignment 12
Hiding conservation header for alignment 12
Chains used in RMSD evaluation for alignment 12: 7wlt.pdb #2/C, rhlf-0814 #3/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 12
RMSD between 303 pruned atom pairs is 1.225 angstroms; (across all 3822 pairs:
30.759)
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #4/A#4/B#4/C to #2/A#2/B#2/C pairing ss ssFraction false
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlt.pdb, chain A (#2) with rhlc, chain A (#4), sequence alignment
score = 7252
Matchmaker 7wlt.pdb, chain B (#2) with rhlc, chain B (#4), sequence alignment
score = 7252
Matchmaker 7wlt.pdb, chain C (#2) with rhlc, chain C (#4), sequence alignment
score = 7252
RMSD between 1532 pruned atom pairs is 1.144 angstroms; (across all 4059
pairs: 6.889)
> hide #!4 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #5/A#5/B#5/C to #2/A#2/B#2/C pairing ss ssFraction false
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlt.pdb, chain A (#2) with 8ixo.pdb, chain A (#5), sequence
alignment score = 13421
Matchmaker 7wlt.pdb, chain B (#2) with 8ixo.pdb, chain B (#5), sequence
alignment score = 13421
Matchmaker 7wlt.pdb, chain C (#2) with 8ixo.pdb, chain C (#5), sequence
alignment score = 13421
RMSD between 453 pruned atom pairs is 0.925 angstroms; (across all 3747 pairs:
20.776)
> ui tool show Matchmaker
> show #!6 models
> hide #!5 models
> matchmaker #6/A#6/B#6/C to #2/A#2/B#2/C pairing ss ssFraction false
Different number of reference/match chains (3 ref, 4 match)
> select add #6.1
45 pseudobonds, 1 model selected
> select subtract #6.1
Nothing selected
> show #6.1 models
> hide #6.1 models
> select #6/ E
141 atoms, 141 bonds, 21 residues, 1 model selected
> show sel cartoons
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> show sel cartoons
> select subtract #6.1
31599 atoms, 32357 bonds, 3903 residues, 1 model selected
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> select #6/ E
141 atoms, 141 bonds, 21 residues, 1 model selected
> select #6 : 2490-2547
852 atoms, 867 bonds, 96 residues, 1 model selected
> select ~sel & ##selected
30747 atoms, 31490 bonds, 45 pseudobonds, 3807 residues, 2 models selected
> hide sel cartoons
> view orient
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> matchmaker #6/A#6/B#6/C to #2/A#2/B#2/C pairing ss ssFraction false
Different number of reference/match chains (3 ref, 4 match)
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> show sel cartoons
> select subtract #6
Nothing selected
> select #6/C
10535 atoms, 10788 bonds, 15 pseudobonds, 1301 residues, 2 models selected
> ui tool show "Side View"
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> ui mousemode right select
Drag select of 21 residues
Drag select of 7 residues
Drag select of 10 residues
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> select #6: 227-247
423 atoms, 423 bonds, 63 residues, 1 model selected
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
Drag select of 8 residues
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
Drag select of 23 residues
Drag select of 5 residues
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
Drag select of 23 residues
> select #6/E
141 atoms, 141 bonds, 21 residues, 1 model selected
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
Drag select of 23 residues
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> hide #!6 models
> show #!6 models
> close #6
> open /Users/chenxi/Desktop/PDB/8yfg_hp1_RH_mdfic.pdb
8yfg_hp1_RH_mdfic.pdb title:
Human PIEZO1-R2456H_mdfic [more info...]
Chain information for 8yfg_hp1_RH_mdfic.pdb #6
---
Chain | Description | UniProt
A B D | piezo-type mechanosensitive ion channel component 1 | PIEZ1_HUMAN 1-2521
C E F | myod family inhibitor domain-containing protein | MDFIC_HUMAN 2-247
Associated 8yfg_hp1_RH_mdfic.pdb chain A to 7wlt.pdb with 1 mismatch
Associated 8yfg_hp1_RH_mdfic.pdb chain B to 7wlt.pdb with 1 mismatch
Associated 8yfg_hp1_RH_mdfic.pdb chain D to 7wlt.pdb with 1 mismatch
Chains used in RMSD evaluation for alignment 1: 7wlu-rechain #1/A, 7wlt.pdb
#2/A, 8yfg_hp1_RH_mdfic.pdb #6/D
Associated 8yfg_hp1_RH_mdfic.pdb chain A to
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb with 1 mismatch
Associated 8yfg_hp1_RH_mdfic.pdb chain B to
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb with 1 mismatch
Associated 8yfg_hp1_RH_mdfic.pdb chain D to
rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb with 1 mismatch
Chains used in RMSD evaluation for alignment 2: 7wlu-rechain #1/A, rhlf-0814
#3/A, 8yfg_hp1_RH_mdfic.pdb #6/D
Associated 8yfg_hp1_RH_mdfic.pdb chain A to 8ixo.pdb with 1 mismatch
Associated 8yfg_hp1_RH_mdfic.pdb chain B to 8ixo.pdb with 1 mismatch
Associated 8yfg_hp1_RH_mdfic.pdb chain D to 8ixo.pdb with 1 mismatch
Chains used in RMSD evaluation for alignment 4: 7wlu-rechain #1/A, 8ixo.pdb
#5/A, 8yfg_hp1_RH_mdfic.pdb #6/D
Associated 8yfg_hp1_RH_mdfic.pdb chain A to 8yfg_hp1_RH_mdfic.pdb, chain A
with 0 mismatches
Associated 8yfg_hp1_RH_mdfic.pdb chain B to 8yfg_hp1_RH_mdfic.pdb, chain A
with 0 mismatches
Associated 8yfg_hp1_RH_mdfic.pdb chain D to 8yfg_hp1_RH_mdfic.pdb, chain A
with 0 mismatches
Chains used in RMSD evaluation for alignment 8: 7wlu-rechain #1/A,
8yfg_hp1_RH_mdfic.pdb #6/D
> view
> ui tool show "Side View"
> view orient
> show #!2,6 cartoons
> hide #!2 models
> show #!6 cartoons
> hide #6 target a
> cartoon style #6 modeHelix tube sides 20
> ui tool show "Color Actions"
> color indian red
> undo
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> ui tool show "Color Actions"
> color sel indian red
> hide #6.1 models
> select subtract #6.1
31599 atoms, 32357 bonds, 3903 residues, 1 model selected
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> select #6: 2490-2547
852 atoms, 867 bonds, 96 residues, 1 model selected
> select ~sel & ##selected
30747 atoms, 31490 bonds, 45 pseudobonds, 3807 residues, 2 models selected
> hide sel cartoons
> select subtract #6.1
30747 atoms, 31490 bonds, 3807 residues, 1 model selected
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> select #2: 2490-2547
1515 atoms, 1542 bonds, 174 residues, 1 model selected
> select ~sel & ##selected
32397 atoms, 33165 bonds, 33 pseudobonds, 3912 residues, 2 models selected
> hide sel cartoons
> hide #!6 models
> select add #2
33912 atoms, 34707 bonds, 33 pseudobonds, 4086 residues, 3 models selected
> select subtract #2
Nothing selected
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> select #6: 2490-2547
852 atoms, 867 bonds, 96 residues, 1 model selected
> show sel cartoons
> select #2: 2490-2547
1515 atoms, 1542 bonds, 174 residues, 1 model selected
> select add #2
33912 atoms, 34707 bonds, 33 pseudobonds, 4086 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #!3 models
> select #6: 2490-2547
852 atoms, 867 bonds, 96 residues, 1 model selected
> select ~sel & ##selected
30747 atoms, 31490 bonds, 45 pseudobonds, 3807 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> select subtract #6
Nothing selected
> matchmaker #6/A#6/B#6/D to #2/A#2/B#2/C pairing ss ssFraction false
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlt.pdb, chain A (#2) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6),
sequence alignment score = 10759
Matchmaker 7wlt.pdb, chain B (#2) with 8yfg_hp1_RH_mdfic.pdb, chain B (#6),
sequence alignment score = 10759
Matchmaker 7wlt.pdb, chain C (#2) with 8yfg_hp1_RH_mdfic.pdb, chain D (#6),
sequence alignment score = 10759
RMSD between 800 pruned atom pairs is 1.358 angstroms; (across all 3504 pairs:
10.161)
Chains used in RMSD evaluation for alignment 1: 7wlu-rechain #1/A, 7wlt.pdb
#2/A, 8yfg_hp1_RH_mdfic.pdb #6/A
Chains used in RMSD evaluation for alignment 2: 7wlu-rechain #1/A, rhlf-0814
#3/A, 8yfg_hp1_RH_mdfic.pdb #6/A
Chains used in RMSD evaluation for alignment 4: 7wlu-rechain #1/A, 8ixo.pdb
#5/A, 8yfg_hp1_RH_mdfic.pdb #6/A
Chains used in RMSD evaluation for alignment 8: 7wlu-rechain #1/A,
8yfg_hp1_RH_mdfic.pdb #6/A
> hide #!6 models
> show #!7 models
> view orient
> ui tool show Matchmaker
> matchmaker #7/A#7/B#7/C to #2/A#2/B#2/C pairing ss ssFraction false
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlt.pdb, chain A (#2) with rhdc, chain A (#7), sequence alignment
score = 8828
Matchmaker 7wlt.pdb, chain B (#2) with rhdc, chain B (#7), sequence alignment
score = 8828
Matchmaker 7wlt.pdb, chain C (#2) with rhdc, chain C (#7), sequence alignment
score = 8828
RMSD between 1801 pruned atom pairs is 1.163 angstroms; (across all 4059
pairs: 4.567)
> hide #!7 models
> hide #!2 models
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select add #2
68673 atoms, 70251 bonds, 72 pseudobonds, 8583 residues, 5 models selected
> select add #3
102948 atoms, 105306 bonds, 117 pseudobonds, 13029 residues, 7 models selected
> select add #4
140553 atoms, 143826 bonds, 153 pseudobonds, 17568 residues, 9 models selected
> select add #5
172665 atoms, 176625 bonds, 192 pseudobonds, 21768 residues, 12 models
selected
> select add #6
204264 atoms, 208982 bonds, 237 pseudobonds, 25671 residues, 14 models
selected
> select add #7
249780 atoms, 255638 bonds, 288 pseudobonds, 31242 residues, 16 models
selected
> select subtract #1
215019 atoms, 220094 bonds, 249 pseudobonds, 26745 residues, 14 models
selected
> select subtract #2
181107 atoms, 185387 bonds, 216 pseudobonds, 22659 residues, 11 models
selected
> select subtract #3
146832 atoms, 150332 bonds, 171 pseudobonds, 18213 residues, 9 models selected
> select subtract #5
114720 atoms, 117533 bonds, 132 pseudobonds, 14013 residues, 6 models selected
> select subtract #6
83121 atoms, 85176 bonds, 87 pseudobonds, 10110 residues, 4 models selected
> select subtract #7
37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> show sel cartoons
> select subtract #1
Nothing selected
> hide #!1 models
> select add #2
33912 atoms, 34707 bonds, 33 pseudobonds, 4086 residues, 3 models selected
> show sel cartoons
> select subtract #2
Nothing selected
> hide #!2 models
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> show sel cartoons
> select subtract #3
Nothing selected
> hide #!3 models
> select add #4
37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected
> show sel cartoons
> select subtract #4
Nothing selected
> hide #!4 models
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> show sel cartoons
> select subtract #5
Nothing selected
> hide #!5 models
> select add #6
31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected
> show sel cartoons
> select subtract #6
Nothing selected
> hide #!6 models
> select add #7
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected
> show sel cartoons
> select subtract #7
Nothing selected
> hide #!7 models
> show #!2 models
> show #!3 models
> view orient
> turn x 90
> turn x 180
> turn y -20
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> show #!1 models
> view
> ui tool show "Side View"
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> select #1-7: 2476
159 atoms, 138 bonds, 21 residues, 7 models selected
> color sel red
> select clear
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> save "/Users/chenxi/Desktop/RH-figure/model align/7wlt.png" width 2000
> height 1237 supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> save "/Users/chenxi/Desktop/RH-figure/model align/7wlt.png" width 2000
> height 1237 supersample 3 transparentBackground true
> hide #!1 models
> show #!3 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf.png" width 2000
> height 1237 supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlc.png" width 2000
> height 1237 supersample 3 transparentBackground true
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhdc.png" width 2000
> height 1237 supersample 3 transparentBackground true
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!5 models
> select #5: 2116-2492
8814 atoms, 9045 bonds, 3 pseudobonds, 1101 residues, 2 models selected
> select ~sel & ##selected
23298 atoms, 23754 bonds, 36 pseudobonds, 3099 residues, 2 models selected
> hide sel cartoons
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> select subtract #5
Nothing selected
> show #!1 models
> select #1: 2116-2492
8724 atoms, 8949 bonds, 6 pseudobonds, 1089 residues, 2 models selected
> hide sel cartoons
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf+7wlu.png" width 2000
> height 1237 supersample 3 transparentBackground true
> save "/Users/chenxi/Desktop/RH-figure/model align/sehole+wtlf.png" width
> 2000 height 1237 supersample 3 transparentBackground true
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!3 models
> show #!1 models
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> show sel cartoons
> select subtract #1
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> select add #5
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> show sel cartoons
> select subtract #5
Nothing selected
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!5 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf+8ixo.png" width 2000
> height 1237 supersample 3 transparentBackground true
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!2 models
> save "/Users/chenxi/Desktop/RH-figure/model align/8yfg+7wlt.png" width 2000
> height 1237 supersample 3 transparentBackground true
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> save "/Users/chenxi/Desktop/RH-figure/model align/rhdc+7wlt.png" width 2000
> height 1237 supersample 3 transparentBackground true
> save "/Users/chenxi/Desktop/RH-figure/model align/model-align.cxs"
> includeMaps true
> hide #!2 models
> show #!1 models
> hide #!7 models
> show #!3 models
> select #1,3: 2490-2547
3012 atoms, 3066 bonds, 348 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #3/A#3/B#3/C & sel to #1/A#1/B#1/C & sel pairing ss ssFraction
> false
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker 7wlu-rechain, chain A (#1) with rhlf-0814, chain A (#3), sequence
alignment score = 301
Matchmaker 7wlu-rechain, chain C (#1) with rhlf-0814, chain C (#3), sequence
alignment score = 301
Matchmaker 7wlu-rechain, chain B (#1) with rhlf-0814, chain B (#3), sequence
alignment score = 301
RMSD between 159 pruned atom pairs is 1.210 angstroms; (across all 174 pairs:
1.320)
> select add #1
36267 atoms, 37077 bonds, 39 pseudobonds, 4671 residues, 3 models selected
> select add #3
69036 atoms, 70599 bonds, 84 pseudobonds, 8943 residues, 4 models selected
> select subtract #1
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> select add #1
69036 atoms, 70599 bonds, 84 pseudobonds, 8943 residues, 4 models selected
> select subtract #1
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> select subtract #3
Nothing selected
> lighting simple
> lighting soft
> ui tool show "Side View"
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf+7wlu.png" width 2000
> height 1237 supersample 3 transparentBackground true
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting soft
> ui tool show "Side View"
> select #3,5: 2490-2547
3006 atoms, 3060 bonds, 348 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #5/A#5/B#5/C & sel to #3/A#3/B#3/C & sel pairing ss ssFraction
> false
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker rhlf-0814, chain A (#3) with 8ixo.pdb, chain C (#5), sequence
alignment score = 301
Matchmaker rhlf-0814, chain C (#3) with 8ixo.pdb, chain A (#5), sequence
alignment score = 301
Matchmaker rhlf-0814, chain B (#3) with 8ixo.pdb, chain B (#5), sequence
alignment score = 301
RMSD between 7 pruned atom pairs is 0.900 angstroms; (across all 174 pairs:
20.592)
> select ~sel & ##selected
63381 atoms, 64794 bonds, 84 pseudobonds, 8298 residues, 4 models selected
> hide sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #5/A#5/B#5/C to #3/A#3/B#3/C pairing ss ssFraction false
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 2
Matchmaker rhlf-0814, chain A (#3) with 8ixo.pdb, chain A (#5), sequence
alignment score = 7062
Matchmaker rhlf-0814, chain B (#3) with 8ixo.pdb, chain B (#5), sequence
alignment score = 7062
Matchmaker rhlf-0814, chain C (#3) with 8ixo.pdb, chain C (#5), sequence
alignment score = 7062
RMSD between 255 pruned atom pairs is 1.217 angstroms; (across all 4116 pairs:
23.493)
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> select add #5
66387 atoms, 67854 bonds, 84 pseudobonds, 8646 residues, 5 models selected
> show sel cartoons
> select subtract #3
32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected
> select subtract #5
Nothing selected
> view
> ui tool show "Side View"
> view orient
> turn x 90
> turn y -20
> turn y -5
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf+8ixo.png" width 2000
> height 1237 supersample 3 transparentBackground true
> ui tool show "Side View"
> save "/Users/chenxi/Desktop/RH-figure/model align/rhlf+8ixo.png" width 2000
> height 1237 supersample 3 transparentBackground true
> show #!1 models
> hide #!5 models
> select #1,3: 2116-2213
4872 atoms, 5010 bonds, 588 residues, 2 models selected
> select ~sel & ##selected
64164 atoms, 65589 bonds, 84 pseudobonds, 8355 residues, 4 models selected
> hide sel cartoons
> select #1,3: 2417-2492
3165 atoms, 3246 bonds, 6 pseudobonds, 408 residues, 4 models selected
> show sel cartoons
> hide sel cartoons
> select #1,3: 2465-2492
1281 atoms, 1308 bonds, 168 residues, 2 models selected
> select #1,3: 2476
42 atoms, 36 bonds, 6 residues, 2 models selected
Drag select of 9 residues
> select clear
> select #1,3: 2476
42 atoms, 36 bonds, 6 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #1,3: 2465-2492
1281 atoms, 1308 bonds, 168 residues, 2 models selected
> show sel cartoons
> select clear
> ui tool show "Side View"
Drag select of 3 residues
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> select subtract #3
Nothing selected
> select #1,3: 2417-2492
3165 atoms, 3246 bonds, 6 pseudobonds, 408 residues, 4 models selected
> show sel cartoons
> select clear
> show #3.1 models
> show #1.1 models
> ui tool show "Side View"
> select #1,3/A
23012 atoms, 23533 bonds, 28 pseudobonds, 2981 residues, 4 models selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> undo
> select #1,3/A,B
46024 atoms, 47066 bonds, 56 pseudobonds, 5962 residues, 4 models selected
> color (#!1,3 & sel) dark gray
> color (#!1,3 & sel) white
> lighting flat
> select clear
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting simple
> lighting soft
> select #1/C:2475
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1
34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected
> select subtract #1
Nothing selected
> ui tool show "Side View"
> save "/Users/chenxi/Desktop/RH-figure/model align/IH-OH-rhlf-7wlu.png" width
> 2000 height 1237 supersample 3 transparentBackground true
> select #1,3: 2214-2465
11316 atoms, 11589 bonds, 15 pseudobonds, 1428 residues, 4 models selected
> select ~sel & ##selected
57720 atoms, 59010 bonds, 69 pseudobonds, 7515 residues, 4 models selected
> hide sel cartoons
> select #1,3: 2214-2465
11316 atoms, 11589 bonds, 15 pseudobonds, 1428 residues, 4 models selected
> show sel cartoons
> select #1,3: 2200-2470
12258 atoms, 12567 bonds, 15 pseudobonds, 1542 residues, 4 models selected
> show sel cartoons
> select #1,3: 2200-2476
12516 atoms, 12825 bonds, 15 pseudobonds, 1578 residues, 4 models selected
> show sel cartoons
> select clear
> select #1,3: 2185-2492
13977 atoms, 14325 bonds, 15 pseudobonds, 1764 residues, 4 models selected
> show sel cartoons
> select clear
> save "/Users/chenxi/Desktop/RH-figure/model align/capside-rhlf-7wlu.png"
> width 2000 height 1237 supersample 3 transparentBackground true
> view orient
> turn y 90
> turn z 90
> turn y 90
> turn x 90
> turn z 90
> view orient
> turn z 90
> view orient
> turn x 90
> turn y 90
> turn x 90
> ui tool show "Side View"
> save "/Users/chenxi/Desktop/RH-figure/model align/captop-rhlf-7wlu.png"
> width 2000 height 1237 supersample 3 transparentBackground true
> hide #1.1 models
> hide #3.1 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLXY3CH/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 17天13小时28分钟
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
YOGA27_APH8:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 1280 x 720 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 8 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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