![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Last modified 7 months ago
#17325 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.4-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020184bac0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, 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._minpack2, 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._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 124)
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{
"uptime" : 2500000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 1825,
"osVersion" : {
"train" : "macOS 14.4",
"build" : "23E214",
"releaseType" : "User"
},
"captureTime" : "2025-04-08 21:08:04.3390 +0800",
"codeSigningMonitor" : 1,
"incident" : "BB84EA3C-6556-44AF-8C71-E2C8648A2D21",
"pid" : 76887,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-01 21:18:08.3253 +0800",
"procStartAbsTime" : 53401234958656,
"procExitAbsTime" : 62004766438961,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"49F00EFF-C531-5FD5-8F10-11418D9C2A6A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8BF29B20-E336-8E38-8810-E698BC388B76",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 20154,
"sleepWakeUUID" : "7C640D44-C103-4CE4-AFA1-C3D4218CEAC2",
"sip" : "enabled",
"vmRegionInfo" : "0x3ba636d2c2c8 is not in any region. Bytes after previous region: 65104034054857 Bytes before following region: 39968045874488\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00003ba636d2c2c8","rawCodes":[1,65585070392008],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00003ba636d2c2c8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":76887},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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"faultingThread" : 0,
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"name" : "AppKit",
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"name" : "CoreFoundation",
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"uuid" : "08c4329e-407f-310b-b037-75a8020b2963",
"path" : "\/usr\/lib\/libc++.1.dylib",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=55.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=55.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1152K 9 \nActivity Tracing 256K 1 \nCG image 2448K 63 \nColorSync 736K 36 \nCoreAnimation 5312K 224 \nCoreGraphics 48K 3 \nCoreImage 80K 5 \nCoreServices 624K 2 \nCoreUI image data 3968K 28 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 53.8G 316 \nMALLOC guard page 384K 24 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 57.0M 61 \nStack 167.1M 61 \nVM_ALLOCATE 893.0M 1004 \nVM_ALLOCATE (reserved) 544.0M 7 reserved VM address space (unallocated)\n__AUTH 2212K 410 \n__AUTH_CONST 31.9M 629 \n__CTF 824 1 \n__DATA 24.5M 857 \n__DATA_CONST 43.8M 859 \n__DATA_DIRTY 2030K 234 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 562.2M 225 \n__OBJC_RO 71.7M 1 \n__OBJC_RW 2195K 1 \n__TEXT 980.6M 876 \ndyld private memory 592K 7 \nmapped file 789.2M 131 \nshared memory 4096K 34 \n=========== ======= ======= \nTOTAL 57.9G 6122 \nTOTAL, minus reserved VM space 57.4G 6122 \n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.cxs"
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400,
pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.083, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Log from Thu Mar 27 15:32:10 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/wujingyi/Desktop/figure/figure4/state1_Fo侧视atom+map.cxs
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400,
pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.083, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Log from Tue Mar 18 21:19:53 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/wujingyi/Desktop/RfxATPase_figure/figure_5/Rfxatp_state1_hollow.cxs
Log from Mon Aug 12 10:58:14 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2hollow.pdb"
> hide #1 models
> show #1 models
> select add #1
4431 atoms, 3493 bonds, 4431 residues, 1 model selected
> show sel surfaces
> set bgColor white
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/state_1_Fo.pdb"
Chain information for state_1_Fo.pdb #2
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide sel atoms
[Repeated 2 time(s)]
> select add #2
15578 atoms, 14854 bonds, 2 pseudobonds, 5912 residues, 7 models selected
> hide sel atoms
> show sel cartoons
> select subtract #1
11147 atoms, 11361 bonds, 2 pseudobonds, 1481 residues, 6 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #2.13
10824 atoms, 11031 bonds, 2 pseudobonds, 1443 residues, 18 models selected
> select add #2.13
11147 atoms, 11031 bonds, 2 pseudobonds, 1481 residues, 17 models selected
> hide #2.13 models
> show #2.13 models
> select add #2
11147 atoms, 11361 bonds, 2 pseudobonds, 1481 residues, 18 models selected
> select subtract #2
16 models selected
> select add #2.13
323 atoms, 38 residues, 1 model selected
> select add #2.16
629 atoms, 74 residues, 2 models selected
> select subtract #2.16
323 atoms, 38 residues, 3 models selected
> select add #2.14
629 atoms, 74 residues, 2 models selected
> hide sel cartoons
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo.pdb"
Chain information for RfxATP_state_1_Fo.pdb #3
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide sel cartoons
> hide sel atoms
> select add #3
11776 atoms, 11365 bonds, 2 pseudobonds, 1555 residues, 5 models selected
> select add #2
22294 atoms, 22726 bonds, 4 pseudobonds, 2962 residues, 6 models selected
> hide sel atoms
> show sel cartoons
> 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
> 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
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> show sel surfaces
> hide sel surfaces
> select subtract #3
16 models selected
> select add #3.13
323 atoms, 38 residues, 1 model selected
> select add #3.15
646 atoms, 76 residues, 2 models selected
> hide sel cartoons
> select add #3.14
952 atoms, 112 residues, 3 models selected
> select add #3.16
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> select add #3.2
1808 atoms, 224 residues, 5 models selected
> select add #3.3
2331 atoms, 297 residues, 6 models selected
> select add #3.4
2873 atoms, 372 residues, 7 models selected
> select add #3.5
3415 atoms, 447 residues, 8 models selected
> select add #3.6
3965 atoms, 523 residues, 9 models selected
> select add #3.7
4507 atoms, 598 residues, 10 models selected
> select add #3.8
5049 atoms, 673 residues, 11 models selected
> select add #3.9
5599 atoms, 749 residues, 12 models selected
> select add #3.10
6149 atoms, 825 residues, 13 models selected
> select add #3.11
6683 atoms, 899 residues, 14 models selected
> hide sel cartoons
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa1_inlet_hollow.pdb"
> select add #2
13913 atoms, 5473 bonds, 8129 residues, 16 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #3.2
13363 atoms, 5473 bonds, 8053 residues, 16 models selected
> show sel surfaces
> hide sel surfaces
> select add #3
18377 atoms, 16838 bonds, 2 pseudobonds, 8711 residues, 16 models selected
> select subtract #3
7230 atoms, 5473 bonds, 7230 residues, 17 models selected
> show sel surfaces
> select subtract #2
4 models selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> hide sel surfaces
> hide sel atoms
> select subtract #2
4 models selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> show sel atoms
> select subtract #2
4 models selected
> select add #2.1
1460 atoms, 1460 residues, 1 model selected
> select add #2.2
5673 atoms, 5673 residues, 2 models selected
> select add #2.3
7208 atoms, 7208 residues, 3 models selected
> select add #2.4
7230 atoms, 7230 residues, 4 models selected
> select subtract #2.4
7208 atoms, 7208 residues, 5 models selected
> show sel cartoons
> show sel surfaces
> select add #2.4
7230 atoms, 7230 residues, 4 models selected
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> show sel surfaces
> select subtract #2.4
7208 atoms, 7208 residues, 5 models selected
> show sel surfaces
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 4 models selected
> select subtract #2.4
7208 atoms, 5454 bonds, 7208 residues, 5 models selected
> select add #2.4
7230 atoms, 5454 bonds, 7230 residues, 4 models selected
> hide sel surfaces
> select subtract #2.4
7208 atoms, 5454 bonds, 7208 residues, 5 models selected
> show sel surfaces
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 4 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #2.4
7208 atoms, 5454 bonds, 7208 residues, 5 models selected
> show sel surfaces
> color #2.1 #87ceeb90
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 4 models selected
> hide sel atoms
> color #2.1 #87ceeb82
> color #2.1 #87ceeb80
> color #2.2 #87ceeb80
> color #2.3 #87ceeb82
> color #2.3 #87ceeb80
> select subtract #2.4
7208 atoms, 5454 bonds, 7208 residues, 5 models selected
> select subtract #2.3
5673 atoms, 4370 bonds, 5673 residues, 4 models selected
> select subtract #2.2
1460 atoms, 1278 bonds, 1460 residues, 3 models selected
> select subtract #2.1
1 model selected
> hide #!3 models
> show #!3 models
> hide #!1 models
> select add #3.2
550 atoms, 76 residues, 1 model selected
> select add #3.3
1073 atoms, 149 residues, 2 models selected
> select add #3.4
1615 atoms, 224 residues, 3 models selected
> select add #3.5
2157 atoms, 299 residues, 4 models selected
> show sel cartoons
> hide sel cartoons
> select subtract #3.2
1607 atoms, 223 residues, 5 models selected
> select subtract #3.3
1084 atoms, 150 residues, 4 models selected
> select subtract #3.4
542 atoms, 75 residues, 3 models selected
> select subtract #3.5
1 model selected
> select add #3.6
550 atoms, 76 residues, 1 model selected
> select add #3.7
1092 atoms, 151 residues, 2 models selected
> select add #3.8
1634 atoms, 226 residues, 3 models selected
> select add #3.9
2184 atoms, 302 residues, 4 models selected
> select add #3.10
2734 atoms, 378 residues, 5 models selected
> select add #3.11
3268 atoms, 452 residues, 6 models selected
> select add #3.12
5500 atoms, 743 residues, 7 models selected
> select subtract #3.12
3268 atoms, 452 residues, 8 models selected
> show sel cartoons
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa1_outlet_hollow2.pdb"
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2_intlet_hollow.pdb"
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2_outlet_hollow.pdb"
> select add #1
7699 atoms, 3493 bonds, 4883 residues, 8 models selected
> select add #3
15578 atoms, 14858 bonds, 2 pseudobonds, 5912 residues, 13 models selected
> select subtract #3
4431 atoms, 3493 bonds, 4431 residues, 21 models selected
> close #1
> select add #6
5690 atoms, 4616 bonds, 5690 residues, 1 model selected
> select add #5
12781 atoms, 9914 bonds, 12781 residues, 2 models selected
> select add #4
19169 atoms, 14970 bonds, 19169 residues, 3 models selected
> show sel surfaces
> select subtract #4
12781 atoms, 9914 bonds, 12781 residues, 13 models selected
> select subtract #5
5690 atoms, 4616 bonds, 5690 residues, 8 models selected
> select subtract #6
3 models selected
> select add #5.4
860 atoms, 860 residues, 1 model selected
> select add #5.3
4775 atoms, 4775 residues, 2 models selected
> select add #5.2
7013 atoms, 7013 residues, 3 models selected
> select subtract #5.2
4775 atoms, 4775 residues, 4 models selected
> select add #5.1
4853 atoms, 4853 residues, 3 models selected
> select subtract #5.1
4775 atoms, 4775 residues, 4 models selected
> select subtract #5.3
860 atoms, 860 residues, 3 models selected
> select subtract #5.4
1 model selected
> select add #5.2
2238 atoms, 2238 residues, 1 model selected
> select subtract #5.2
1 model selected
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> show sel cartoons
> select subtract #3
16 models selected
> select add #3.13
323 atoms, 38 residues, 1 model selected
> select add #3.14
629 atoms, 74 residues, 2 models selected
> select add #3.16
935 atoms, 110 residues, 3 models selected
> select add #3.15
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 11147 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> undo
[Repeated 5 time(s)]
> select add #3.16
306 atoms, 36 residues, 1 model selected
> select add #3.15
629 atoms, 74 residues, 2 models selected
> select add #3.14
935 atoms, 110 residues, 3 models selected
> select add #3.13
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 6 models selected
> select subtract #3
16 models selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> select add #6
12920 atoms, 10089 bonds, 12920 residues, 6 models selected
> select add #5
20011 atoms, 15387 bonds, 20011 residues, 10 models selected
> select add #4
26399 atoms, 20443 bonds, 26399 residues, 15 models selected
> show sel surfaces
> select subtract #2
19169 atoms, 14970 bonds, 19169 residues, 18 models selected
> select subtract #4
12781 atoms, 9914 bonds, 12781 residues, 13 models selected
> select subtract #5
5690 atoms, 4616 bonds, 5690 residues, 8 models selected
> select subtract #6
3 models selected
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> cartoon style (#!3 & sel) modeHelix tube sides 20
> select subtract #3.1
11147 atoms, 11365 bonds, 1481 residues, 17 models selected
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 18 models selected
> select subtract #3
16 models selected
> select add #3.2
550 atoms, 76 residues, 1 model selected
> select add #3.3
1073 atoms, 149 residues, 2 models selected
> select add #3.4
1615 atoms, 224 residues, 3 models selected
> select add #3.5
2157 atoms, 299 residues, 4 models selected
> select add #3.6
2707 atoms, 375 residues, 5 models selected
> select add #3.7
3249 atoms, 450 residues, 6 models selected
> select add #3.8
3791 atoms, 525 residues, 7 models selected
> select add #3.9
4341 atoms, 601 residues, 8 models selected
> select add #3.10
4891 atoms, 677 residues, 9 models selected
> select add #3.11
5425 atoms, 751 residues, 10 models selected
> color (#!3 & sel) #f5ccdcff
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected
> select subtract #3
16 models selected
> select add #3.12
2232 atoms, 291 residues, 1 model selected
> select add #3.14
2538 atoms, 327 residues, 2 models selected
> color (#!3 & sel) forest green
> select subtract #3.14
2232 atoms, 291 residues, 3 models selected
> select add #3.17
4464 atoms, 582 residues, 2 models selected
> color (#!3 & sel) forest green
> select subtract #3.17
2232 atoms, 291 residues, 3 models selected
> select add #3.10
2782 atoms, 367 residues, 2 models selected
> select add #3.9
3332 atoms, 443 residues, 3 models selected
> select add #3.8
3874 atoms, 518 residues, 4 models selected
> select add #3.7
4416 atoms, 593 residues, 5 models selected
> select add #3.6
4966 atoms, 669 residues, 6 models selected
> select add #3.5
5508 atoms, 744 residues, 7 models selected
> select add #3.4
6050 atoms, 819 residues, 8 models selected
> select add #3.3
6573 atoms, 892 residues, 9 models selected
> select add #3.2
7123 atoms, 968 residues, 10 models selected
> hide sel cartoons
> select add #3.11
7657 atoms, 1042 residues, 11 models selected
> select subtract #3.12
5425 atoms, 751 residues, 12 models selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> select add #3.17
7657 atoms, 1042 residues, 11 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 13 models selected
> select subtract #3
16 models selected
> select add #3.14
306 atoms, 36 residues, 1 model selected
> select add #3.12
2538 atoms, 327 residues, 2 models selected
> show sel cartoons
> select subtract #3.14
2232 atoms, 291 residues, 3 models selected
> select add #3.17
4464 atoms, 582 residues, 2 models selected
> show sel cartoons
> select add #3.14
4770 atoms, 618 residues, 3 models selected
> select subtract #3.12
2538 atoms, 327 residues, 4 models selected
> select subtract #3.17
306 atoms, 36 residues, 3 models selected
> hide sel cartoons
> color #3.14 #917297ff
> select subtract #3.14
1 model selected
> lighting soft
> select add #3.2
550 atoms, 76 residues, 1 model selected
> select add #3.3
1073 atoms, 149 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/H #3/L #3/O #3/P
Alignment identifier is 1
> sequence chain #3/I
Alignment identifier is 3/I
> sequence chain #3/J #3/K #3/M #3/N
Alignment identifier is 2
> sequence chain #3/Q
Alignment identifier is 3/Q
> select #3/Q:3-39,41-74
508 atoms, 515 bonds, 71 residues, 1 model selected
> select #3/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color (#!3 & sel) byhetero
> select #3/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> color (#!3 & sel) byhetero
> select #3/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> color (#!3 & sel) byhetero
> select #3/H,L,O-P:3-39,41-74
2032 atoms, 2060 bonds, 284 residues, 1 model selected
> ui mousemode right select
> select clear
Drag select of 6 residues
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/T #3/Z
Alignment identifier is 3
> select #3/T,Z:259
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/T,Z:259
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color (#!3 & sel) byhetero
> select clear
Drag select of 9 atoms, 8 bonds
> select clear
[Repeated 1 time(s)]
> select add #3.11
534 atoms, 74 residues, 1 model selected
> select add #3.10
1084 atoms, 150 residues, 2 models selected
> select subtract #3.11
550 atoms, 76 residues, 3 models selected
> select subtract #3.10
1 model selected
> select #3/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color (#!3 & sel) byhetero
> select clear
> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc
Opened J276_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.95,
shown at level 0.101, step 2, values float32
Drag select of rfxa2_intlet_hollow.pdb_E SES surface, 208 of 3672 triangles,
rfxa2_intlet_hollow.pdb_F SES surface, 464 of 25208 triangles, 8 atoms, 8
bonds, 1 J276_003_volume_map_sharp.mrc
> volume #1 step 1
> volume #1 level 0.2498
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 7 models selected
> hide #!3 models
> hide #3.1 models
> hide #3.2 models
> show #3.1 models
> hide #!2 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> select clear
[Repeated 1 time(s)]
> close #1
> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc
Opened J276_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.95,
shown at level 0.101, step 2, values float32
> volume zlip #1
Expected a density maps specifier or a keyword
> volume #1 step 1
> volume #1 level 0.224
> volume zlip #1
Expected a density maps specifier or a keyword
> volume zflip #1
Expected a density maps specifier or a keyword
> volume flip #1
Opened J276_003_volume_map_sharp.mrc z flip as #7, grid size 400,400,400,
pixel 0.95, shown at step 1, values float32
> save /Users/wujingyi/Downloads/RfxATP_state1_withoutADP_F1.mrc models #7
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RFXATPase_state1_2.98A-1.pdb"
Chain information for RFXATPase_state1_2.98A-1.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
R | No description available
S | No description available
T Z | No description available
U X | No description available
V | No description available
W | No description available
Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select clear
> hide #!8 atoms
> show #!8 cartoons
> select add #7
2 models selected
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 15 residues
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,-1.2628,0,1,0,0.47837,0,0,1,-1.2591,#8,1,0,0,-1.2628,0,1,0,0.47837,0,0,1,-1.2591
> view matrix models
> #7,1,0,0,-1.7005,0,1,0,0.32181,0,0,1,0.34779,#8,1,0,0,-1.7005,0,1,0,0.32181,0,0,1,0.34779
> view matrix models
> #7,1,0,0,-1.3832,0,1,0,1.3436,0,0,1,-6.5748,#8,1,0,0,-1.3832,0,1,0,1.3436,0,0,1,-6.5748
> ui mousemode right select
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 9 residues
> select subtract #7
69 atoms, 9 residues, 1 model selected
> select add #7
69 atoms, 9 residues, 3 models selected
> select subtract #7
69 atoms, 9 residues, 1 model selected
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 3 residues
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 24 residues
> select #8/X:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,-1.6308,0,1,0,1.9901,0,0,1,-10.325
> view matrix models #8,1,0,0,17.812,0,1,0,-0.57249,0,0,1,-3.5122
> view matrix models #8,1,0,0,8.9735,0,1,0,15.372,0,0,1,-18.231
> view matrix models #8,1,0,0,6.1384,0,1,0,40.464,0,0,1,-18.769
> view matrix models #8,1,0,0,0.28461,0,1,0,11.462,0,0,1,-11.994
> ui mousemode right select
> select clear
> volume #7 level 0.1787
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 18 residues
> select clear
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.90579,0.37073,-0.20519,328.38,-0.30373,-0.90572,-0.29566,478.69,-0.29545,-0.20548,0.933,94.403
> view matrix models
> #8,-0.96264,0.27066,0.0076537,318.46,-0.26006,-0.91632,-0.3045,474.07,-0.075404,-0.29512,0.95248,66.029
> view matrix models
> #8,-0.92958,-0.23864,0.28095,356.73,0.29128,-0.94264,0.16308,288.68,0.22591,0.23343,0.94577,-88.104
> view matrix models
> #8,-0.84595,0.16919,0.50571,223.41,-0.021766,-0.9585,0.28426,328.28,0.53282,0.22946,0.81452,-121
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.84595,0.16919,0.50571,235.2,-0.021766,-0.9585,0.28426,367.87,0.53282,0.22946,0.81452,-65.315
> view matrix models
> #8,-0.84595,0.16919,0.50571,220.58,-0.021766,-0.9585,0.28426,321.34,0.53282,0.22946,0.81452,-116.96
> view matrix models
> #8,-0.84595,0.16919,0.50571,221.54,-0.021766,-0.9585,0.28426,322.24,0.53282,0.22946,0.81452,-114.19
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.83579,0.078648,0.54339,229.55,-0.07592,-0.99673,0.027491,386.99,0.54378,-0.018278,0.83903,-74.584
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.83579,0.078648,0.54339,222.57,-0.07592,-0.99673,0.027491,390.28,0.54378,-0.018278,0.83903,-87.165
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.91118,0.13459,0.38941,254.79,-0.039499,-0.96932,0.2426,338.58,0.41011,0.20567,0.88854,-112.87
> view matrix models
> #8,-0.97717,-0.025638,0.21089,330.07,0.044447,-0.99539,0.084934,356.72,0.20775,0.092368,0.97381,-69.326
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.97717,-0.025638,0.21089,338.54,0.044447,-0.99539,0.084934,351.74,0.20775,0.092368,0.97381,-56.344
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.87329,0.37091,0.31591,-103.7,-0.46999,0.81218,0.34565,63.53,-0.12837,-0.45033,0.88359,124.89
> view matrix models
> #8,0.87251,0.34682,0.34414,-104.27,-0.46902,0.79188,0.39108,58.745,-0.13689,-0.50263,0.85359,141.79
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.87251,0.34682,0.34414,-88.442,-0.46902,0.79188,0.39108,76.727,-0.13689,-0.50263,0.85359,134.61
> select add #7
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 4 models selected
> view matrix models
> #7,1,0,0,-6.297,0,1,0,-4.732,0,0,1,-10.051,#8,0.87251,0.34682,0.34414,-93.356,-0.46902,0.79188,0.39108,70.651,-0.13689,-0.50263,0.85359,131.13
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99677,-0.0017702,0.080268,-20.213,-0.0060842,0.99522,0.097502,-20.723,-0.080056,-0.097676,0.99199,25.283,#8,0.85954,0.30395,0.41086,-95.792,-0.48544,0.73697,0.47034,68.595,-0.15983,-0.60372,0.78101,164.94
> select subtract #8
2 models selected
> view matrix models
> #7,0.95476,-0.047178,0.29362,-43.084,-0.0629,0.93296,0.35444,-45.638,-0.29066,-0.35687,0.88778,134.06
> view matrix models
> #7,-0.88421,-0.21366,0.41537,319.19,0.41454,-0.76875,0.48701,159.82,0.21526,0.60281,0.7683,-122.46
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.88421,-0.21366,0.41537,329.35,0.41454,-0.76875,0.48701,172.07,0.21526,0.60281,0.7683,-126.96
> view matrix models
> #7,-0.88421,-0.21366,0.41537,332.67,0.41454,-0.76875,0.48701,178.44,0.21526,0.60281,0.7683,-131.73
> view matrix models
> #7,-0.88421,-0.21366,0.41537,331.46,0.41454,-0.76875,0.48701,179.89,0.21526,0.60281,0.7683,-135.36
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.94832,0.25093,0.19421,-67.519,-0.30926,0.86791,0.38872,27.724,-0.071014,-0.42869,0.90066,90.153
> view matrix models
> #7,0.70521,0.58704,0.39757,-122.03,-0.69527,0.68242,0.22562,167.18,-0.13886,-0.43553,0.8894,106.57
> view matrix models
> #7,0.82451,0.45778,0.33259,-108.48,-0.56304,0.72221,0.40175,101.62,-0.056283,-0.51851,0.85322,113.1
> view matrix models
> #7,0.82328,0.52176,0.22356,-100.14,-0.5672,0.77161,0.28794,114.17,-0.022268,-0.36385,0.93119,62.872
> view matrix models
> #7,0.67235,0.54008,0.50622,-126.97,-0.70093,0.68439,0.20079,172.5,-0.23801,-0.48982,0.83871,145.28
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.67235,0.54008,0.50622,-119.87,-0.70093,0.68439,0.20079,159.37,-0.23801,-0.48982,0.83871,140.99
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.69879,0.54006,0.46907,-118.06,-0.69186,0.67684,0.25141,149.67,-0.18171,-0.50022,0.84662,130.67
> view matrix models
> #7,0.83451,0.45787,0.30652,-98.483,-0.50917,0.85342,0.11141,107.12,-0.21058,-0.24905,0.94532,70.441
> view matrix models
> #7,0.89321,0.41571,0.17135,-76.748,-0.44856,0.85022,0.27554,65.671,-0.031139,-0.32297,0.9459,49.832
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.85265,0.28815,0.43585,-93.839,-0.38349,0.91169,0.14749,65.269,-0.35486,-0.2929,0.88785,117.1
> ui tool show "Fit in Map"
> fitmap #8 inMap #7
Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms
average map value = 0.0361, steps = 248
shifted from previous position = 3.32
rotated from previous position = 3.59 degrees
atoms outside contour = 36794, contour level = 0.17874
Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#7) coordinates:
Matrix rotation and translation
0.97702481 0.20658623 -0.05238958 -29.62036884
-0.18232674 0.93747643 0.29647078 -1.24036171
0.11036078 -0.28010728 0.95360391 47.42560830
Axis -0.80722577 -0.22785516 -0.54448928
Axis point 0.00000000 159.66635676 39.10884363
Rotation angle (degrees) 20.92438479
Shift along axis -1.62978743
> volume #7 level 0.3325
> volume #7 level 0.191
> surface dust #7 size 9.5
> volume #7 level 0.08035
> surface dust #7 size 9.5
[Repeated 1 time(s)]
> volume #7 level 0.0503
> volume #7 level 0.103
> ui mousemode right select
> select clear
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> surface dust #7 size 9.5
> show #!8 models
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 60 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.81858,0.56012,0.12724,-82.604,-0.57128,0.81694,0.079034,132.39,-0.059679,-0.13738,0.98872,13.357,#8,0.7117,0.65856,0.24451,-101.51,-0.69838,0.62571,0.3475,152.04,0.075857,-0.41807,0.90524,62.186
> select subtract #7
471 atoms, 60 residues, 1 model selected
> view matrix models
> #8,-0.66704,-0.73627,0.11385,442.68,0.72058,-0.6764,-0.15248,219.63,0.18927,-0.019677,0.98173,-47.612
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> select add #7
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.81858,0.56012,0.12724,-107.08,-0.57128,0.81694,0.079034,119.88,-0.059679,-0.13738,0.98872,13.446,#8,-0.66704,-0.73627,0.11385,418.2,0.72058,-0.6764,-0.15248,207.12,0.18927,-0.019677,0.98173,-47.523
> select subtract #8
2 models selected
> select subtract #7
Nothing selected
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> view matrix models
> #8,-0.66704,-0.73627,0.11385,415.23,0.72058,-0.6764,-0.15248,205.72,0.18927,-0.019677,0.98173,-48.196
> view matrix models
> #8,-0.66704,-0.73627,0.11385,414.92,0.72058,-0.6764,-0.15248,206.56,0.18927,-0.019677,0.98173,-49.48
> view matrix models
> #8,-0.66704,-0.73627,0.11385,413.85,0.72058,-0.6764,-0.15248,208.31,0.18927,-0.019677,0.98173,-47.84
> select subtract #8
Nothing selected
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.82946,0.54181,0.1358,-107.14,-0.55482,0.8273,0.088006,113.07,-0.064669,-0.14834,0.98682,16.887
> view matrix models
> #7,0.82794,0.53632,0.16394,-110.95,-0.54873,0.83508,0.03928,119.35,-0.11584,-0.12248,0.98569,21.764
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.82794,0.53632,0.16394,-116.9,-0.54873,0.83508,0.03928,129.66,-0.11584,-0.12248,0.98569,21.897
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.80067,0.55879,0.21605,-125.69,-0.57153,0.82057,-0.0042587,144.83,-0.17966,-0.12007,0.97637,35.272
> view matrix models
> #7,0.81894,0.56477,0.1019,-109.35,-0.54936,0.82283,-0.14542,166.11,-0.16597,0.063107,0.98411,-4.5857
> select subtract #7
Nothing selected
> hide #!7 models
> show #!7 models
> fitmap #8 inMap #7
Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms
average map value = 0.04304, steps = 80
shifted from previous position = 1.27
rotated from previous position = 1.72 degrees
atoms outside contour = 33294, contour level = 0.103
Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#7) coordinates:
Matrix rotation and translation
-0.97766050 -0.21015754 0.00371096 411.17643737
0.21004182 -0.97748108 -0.02032708 335.92463186
0.00789929 -0.01909353 0.99978651 8.97038534
Axis 0.00293548 -0.00996693 0.99994602
Axis point 187.72593879 189.84909480 0.00000000
Rotation angle (degrees) 167.87114146
Shift along axis 6.82876360
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/Rfx ATPase ADP map/Rfx ATPase overall
> map/J68_10.48w_2.89A_volumeZ_map.mrc.mrc"
Opened J68_10.48w_2.89A_volumeZ_map.mrc.mrc as #9, grid size 400,400,400,
pixel 0.93, shown at level 0.0643, step 2, values float32
> select add #9
2 models selected
> view matrix models
> #9,0.94781,0.29555,0.11964,-65.963,-0.30155,0.9528,0.035199,59.073,-0.10359,-0.069439,0.99219,33.644
> view matrix models
> #9,-0.16235,-0.98146,-0.10184,417.29,0.97581,-0.14439,-0.16413,56.511,0.14638,-0.12602,0.98117,-0.95683
> view matrix models
> #9,-0.64648,-0.75883,0.079063,434.97,0.74348,-0.64985,-0.15787,192.08,0.17118,-0.04328,0.98429,-21.402
> hide #!7 models
> view matrix models
> #9,-0.63471,-0.72188,0.27572,390.81,0.71277,-0.68474,-0.15195,203.21,0.29849,0.10008,0.94915,-65.43
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.63471,-0.72188,0.27572,444.16,0.71277,-0.68474,-0.15195,299.14,0.29849,0.10008,0.94915,-102.44
> view matrix models
> #9,-0.63471,-0.72188,0.27572,377.16,0.71277,-0.68474,-0.15195,204.9,0.29849,0.10008,0.94915,-87.29
> view matrix models
> #9,-0.63471,-0.72188,0.27572,380.26,0.71277,-0.68474,-0.15195,209.91,0.29849,0.10008,0.94915,-89.722
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.81475,-0.54434,0.19968,395.03,0.53788,-0.83818,-0.09021,259.98,0.21648,0.033908,0.9757,-66.876
> view matrix models
> #9,-0.81553,-0.55997,0.14609,407.63,0.53884,-0.82683,-0.16124,270.41,0.21109,-0.052776,0.97604,-49.973
> view matrix models
> #9,-0.72178,-0.67644,0.14653,411.36,0.64266,-0.7336,-0.22095,244.41,0.25695,-0.065305,0.96421,-54.174
> view matrix models
> #9,-0.70922,-0.70009,0.082935,424.72,0.68767,-0.71291,-0.1374,217.21,0.15532,-0.040416,0.98704,-43.731
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.70922,-0.70009,0.082935,420.42,0.68767,-0.71291,-0.1374,222.59,0.15532,-0.040416,0.98704,-41.757
> show #!7 models
> select subtract #9
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,0.81894,0.56477,0.1019,-109.07,-0.54936,0.82283,-0.14542,166.67,-0.16597,0.063107,0.98411,-8.6208
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.82136,0.57001,0.021207,-95.736,-0.56458,0.81772,-0.11217,164.45,-0.081282,0.080162,0.99346,-29.777
> view matrix models
> #7,-0.8497,-0.52724,0.0058055,439.44,0.52217,-0.84296,-0.12945,285.87,0.073144,-0.10696,0.99157,-22.184
> select subtract #7
Nothing selected
> hide #!9 models
> select add #7
2 models selected
> view matrix models
> #7,-0.83572,-0.53982,0.10088,421.78,0.53709,-0.84174,-0.054778,269.08,0.11449,0.0084053,0.99339,-52.947
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.83572,-0.53982,0.10088,417.08,0.53709,-0.84174,-0.054778,262.64,0.11449,0.0084053,0.99339,-42.059
> select subtract #7
Nothing selected
> fitmap #8 inMap #7
Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms
average map value = 0.04408, steps = 112
shifted from previous position = 3.13
rotated from previous position = 2.25 degrees
atoms outside contour = 33470, contour level = 0.103
Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#7) coordinates:
Matrix rotation and translation
0.97622445 0.21492117 -0.02819088 -26.72514574
-0.21024437 0.97048116 0.11816781 32.35392173
0.05275548 -0.10943133 0.99259340 14.03890220
Axis -0.46543944 -0.16553502 -0.86946207
Axis point 128.83594929 149.69566655 0.00000000
Rotation angle (degrees) 14.15223914
Shift along axis -5.12306287
> open "/Volumes/暴躁的喷火龙/Rfx ATPase
> 相关/RfxATPaseRefine/RealSpaceRefine_17/RealSpaceRefine_3/RFXATP_state3_2.98A.pdb"
Chain information for RFXATP_state3_2.98A.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H J K L M N O P | No description available
I | No description available
Q | No description available
R | No description available
S | No description available
T Z | No description available
U X | No description available
V | No description available
W | No description available
Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!8,10 atoms
> show #!8,10 cartoons
> select add #10
41664 atoms, 42310 bonds, 2 pseudobonds, 5415 residues, 2 models selected
> view matrix models #10,1,0,0,-10.589,0,1,0,-7.4647,0,0,1,-9.3559
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.76052,0.64884,0.024792,-93.638,-0.62796,0.74469,-0.22605,199.08,-0.16514,0.15635,0.9738,-3.506
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.76052,0.64884,0.024792,-86.508,-0.62796,0.74469,-0.22605,209.64,-0.16514,0.15635,0.9738,-11.296
> close #10
> select add #7
2 models selected
> view matrix models
> #7,-0.83572,-0.53982,0.10088,415.05,0.53709,-0.84174,-0.054778,260.68,0.11449,0.0084053,0.99339,-39.287
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.95714,0.16723,0.23649,-89.037,-0.1543,0.98537,-0.072306,37.936,-0.24512,0.032717,0.96894,28.818
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.95714,0.16723,0.23649,-87.29,-0.1543,0.98537,-0.072306,40.751,-0.24512,0.032717,0.96894,27.221
> view matrix models
> #7,0.95714,0.16723,0.23649,-86.543,-0.1543,0.98537,-0.072306,42.25,-0.24512,0.032717,0.96894,24.956
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.92321,0.37982,0.058404,-88.959,-0.38192,0.92371,0.029897,78.808,-0.042593,-0.049907,0.99785,-2.6972
> view matrix models
> #7,0.91969,0.39205,-0.021748,-75.952,-0.39242,0.91582,-0.085316,103.52,-0.01353,0.086998,0.99612,-34.686
> view matrix models
> #7,0.92247,0.38437,0.036047,-85.6,-0.38453,0.92311,-0.0026085,85.396,-0.034278,-0.011455,0.99935,-12.076
> view matrix models
> #7,0.76202,0.644,0.067666,-111.69,-0.64537,0.76387,-0.002207,166.06,-0.053109,-0.041988,0.99771,-2.2214
> view matrix models
> #7,0.65427,0.75569,0.029352,-106.02,-0.75604,0.65266,0.049297,199.4,0.018097,-0.054445,0.99835,-13.441
> view matrix models
> #7,0.95204,-0.28314,-0.11602,67.299,0.24823,0.93635,-0.24825,7.6394,0.17892,0.20754,0.96172,-88.537
> view matrix models
> #7,0.94298,-0.2658,-0.20036,81.127,0.22255,0.95108,-0.21431,3.4041,0.24752,0.1575,0.956,-90.737
> view matrix models
> #7,0.96073,-0.23679,-0.14467,61.843,0.22866,0.97094,-0.070685,-28.033,0.1572,0.034829,0.98695,-55.257
> view matrix models
> #7,0.9619,0.21075,-0.17416,-20.507,-0.22712,0.97058,-0.079934,60.391,0.15219,0.11644,0.98147,-69.263
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.9619,0.21075,-0.17416,-18.141,-0.22712,0.97058,-0.079934,65.506,0.15219,0.11644,0.98147,-70.438
> view matrix models
> #7,0.9619,0.21075,-0.17416,-9.0196,-0.22712,0.97058,-0.079934,60.113,0.15219,0.11644,0.98147,-77.849
> view matrix models
> #7,0.9619,0.21075,-0.17416,-3.0965,-0.22712,0.97058,-0.079934,65.362,0.15219,0.11644,0.98147,-75.215
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.93248,0.31906,-0.16934,-19.577,-0.3338,0.9403,-0.066405,89.08,0.13804,0.11845,0.98332,-73.257
> view matrix models
> #7,0.9156,0.31072,-0.2552,1.0399,-0.34905,0.92927,-0.1209,104.15,0.19958,0.19978,0.9593,-96.453
> view matrix models
> #7,0.91676,0.39096,-0.081908,-46.718,-0.38877,0.92039,0.041794,83.547,0.091726,-0.0064719,0.99576,-42.301
> view matrix models
> #7,0.91372,0.37945,-0.14535,-32.232,-0.35999,0.92185,0.14354,59.093,0.18846,-0.078833,0.97891,-43.441
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.91372,0.37945,-0.14535,-43.381,-0.35999,0.92185,0.14354,51.397,0.18846,-0.078833,0.97891,-38.445
> view matrix models
> #7,0.91372,0.37945,-0.14535,-74.107,-0.35999,0.92185,0.14354,94.41,0.18846,-0.078833,0.97891,-33.917
> view matrix models
> #7,0.91372,0.37945,-0.14535,-48.806,-0.35999,0.92185,0.14354,-0.85681,0.18846,-0.078833,0.97891,-44.749
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.93287,0.35507,-0.060677,-63.236,-0.36003,0.91353,-0.18932,61.939,-0.011792,0.19845,0.98004,-61.127
> view matrix models
> #7,0.59552,0.72577,-0.34442,-19.476,-0.76545,0.64276,0.030941,151.52,0.24383,0.24521,0.93831,-111.2
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.59552,0.72577,-0.34442,-49.852,-0.76545,0.64276,0.030941,124.52,0.24383,0.24521,0.93831,-101.83
> view matrix models
> #7,0.59552,0.72577,-0.34442,-60.128,-0.76545,0.64276,0.030941,116.16,0.24383,0.24521,0.93831,-94.184
> close #9
> close #8
> close #1
> close #7
> open /Users/wujingyi/Downloads/RfxATP_state1_withoutADP_F1.mrc
Opened RfxATP_state1_withoutADP_F1.mrc as #1, grid size 400,400,400, pixel
0.95, shown at level 0.101, step 2, values float32
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RFXATPase_state1_2.98A-1.pdb"
Chain information for RFXATPase_state1_2.98A-1.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
R | No description available
S | No description available
T Z | No description available
U X | No description available
V | No description available
W | No description available
Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!7 atoms
> show #!7 cartoons
> surface dust #1 size 9.5
> fitmap #7 inMap #1
Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41723 atoms
average map value = 0.04077, steps = 136
shifted from previous position = 4.02
rotated from previous position = 3.84 degrees
atoms outside contour = 34651, contour level = 0.10124
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
0.99804835 -0.05934006 -0.01944861 16.74869891
0.05979253 0.99793245 0.02357275 -13.35557001
0.01800960 -0.02468963 0.99953293 4.36796433
Axis -0.36047882 -0.27978089 0.88981890
Axis point 225.78118362 284.45693547 0.00000000
Rotation angle (degrees) 3.83836701
Shift along axis 1.58577930
> volume #1 color #b2b2b24d
> volume #1 color #b2b2b227
> volume #1 color #b22eb227
> volume #1 color #ff80b227
> volume #1 color #ff80b226
> select add #7
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.98144,0.18462,0.051915,-38.788,-0.18689,0.98144,0.043017,32.642,-0.04301,-0.051921,0.99772,21.285
> view matrix models
> #7,0.97737,0.20827,-0.037143,-25.986,-0.20456,0.97514,0.085249,29.35,0.053975,-0.075722,0.99567,7.8166
> view matrix models
> #7,0.3135,0.89632,0.31357,-93.877,-0.94688,0.31999,0.032003,301.32,-0.071653,-0.30695,0.94903,83.234
> view matrix models
> #7,0.27847,0.948,0.1541,-67.461,-0.95389,0.25426,0.15953,291.34,0.11206,-0.19141,0.97509,22.238
> view matrix models
> #7,-0.89188,-0.12145,0.43567,300.64,-0.070548,-0.91412,-0.39926,445.84,0.44674,-0.38683,0.80671,26.663
> view matrix models
> #7,-0.97781,-0.1101,0.17823,362.26,0.097028,-0.99202,-0.080488,369.91,0.18567,-0.061408,0.98069,-16.918
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.97781,-0.1101,0.17823,369.79,0.097028,-0.99202,-0.080488,367.47,0.18567,-0.061408,0.98069,-16.517
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.95046,-0.2701,0.15386,398.97,0.25491,-0.96051,-0.11154,337.56,0.17791,-0.066792,0.98178,-14.251
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.95046,-0.2701,0.15386,397.21,0.25491,-0.96051,-0.11154,335.28,0.17791,-0.066792,0.98178,-14.171
> select subtract #7
Nothing selected
> fitmap #7 inMap #1
Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41723 atoms
average map value = 0.04023, steps = 80
shifted from previous position = 2.74
rotated from previous position = 1.81 degrees
atoms outside contour = 34774, contour level = 0.10124
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
-0.94648353 -0.29356976 0.13411086 404.06536557
0.27833502 -0.95279058 -0.12132491 329.83743239
0.16339689 -0.07750428 0.98351133 -12.14291093
Axis 0.07629892 -0.05099179 0.99578025
Axis point 178.19941142 194.35490456 0.00000000
Rotation angle (degrees) 163.31174632
Shift along axis 1.91907946
> select add #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99784,0.031519,-0.057702,3.7445,-0.041622,0.98218,-0.18327,41.551,0.050897,0.18527,0.98137,-42.827
> view matrix models
> #1,0.99784,0.031523,-0.057713,3.7455,-0.04163,0.98218,-0.1833,41.559,0.050906,0.18531,0.98136,-42.834
> view matrix models
> #1,0.99858,0.026368,-0.046311,2.7359,-0.033003,0.9883,-0.14892,33.065,0.041843,0.15024,0.98776,-35.309
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99858,0.026368,-0.046311,26.097,-0.033003,0.9883,-0.14892,38.648,0.041843,0.15024,0.98776,-34.996
> view matrix models
> #1,0.99858,0.026368,-0.046311,25.542,-0.033003,0.9883,-0.14892,29.187,0.041843,0.15024,0.98776,-37.84
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99824,0.026046,-0.053332,26.825,-0.033706,0.98839,-0.14818,29.182,0.048853,0.14972,0.98752,-39.032
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99824,0.026046,-0.053332,8.1344,-0.033706,0.98839,-0.14818,30.937,0.048853,0.14972,0.98752,-37.661
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.97824,0.040182,0.20356,-33.084,-0.0047157,0.98512,-0.17179,29.942,-0.20744,0.16709,0.96387,11.601
> fitmap #7 inMap #1
Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41723 atoms
average map value = 0.04286, steps = 136
shifted from previous position = 3.45
rotated from previous position = 1.82 degrees
atoms outside contour = 34360, contour level = 0.10124
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
-0.96674099 -0.23994963 -0.08852139 428.37710337
0.23665701 -0.97049707 0.04613999 318.95845950
-0.09698103 0.02365621 0.99500506 17.97471156
Axis -0.04711490 0.01772721 0.99873216
Axis point 195.28656125 185.29015588 0.00000000
Rotation angle (degrees) 166.19572999
Shift along axis 3.42322358
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> open "/Volumes/暴躁的喷火龙/Rfx ATPase
> 相关/RfxATPaseRefine/RealSpaceRefine_17/RealSpaceRefine_2/RFXATP_state2_3.02A.pdb"
Chain information for RFXATP_state2_3.02A.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H I | No description available
J K | No description available
L | No description available
M N O P Q | No description available
R | No description available
S | No description available
T Z | No description available
U X | No description available
V | No description available
W | No description available
Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Volumes/暴躁的喷火龙/Rfx ATPase
> 相关/RfxATPaseRefine/RealSpaceRefine_17/RealSpaceRefine_3/RFXATP_state3_2.98A.pdb"
Chain information for RFXATP_state3_2.98A.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H J K L M N O P | No description available
I | No description available
Q | No description available
R | No description available
S | No description available
T Z | No description available
U X | No description available
V | No description available
W | No description available
Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!7-9 atoms
> show #!7-9 cartoons
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select add #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.97037,-0.23901,0.035515,419.91,0.23572,-0.96865,-0.078444,350.65,0.053151,-0.067748,0.99629,2.5777
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.97037,-0.23901,0.035515,416.59,0.23572,-0.96865,-0.078444,339.72,0.053151,-0.067748,0.99629,-1.2446
> hide #!9 models
> show #!8 models
> view matrix models
> #1,-0.97037,-0.23901,0.035515,345.96,0.23572,-0.96865,-0.078444,363.39,0.053151,-0.067748,0.99629,-2.3113
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.92075,-0.19413,0.33842,-72.485,0.27823,0.9348,-0.22076,6.7297,-0.2735,0.29743,0.91473,1.8952
> view matrix models
> #1,0.13093,0.98898,0.069111,-109.1,-0.90483,0.1477,-0.39932,415.04,-0.40513,-0.010249,0.9142,87.158
> view matrix models
> #1,-0.23986,0.9708,0.004384,-24.349,-0.96326,-0.23743,-0.12553,456.38,-0.12082,-0.034331,0.99208,24.953
> view matrix models
> #1,-0.21234,0.97717,-0.0064039,-29.056,-0.96114,-0.21003,-0.17918,459.45,-0.17643,-0.031892,0.9838,36.422
> view matrix models
> #1,-0.1936,0.97382,-0.11911,-13.426,-0.96727,-0.20976,-0.14277,454.57,-0.16402,0.087575,0.98256,10.915
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.1936,0.97382,-0.11911,56.039,-0.96727,-0.20976,-0.14277,432.09,-0.16402,0.087575,0.98256,17.749
> fitmap #8 inMap #1
Fit molecule RFXATP_state2_3.02A.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41693 atoms
average map value = 0.03895, steps = 312
shifted from previous position = 2.45
rotated from previous position = 3.63 degrees
atoms outside contour = 35104, contour level = 0.10124
Position of RFXATP_state2_3.02A.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
-0.19496911 -0.96149331 -0.19369476 435.88456688
0.96437624 -0.22392600 0.14083899 31.70371768
-0.17878904 -0.15933537 0.97089996 67.54728992
Axis -0.15400038 -0.00764718 0.98804120
Axis point 210.43375572 191.70784699 0.00000000
Rotation angle (degrees) 102.94393921
Shift along axis -0.62932566
> hide #!8 models
> show #!9 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.20069,-0.93673,-0.28682,458.35,0.97475,-0.22019,0.037087,35.013,-0.097896,-0.27213,0.95727,79.624
> view matrix models
> #1,-0.54665,-0.8357,0.052654,448.59,0.78016,-0.53115,-0.3305,193.28,0.30416,-0.13959,0.94234,-20.326
> view matrix models
> #1,-0.98194,0.18213,0.051307,332.73,-0.18307,-0.983,-0.014229,412.84,0.047843,-0.023365,0.99858,-3.5188
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.98194,0.18213,0.051307,336.15,-0.18307,-0.983,-0.014229,410.41,0.047843,-0.023365,0.99858,-14.129
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.21156,-0.97496,0.068448,412.87,0.88946,-0.22109,-0.39997,120.89,0.40509,-0.023736,0.91397,-68.114
> view matrix models
> #1,-0.23443,-0.96721,-0.097748,443.04,0.90288,-0.17935,-0.39069,108.66,0.36035,-0.17984,0.91532,-29.315
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.23443,-0.96721,-0.097748,435.3,0.90288,-0.17935,-0.39069,108.91,0.36035,-0.17984,0.91532,-28.573
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.30949,-0.92218,0.23194,386.54,0.80312,-0.38409,-0.4555,178.56,0.50914,0.0453,0.85949,-91.7
> view matrix models
> #1,-0.29078,-0.93136,0.21914,386.88,0.95319,-0.30183,-0.017985,61.954,0.082893,0.20365,0.97553,-60.629
> view matrix models
> #1,-0.34211,-0.91713,0.20453,396.27,0.933,-0.35741,-0.042049,80.618,0.11166,0.17644,0.97796,-61.185
> view matrix models
> #1,-0.32848,-0.9432,-0.049801,440.61,0.93446,-0.3322,0.12814,47.414,-0.13741,-0.0044456,0.9905,19.494
> view matrix models
> #1,-0.63985,-0.75621,0.13691,432.6,0.76725,-0.61842,0.16997,128.29,-0.043868,0.2138,0.97589,-38.552
> view matrix models
> #1,-0.55479,-0.79218,0.25428,404.14,0.81426,-0.57975,-0.029596,144.61,0.17086,0.19063,0.96668,-73.367
> fitmap #9 inMap #1
Fit molecule RFXATP_state3_2.98A.pdb (#9) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41664 atoms
average map value = 0.04065, steps = 84
shifted from previous position = 1.73
rotated from previous position = 2.42 degrees
atoms outside contour = 34719, contour level = 0.10124
Position of RFXATP_state3_2.98A.pdb (#9) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
-0.52344947 0.82977819 0.19356862 107.43103314
-0.80993669 -0.55510715 0.18936369 416.56043578
0.26458118 -0.05765600 0.96263834 -22.37825674
Axis -0.14883064 -0.04278544 -0.98793666
Axis point 167.56416462 180.27267990 0.00000000
Rotation angle (degrees) 123.91477585
Shift along axis -11.70344924
> hide #!9 models
> show #!7 models
> view matrix models
> #1,0.90249,0.36148,0.23419,-95.305,-0.32338,0.92782,-0.18593,92.182,-0.2845,0.092068,0.95425,34.586
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.90249,0.36148,0.23419,-92.259,-0.32338,0.92782,-0.18593,106.85,-0.2845,0.092068,0.95425,39.176
> view matrix models
> #1,0.90249,0.36148,0.23419,-87.379,-0.32338,0.92782,-0.18593,104.13,-0.2845,0.092068,0.95425,40.688
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.90519,0.41617,-0.086184,-45.877,-0.42093,0.90589,-0.046645,104.06,0.058661,0.0785,0.99519,-28.692
> view matrix models
> #1,0.8977,0.43274,-0.082866,-48.236,-0.43682,0.8987,-0.039055,107.25,0.057571,0.071257,0.9958,-27.17
> view matrix models
> #1,0.90611,0.39509,0.15124,-80.989,-0.38925,0.91864,-0.067724,99.013,-0.16569,0.0024974,0.98617,30.333
> view matrix models
> #1,0.91513,0.39842,0.061622,-68.615,-0.39628,0.91706,-0.044261,96.8,-0.074145,0.016085,0.99712,8.4582
> select subtract #1
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,-0.52084,0.83782,-0.16368,155.82,-0.6798,-0.52304,-0.51411,509.47,-0.51634,-0.1565,0.84196,151.85
> view matrix models
> #1,-0.74213,-0.64735,-0.17371,489.82,0.66907,-0.73089,-0.13472,231.02,-0.039753,-0.2162,0.97554,50.859
> view matrix models
> #1,-0.7533,-0.58651,0.29758,402.52,0.52674,-0.80896,-0.26102,294.14,0.39382,-0.039881,0.91832,-56.687
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.7533,-0.58651,0.29758,415.76,0.52674,-0.80896,-0.26102,290.08,0.39382,-0.039881,0.91832,-56.792
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> color #1 #ff80b2ff models
> select add #1
2 models selected
> view matrix models
> #1,-0.7533,-0.58651,0.29758,442.79,0.52674,-0.80896,-0.26102,380.85,0.39382,-0.039881,0.91832,-55.44
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.7533,-0.58651,0.29758,446.69,0.52674,-0.80896,-0.26102,388.45,0.39382,-0.039881,0.91832,-48.116
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.81746,-0.57568,0.018822,502.64,0.57225,-0.81545,-0.087036,352.43,0.065453,-0.060377,0.99603,5.5883
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.81746,-0.57568,0.018822,510.94,0.57225,-0.81545,-0.087036,371.17,0.065453,-0.060377,0.99603,-4.0051
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.9404,-0.30666,-0.14699,151.16,0.31054,0.95055,0.0036449,60.933,0.1386,-0.049073,0.98913,-18.999
> view matrix models
> #1,0.94258,0.27118,0.19494,-18.434,-0.26437,0.96251,-0.060662,178.57,-0.20408,0.0056438,0.97894,37.191
> view matrix models
> #1,0.97155,0.18858,-0.14329,47.837,-0.17573,0.97958,0.09769,132.32,0.15878,-0.06973,0.98485,-18.097
> view matrix models
> #1,0.98671,0.15401,0.051892,19.6,-0.15475,0.9879,0.010558,141.03,-0.049638,-0.018449,0.9986,9.2778
> view matrix models
> #1,0.99318,0.11653,-0.0048243,35.025,-0.11623,0.99236,0.041337,127.77,0.0096042,-0.040494,0.99913,2.2251
> view matrix models
> #1,0.99089,0.11403,-0.071604,46.933,-0.12143,0.98656,-0.1093,154.67,0.058179,0.11699,0.99143,-36.527
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98298,0.1349,0.12469,12.068,-0.11416,0.98038,-0.16069,162.95,-0.14392,0.14372,0.9791,-1.2664
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.98298,0.1349,0.12469,-19.664,-0.11416,0.98038,-0.16069,157.99,-0.14392,0.14372,0.9791,-0.011895
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99106,0.12059,0.057146,-7.2929,-0.11296,0.98609,-0.12195,150.27,-0.071058,0.11441,0.99089,-10.087
> view matrix models
> #1,0.99366,0.11208,0.0085199,1.8747,-0.11123,0.9914,-0.069006,140.2,-0.016181,0.067621,0.99758,-12.487
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99366,0.11208,0.0085199,-8.3383,-0.11123,0.9914,-0.069006,179.3,-0.016181,0.067621,0.99758,-13.796
> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc
Opened J276_003_volume_map_sharp.mrc as #10, grid size 400,400,400, pixel
0.95, shown at level 0.101, step 2, values float32
> volume flip #10
Opened J276_003_volume_map_sharp.mrc z flip as #11, grid size 400,400,400,
pixel 0.95, shown at step 1, values float32
> surface dust #1 size 9.5
[Repeated 2 time(s)]
> volume #11 level 0.1898
> view matrix models
> #1,0.99366,0.11208,0.0085199,-8.5676,-0.11123,0.9914,-0.069006,175.82,-0.016181,0.067621,0.99758,-8.4965
> select add #11
4 models selected
> close #10
> view matrix models
> #1,0.99366,0.11208,0.0085199,-9.271,-0.11123,0.9914,-0.069006,174.67,-0.016181,0.067621,0.99758,-8.5799,#11,1,0,0,-0.70339,0,1,0,-1.151,0,0,1,-0.083462
> select subtract #1
2 models selected
> view matrix models #11,1,0,0,-24.883,0,1,0,-115.17,0,0,1,-3.4578
> view matrix models #11,1,0,0,-14.96,0,1,0,-8.1909,0,0,1,-4.9614
> view matrix models #11,1,0,0,-12.667,0,1,0,-129.71,0,0,1,-22.609
> select add #1
4 models selected
> view matrix models
> #1,0.99366,0.11208,0.0085199,-7.888,-0.11123,0.9914,-0.069006,154.52,-0.016181,0.067621,0.99758,-11.139,#11,1,0,0,-11.284,0,1,0,-149.87,0,0,1,-25.167
> select subtract #11
2 models selected
> view matrix models
> #1,0.99366,0.11208,0.0085199,-6.4335,-0.11123,0.9914,-0.069006,158.49,-0.016181,0.067621,0.99758,-0.46871
> view matrix models
> #1,0.99366,0.11208,0.0085199,-7.6761,-0.11123,0.9914,-0.069006,152,-0.016181,0.067621,0.99758,0.52332
> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc
Opened J276_003_volume_map_sharp.mrc as #10, grid size 400,400,400, pixel
0.95, shown at level 0.101, step 2, values float32
> close #11
> volume #10 step 1
> surface dust #1 size 9.5
> volume #10 level 0.1812
> surface dust #1 size 9.5
> fitmap #10 inMap #1
Fit map J276_003_volume_map_sharp.mrc in map RfxATP_state1_withoutADP_F1.mrc
using 188089 points
correlation = -0.006151, correlation about mean = 0.01165, overlap = -25.22
steps = 124, shift = 3.02, angle = 1.44 degrees
Position of J276_003_volume_map_sharp.mrc (#10) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
0.99219120 -0.11872377 -0.03822681 33.00709102
0.12081950 0.99096707 0.05819723 -151.45253231
0.03097211 -0.06236133 0.99757295 3.22774595
Axis -0.43530083 -0.24985658 0.86491900
Axis point 1221.20725162 293.99472165 0.00000000
Rotation angle (degrees) 7.95974301
Shift along axis 26.26513589
> select add #10
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.97091,0.099541,-0.21778,40.434,-0.10837,0.99369,-0.028932,143.66,0.21353,0.05169,0.97557,-37.684,#10,0.96861,-0.0030468,-0.24857,56.703,0.011641,0.99938,0.033111,-10.51,0.24832,-0.034965,0.96805,-35.316
> select subtract #1
2 models selected
> view matrix models
> #10,-0.9324,0.29299,-0.21165,358.89,0.29835,0.95443,0.0068452,-52.02,0.20401,-0.056764,-0.97732,354.17
> view matrix models
> #10,-0.93215,0.31812,-0.17292,346.59,0.28997,0.94188,0.16965,-79.574,0.21684,0.108,-0.97021,319.18
> view matrix models
> #10,-0.95209,0.30384,-0.034637,326.33,0.29532,0.94293,0.15383,-77.736,0.079399,0.13623,-0.98749,343.6
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.95209,0.30384,-0.034637,325.96,0.29532,0.94293,0.15383,-75.425,0.079399,0.13623,-0.98749,332.17
> fitmap #10 inMap #1
Fit map J276_003_volume_map_sharp.mrc in map RfxATP_state1_withoutADP_F1.mrc
using 188089 points
correlation = -0.007304, correlation about mean = 0.01435, overlap = -29.43
steps = 128, shift = 0.762, angle = 2.55 degrees
Position of J276_003_volume_map_sharp.mrc (#10) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
-0.94519797 0.18352083 -0.27003869 390.20153472
0.17116532 0.98283540 0.06882591 -159.08409996
0.27803458 0.01883286 -0.96038643 307.90980210
Axis -0.09081601 -0.99561473 -0.02244469
Axis point 180.47276345 0.00000000 183.99021934
Rotation angle (degrees) 164.02346511
Shift along axis 116.03898949
> surface dust #10 size 9.5
> hide #!1 models
> volume #10 level 0.1163
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.96121,0.27191,-0.046177,336.43,0.26447,0.9562,0.12544,-67.366,0.078264,0.10836,-0.99103,338.37
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.95945,0.26317,-0.10101,349.53,0.24157,0.95229,0.1865,-75.323,0.14527,0.15454,-0.97725,313.7
> view matrix models
> #10,-0.941,0.32028,-0.10925,336.66,0.2949,0.93447,0.19949,-84.745,0.16598,0.1555,-0.97379,308.85
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.941,0.32028,-0.10925,336.51,0.2949,0.93447,0.19949,-85.007,0.16598,0.1555,-0.97379,311.62
> view matrix models
> #10,-0.941,0.32028,-0.10925,335.02,0.2949,0.93447,0.19949,-82.234,0.16598,0.1555,-0.97379,307.58
> view matrix models
> #10,-0.941,0.32028,-0.10925,337.07,0.2949,0.93447,0.19949,-81.211,0.16598,0.1555,-0.97379,307.08
> fitmap #10 inMap #1
Fit map J276_003_volume_map_sharp.mrc in map RfxATP_state1_withoutADP_F1.mrc
using 412809 points
correlation = 0.003388, correlation about mean = -0.01098, overlap = 26.25
steps = 188, shift = 2.96, angle = 3.45 degrees
Position of J276_003_volume_map_sharp.mrc (#10) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
-0.88776004 0.24481426 -0.38980519 394.83049540
0.20167323 0.96809819 0.14870711 -177.87661799
0.41377531 0.05340296 -0.90881137 261.15290888
Axis -0.11760697 -0.99163221 -0.05323677
Axis point 179.43195104 0.00000000 178.94673905
Rotation angle (degrees) 156.09754779
Shift along axis 116.05042942
> select subtract #10
Nothing selected
> select add #10
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.93304,0.31032,-0.18203,355.25,0.28502,0.94634,0.15235,-72.252,0.21954,0.090268,-0.97142,307.64
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.93304,0.31032,-0.18203,353.2,0.28502,0.94634,0.15235,-85.848,0.21954,0.090268,-0.97142,311.78
> view matrix models
> #10,-0.93304,0.31032,-0.18203,353.31,0.28502,0.94634,0.15235,-85.037,0.21954,0.090268,-0.97142,312.82
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.9315,0.30464,-0.19874,357.71,0.31409,0.94924,-0.017144,-54.858,0.18343,-0.078393,-0.9799,354.37
> fitmap #10 inMap #1
Fit map J276_003_volume_map_sharp.mrc in map RfxATP_state1_withoutADP_F1.mrc
using 412809 points
correlation = 0.003971, correlation about mean = -0.01138, overlap = 29.2
steps = 76, shift = 1.45, angle = 1.05 degrees
Position of J276_003_volume_map_sharp.mrc (#10) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:
Matrix rotation and translation
-0.89202044 0.17867377 -0.41518095 415.57480664
0.23668091 0.96719546 -0.09227724 -144.51510345
0.38507361 -0.18057859 -0.90504679 317.47235545
Axis -0.10939237 -0.99139756 0.07186231
Axis point 182.93569343 0.00000000 199.07523474
Rotation angle (degrees) 156.19662314
Shift along axis 120.62550380
> select subtract #10
Nothing selected
> fitmap #7 inMap #10
Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
J276_003_volume_map_sharp.mrc (#10) using 41723 atoms
average map value = 0.03999, steps = 92
shifted from previous position = 2.94
rotated from previous position = 3.89 degrees
atoms outside contour = 34568, contour level = 0.11631
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
J276_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99939912 -0.03433994 -0.00470912 14.18609868
-0.03465788 -0.98811995 -0.14972575 409.89756479
0.00048839 0.14979899 -0.98871635 348.63431455
Axis 0.99984892 -0.01734993 -0.00106133
Axis point 0.00000000 191.94050757 189.76759693
Rotation angle (degrees) 171.38553254
Shift along axis 6.70224576
> select add #10
2 models selected
> view matrix models
> #10,-0.96568,0.16527,-0.20039,392.73,0.18193,0.98098,-0.067662,-24.382,0.1854,-0.1018,-0.97738,358.48
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.96568,0.16527,-0.20039,389.82,0.18193,0.98098,-0.067662,-22.699,0.1854,-0.1018,-0.97738,359.38
> select subtract #10
Nothing selected
> fitmap #7 inMap #10
Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
J276_003_volume_map_sharp.mrc (#10) using 41723 atoms
average map value = 0.1675, steps = 388
shifted from previous position = 5.7
rotated from previous position = 10.9 degrees
atoms outside contour = 26445, contour level = 0.11631
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
J276_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.98574956 0.16765026 0.01382779 -27.67300286
0.16781986 -0.98574247 -0.01217687 343.80660039
0.01158918 0.01432392 -0.99983025 368.53685588
Axis 0.99643086 0.08417165 0.00637725
Axis point 0.00000000 171.84256163 185.50305705
Rotation angle (degrees) 179.23806648
Shift along axis 3.71478754
> save /Users/wujingyi/Downloads/rfxATPase_withoutADP_F1.mrc models #10
> color #10 #b2b2ff53 models
> color #10 #b2b2ff54 models
> select add #7
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 41723 atom styles
> ui mousemode right select
> select clear
Drag select of 18 atoms, 10 residues, 18 bonds, 10
J276_003_volume_map_sharp.mrc
> volume #10 color #b2b2ff
> select clear
> close #10
> close #9
> close #8
> close #1
> hide #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo-1.pdb"
Chain information for RfxATP_state_1_Fo-1.pdb #1
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1-6 atoms
> show #!1-6 cartoons
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> hide target m
> select subtract #3
16 models selected
> select add #1
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> show #!1 models
> show sel surfaces
> hide sel surfaces
> select subtract #1.2
10597 atoms, 10807 bonds, 2 pseudobonds, 1405 residues, 18 models selected
> select subtract #1.3
10074 atoms, 10276 bonds, 2 pseudobonds, 1332 residues, 17 models selected
> select subtract #1.4
9532 atoms, 9726 bonds, 2 pseudobonds, 1257 residues, 16 models selected
> select subtract #1.5
8990 atoms, 9176 bonds, 2 pseudobonds, 1182 residues, 15 models selected
> select subtract #1.6
8440 atoms, 8618 bonds, 2 pseudobonds, 1106 residues, 14 models selected
> select subtract #1.7
7898 atoms, 8068 bonds, 2 pseudobonds, 1031 residues, 13 models selected
> select subtract #1.8
7356 atoms, 7518 bonds, 2 pseudobonds, 956 residues, 12 models selected
> select subtract #1.9
6806 atoms, 6960 bonds, 2 pseudobonds, 880 residues, 11 models selected
> select add #1
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 10 models selected
> select subtract #1.1
11147 atoms, 11365 bonds, 1481 residues, 17 models selected
> select subtract #1.12
8915 atoms, 9078 bonds, 1190 residues, 17 models selected
> select subtract #1.13
8592 atoms, 8748 bonds, 1152 residues, 16 models selected
> select subtract #1.14
8286 atoms, 8435 bonds, 1116 residues, 15 models selected
> select subtract #1.15
7963 atoms, 8105 bonds, 1078 residues, 14 models selected
> select subtract #1.16
7657 atoms, 7792 bonds, 1042 residues, 13 models selected
> select subtract #1.17
5425 atoms, 5505 bonds, 751 residues, 12 models selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> close #3
> ui tool show "Show Sequence Viewer"
> close #7
> ui tool show "Show Sequence Viewer"
Cell requested for row 0 is out of bounds for table with 22 rows! Resizing
table model.
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H #1/L #1/O #1/P
Alignment identifier is 1
> sequence chain #1/I
Alignment identifier is 1/I
> sequence chain #1/J #1/K #1/M #1/N
Alignment identifier is 2
> sequence chain #1/Q
Alignment identifier is 1/Q
> select #1/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #1/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #1/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> color (#!1 & sel) byhetero
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> color (#!1 & sel) byhetero
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> show #!4 models
> show #!5 models
> show #!6 models
> show #!2 models
> select add #4
6397 atoms, 5064 bonds, 6389 residues, 3 models selected
> select add #2
13627 atoms, 10537 bonds, 13619 residues, 8 models selected
> select add #5
20718 atoms, 15835 bonds, 20710 residues, 13 models selected
> select add #6
26408 atoms, 20451 bonds, 26400 residues, 18 models selected
> show sel surfaces
> select clear
Drag select of RfxATP_state_1_Fo-1.pdb_Q SES surface, 934 of 83818 triangles,
9 atoms, 8 bonds
> hide sel surfaces
> close #1
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo-2.pdb"
Chain information for RfxATP_state_1_Fo-2.pdb #1
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide atoms
> show cartoons
> select add #1
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #1.1
11147 atoms, 11365 bonds, 1481 residues, 17 models selected
> select subtract #1.17
8915 atoms, 9078 bonds, 1190 residues, 17 models selected
> select subtract #1.16
8609 atoms, 8765 bonds, 1154 residues, 16 models selected
> select subtract #1.15
8286 atoms, 8435 bonds, 1116 residues, 15 models selected
> select subtract #1.14
7980 atoms, 8122 bonds, 1080 residues, 14 models selected
> select subtract #1.13
7657 atoms, 7792 bonds, 1042 residues, 13 models selected
> hide sel cartoons
> select subtract #1.12
5425 atoms, 5505 bonds, 751 residues, 12 models selected
> hide sel cartoons
> select add #1.12
7657 atoms, 5505 bonds, 1042 residues, 11 models selected
> select subtract #1.12
5425 atoms, 5505 bonds, 751 residues, 12 models selected
> select add #1
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected
> select subtract #1
16 models selected
> select add #1.12
2232 atoms, 291 residues, 1 model selected
> select add #1.17
4464 atoms, 582 residues, 2 models selected
> show sel cartoons
> select subtract #1.12
2232 atoms, 291 residues, 3 models selected
> select subtract #1.17
1 model selected
> select add #1.16
306 atoms, 36 residues, 1 model selected
> select add #1.15
629 atoms, 74 residues, 2 models selected
> select add #1.13
952 atoms, 112 residues, 3 models selected
> select add #1.14
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> select add #1
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 6 models selected
> select subtract #1
16 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H #1/L #1/O #1/P
Alignment identifier is 1
> sequence chain #1/I
Alignment identifier is 1/I
> sequence chain #1/J #1/K #1/M #1/N
Alignment identifier is 2
> sequence chain #1/Q
Alignment identifier is 1/Q
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 9 atom styles
> color (#!1 & sel) byelement
> select #1/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> color (#!1 & sel) byhetero
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color (#!1 & sel) byhetero
> select #1/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> color (#!1 & sel) byhetero
> show sel atoms
> style sel stick
Changed 36 atom styles
> select clear
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RFXATPase_state1_2.98A-1.pdb"
Chain information for RFXATPase_state1_2.98A-1.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
R | No description available
S | No description available
T Z | No description available
U X | No description available
V | No description available
W | No description available
Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide atoms
> show cartoons
> hide #!3 models
> select add #1.2
550 atoms, 76 residues, 1 model selected
> select add #1.3
1073 atoms, 149 residues, 2 models selected
> select add #1.4
1615 atoms, 224 residues, 3 models selected
> select add #1.5
2157 atoms, 299 residues, 4 models selected
> select add #1.6
2707 atoms, 375 residues, 5 models selected
> select add #1.7
3249 atoms, 450 residues, 6 models selected
> select add #1.8
3791 atoms, 525 residues, 7 models selected
> select add #1.9
4341 atoms, 601 residues, 8 models selected
> select add #1.10
4891 atoms, 677 residues, 9 models selected
> select add #1.11
5425 atoms, 751 residues, 10 models selected
> hide sel cartoons
> select #1/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel atoms
> select clear
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo-3.pdb"
Chain information for RfxATP_state_1_Fo-3.pdb #7
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1-2,4-7 atoms
> show #!1-2,4-7 cartoons
> show #!1-2,4-7 surfaces
> hide #!1-2,4-7 surfaces
> select add #7.2
550 atoms, 76 residues, 1 model selected
> select add #7.3
1073 atoms, 149 residues, 2 models selected
> select add #7.4
1615 atoms, 224 residues, 3 models selected
> select add #7.5
2157 atoms, 299 residues, 4 models selected
> select add #7.6
2707 atoms, 375 residues, 5 models selected
> select add #7.7
3249 atoms, 450 residues, 6 models selected
> select add #7.8
3791 atoms, 525 residues, 7 models selected
> select add #7.9
4341 atoms, 601 residues, 8 models selected
> select add #7.10
4891 atoms, 677 residues, 9 models selected
> select add #7.11
5425 atoms, 751 residues, 10 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H #1/L #1/O #1/P #3/H #3/L #3/O #3/P #7/H #7/L #7/O #7/P
Alignment identifier is 3
> sequence chain #1/I #3/I #7/I
Alignment identifier is 4
> sequence chain #1/J #1/K #1/M #1/N #3/J #3/K #3/M #3/N #7/J #7/K #7/M #7/N
Alignment identifier is 5
> sequence chain #1/Q #3/Q #7/Q
Alignment identifier is 6
> select #1/Q:59 #3/Q:59 #7/Q:59
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1/Q:59 #3/Q:59 #7/Q:59
27 atoms, 24 bonds, 3 residues, 3 models selected
6 [ID: 6] region 3 chains [58] RMSD: 0.294
> show sel & #!7 atoms
> style sel & #!7 stick
Changed 9 atom styles
> color (#!7 & sel) byhetero
> select #1/J-K,M-N:59 #3/J-K,M-N:59 #7/J-K,M-N:59
108 atoms, 96 bonds, 12 residues, 3 models selected
> select #1/J-K,M-N:59-60 #3/J-K,M-N:59-60 #7/J-K,M-N:59-60
168 atoms, 156 bonds, 24 residues, 3 models selected
5 [ID: 5] region 12 chains [58-59] RMSD: 0.425
> select #1/J-K,M-N:59 #3/J-K,M-N:59 #7/J-K,M-N:59
108 atoms, 96 bonds, 12 residues, 3 models selected
> select #1/J-K,M-N:59 #3/J-K,M-N:59 #7/J-K,M-N:59
108 atoms, 96 bonds, 12 residues, 3 models selected
5 [ID: 5] region 12 chains [58] RMSD: 0.411
> color (#!7 & sel) byelement
> color (#!7 & sel) byhetero
> show sel & #!7 atoms
> style sel & #!7 stick
Changed 36 atom styles
> select #1/I:59 #3/I:59 #7/I:59
27 atoms, 24 bonds, 3 residues, 3 models selected
> color (#!7 & sel) byhetero
> select #1/H,L,O-P:59 #3/H,L,O-P:59 #7/H,L,O-P:59
108 atoms, 96 bonds, 12 residues, 3 models selected
> select #1/H,L,O-P:59 #3/H,L,O-P:59 #7/H,L,O-P:59
108 atoms, 96 bonds, 12 residues, 3 models selected
3 [ID: 3] region 12 chains [58] RMSD: 0.353
> color (#!7 & sel) byhetero
> show sel & #!7 atoms
> style sel & #!7 stick
Changed 36 atom styles
> select clear
> select #1/I:59 #3/I:59 #7/I:59
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1/I:59 #3/I:59 #7/I:59
27 atoms, 24 bonds, 3 residues, 3 models selected
4 [ID: 4] region 3 chains [58] RMSD: 0.292
> show sel & #!7 atoms
> style sel & #!7 stick
Changed 9 atom styles
> color (#!7 & sel) byhetero
> select clear
> select add #7.12
2232 atoms, 291 residues, 1 model selected
> select add #7.17
4464 atoms, 582 residues, 2 models selected
> color (#!7 & sel) forest green
> select add #7
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 4 models selected
> select subtract #7.13
10824 atoms, 11035 bonds, 2 pseudobonds, 1443 residues, 18 models selected
> select subtract #7.15
10501 atoms, 10705 bonds, 2 pseudobonds, 1405 residues, 17 models selected
> select subtract #7.14
10195 atoms, 10392 bonds, 2 pseudobonds, 1369 residues, 16 models selected
> select subtract #7.16
9889 atoms, 10079 bonds, 2 pseudobonds, 1333 residues, 15 models selected
> select subtract #7.17
7657 atoms, 7792 bonds, 1 pseudobond, 1042 residues, 14 models selected
> select subtract #7.12
5425 atoms, 5505 bonds, 751 residues, 12 models selected
> color (#!7 & sel) #f5ccdcff
> color (#!7 & sel) byhetero
> select clear
> hide #7.15 models
> hide #7.12 models
> select add #7.15
323 atoms, 38 residues, 1 model selected
> select add #7.13
646 atoms, 76 residues, 2 models selected
> hide sel cartoons
> select add #7.16
952 atoms, 112 residues, 3 models selected
> select add #7.14
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> select clear
> volume flip #10
> view
> cartoon style #2,4-6#7.1-11,13-14,16-17#!7 modeHelix tube sides 20
> view
> show #!1 models
> hide #!1 models
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> select add #4
13618 atoms, 10529 bonds, 13618 residues, 6 models selected
> select add #5
20709 atoms, 15827 bonds, 20709 residues, 11 models selected
> select add #6
26399 atoms, 20443 bonds, 26399 residues, 16 models selected
> show sel surfaces
> select subtract #6
20709 atoms, 15827 bonds, 20709 residues, 18 models selected
> select subtract #4
14321 atoms, 10771 bonds, 14321 residues, 14 models selected
> color (#!2,5 & sel) #f2d6d7ff
> color (#!2,5 & sel) #f2d2d3ff
> color (#!2,5 & sel) #f2cbcdff
> color (#!2,5 & sel) #f2c3c8ff
> color (#!2,5 & sel) #f2b8c5ff
> color (#!2,5 & sel) #f2b2c6ff
> color (#!2,5 & sel) #f2aec7ff
> color (#!2,5 & sel) #f2a9c7ff
> color (#!2,5 & sel) #f2a5c7ff
> color (#!2,5 & sel) #f2a2c9ff
> color (#!2,5 & sel) #f2a0caff
> color (#!2,5 & sel) #f29fc9ff
> color (#!2,5 & sel) #f2a0caff
> color (#!2,5 & sel) #f2a0cbff
> color (#!2,5 & sel) #f2a0ccff
> color (#!2,5 & sel) #f2a1ccff
> color (#!2,5 & sel) #f2a2cdff
> color (#!2,5 & sel) #f2a5d2ff
> color (#!2,5 & sel) #f2a6d5ff
> color (#!2,5 & sel) #f2a9d9ff
> color (#!2,5 & sel) #f2abddff
> color (#!2,5 & sel) #f2aee3ff
> color (#!2,5 & sel) #f2b2edff
> color (#!2,5 & sel) #efb4f2ff
> color (#!2,5 & sel) #e5b3f2ff
> color (#!2,5 & sel) #dcb1f2ff
> color (#!2,5 & sel) #d6aff2ff
> color (#!2,5 & sel) #d4aff2ff
> color (#!2,5 & sel) #d5aff2ff
> color (#!2,5 & sel) #dea2f2ff
> color (#!2,5 & sel) #e29cf2ff
> color (#!2,5 & sel) #e29bf2ff
> color (#!2,5 & sel) #e39bf2ff
> color (#!2,5 & sel) #e49bf2ff
> color (#!2,5 & sel) #e59bf2ff
> color (#!2,5 & sel) #e89bf2ff
> color (#!2,5 & sel) #ea9cf2ff
> color (#!2,5 & sel) #ed9cf2ff
> color (#!2,5 & sel) #f09cf2ff
> color (#!2,5 & sel) #f29cf2ff
> color (#!2,5 & sel) #f29cf0ff
> color (#!2,5 & sel) #f29cefff
[Repeated 1 time(s)]
> color (#!2,5 & sel) #f29ceeff
> color (#!2,5 & sel) #f29cebff
> color (#!2,5 & sel) #f29ce5ff
> color (#!2,5 & sel) #f299dbff
> color (#!2,5 & sel) #f295d2ff
> color (#!2,5 & sel) #f290caff
> color (#!2,5 & sel) #f286bcff
> color (#!2,5 & sel) #f284b8ff
> color (#!2,5 & sel) #f284b7ff
> color (#!2,5 & sel) #f283b7ff
> color (#!2,5 & sel) #f27fb0ff
> color (#!2,5 & sel) #f27eadff
[Repeated 1 time(s)]
> color (#!2,5 & sel) #f27ca9ff
> color (#!2,5 & sel) #f2779dff
> color (#!2,5 & sel) #f27498ff
[Repeated 1 time(s)]
> color (#!2,5 & sel) #f26e91ff
> color (#!2,5 & sel) #f26a8eff
> color (#!2,5 & sel) #f2678bff
> color (#!2,5 & sel) #f26489ff
> color (#!2,5 & sel) #f26388ff
> color (#!2,5 & sel) #f26287ff
> color (#!2,5 & sel) #f26388ff
> color (#!2,5 & sel) #f26589ff
> color (#!2,5 & sel) #f2708bff
> color (#!2,5 & sel) #f27a8eff
> color (#!2,5 & sel) #f28091ff
> color (#!2,5 & sel) #f28494ff
> color (#!2,5 & sel) #f28796ff
> color (#!2,5 & sel) #f28795ff
> color (#!2,5 & sel) #f28796ff
> color (#!2,5 & sel) #f28596ff
> color (#!2,5 & sel) #f28497ff
> color (#!2,5 & sel) #f2819bff
> color (#!2,5 & sel) #f27c9fff
> color (#!2,5 & sel) #f27ba1ff
> color (#!2,5 & sel) #f27ca2ff
> color (#!2,5 & sel) #f27da3ff
> color (#!2,5 & sel) #f27ca3ff
> color (#!2,5 & sel) #f27da4ff
> color (#!2,5 & sel) #f27ea5ff
> color (#!2,5 & sel) #f27da5ff
> select clear
> select add #1
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> select subtract #1
16 models selected
> select add #6
5690 atoms, 4616 bonds, 5690 residues, 1 model selected
> select add #4
12078 atoms, 9672 bonds, 12078 residues, 5 models selected
> color (#!4,6 & sel) cornflower blue
> select subtract #6
6388 atoms, 5056 bonds, 6388 residues, 8 models selected
> select subtract #4
4 models selected
> select add #5
7091 atoms, 5298 bonds, 7091 residues, 1 model selected
> select add #2
14321 atoms, 10771 bonds, 14321 residues, 6 models selected
> select subtract #5
7230 atoms, 5473 bonds, 7230 residues, 9 models selected
> select subtract #2
4 models selected
> color #2 #f27da581
> color #2 #f27da580
> color #5 #f27da580
> color #6 #6495ed80
> color #4 #6495ed7b
> color #4 #6495ed7d
> color #4 #6495ed80
> lighting simple
> lighting soft
> lighting full
> lighting flat
> view
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting flat
> ui tool show "Show Sequence Viewer"
> sequence chain #1/T #1/Z #3/T #3/Z #7/T #7/Z
Alignment identifier is 1
> select #1/T,Z:259 #3/T,Z:259 #7/T,Z:259
66 atoms, 60 bonds, 6 residues, 3 models selected
> select #1/T,Z:259 #3/T,Z:259 #7/T,Z:259
66 atoms, 60 bonds, 6 residues, 3 models selected
1 [ID: 1] region 6 chains [235] RMSD: 0.547
> show sel & #!7 atoms
> style sel & #!7 stick
Changed 22 atom styles
> color (#!7 & sel) byhetero
> select clear
> save /Users/wujingyi/1.cxs
> view
[Repeated 1 time(s)]
> save
> /Users/wujingyi/Desktop/RfxATPase_figure/figure_4/Rfxatp_state1_hollow.cxs
——— End of log from Mon Aug 12 10:58:14 2024 ———
opened ChimeraX session
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RfxATP_state_1_Fo-4-coot-0.pdb"
Chain information for RfxATP_state_1_Fo-4-coot-0.pdb #8
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!2,4-8 atoms
> show #!2,4-8 cartoons
> show #!2,4-8 surfaces
> hide #!2,4-8 surfaces
> hide #!7 models
> select add #8.2
550 atoms, 76 residues, 1 model selected
> select add #8
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 3 models selected
> select subtract #8.17
8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected
> select subtract #8.12
6683 atoms, 6791 bonds, 899 residues, 16 models selected
> select subtract #8.13
6360 atoms, 6461 bonds, 861 residues, 15 models selected
> select subtract #8.14
6054 atoms, 6148 bonds, 825 residues, 14 models selected
> select subtract #8.15
5731 atoms, 5818 bonds, 787 residues, 13 models selected
> select subtract #8.16
5425 atoms, 5505 bonds, 751 residues, 12 models selected
> color (#!8 & sel) #f5ccdcff
> lighting soft
> select add #8
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected
> select subtract #8
16 models selected
> select add #8.12
2232 atoms, 291 residues, 1 model selected
> select add #8.17
4464 atoms, 582 residues, 2 models selected
> color (#!8 & sel) forest green
> select subtract #8.17
2232 atoms, 291 residues, 3 models selected
> select subtract #8.12
1 model selected
> select add #8.14
306 atoms, 36 residues, 1 model selected
> select add #8.16
612 atoms, 72 residues, 2 models selected
> color (#!8 & sel) #9e7bbaff
> select subtract #8.14
306 atoms, 36 residues, 3 models selected
> select subtract #8.16
1 model selected
> select add #8.15
323 atoms, 38 residues, 1 model selected
> select add #8.13
646 atoms, 76 residues, 2 models selected
> color (#!8 & sel) #c5c5ecff
> select subtract #8.13
323 atoms, 38 residues, 3 models selected
> select subtract #8.15
1 model selected
> select add #8.16
306 atoms, 36 residues, 1 model selected
> select add #8.15
629 atoms, 74 residues, 2 models selected
> select add #8.14
935 atoms, 110 residues, 3 models selected
> select add #8.13
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> select subtract #8.13
935 atoms, 110 residues, 5 models selected
> select subtract #8.14
629 atoms, 74 residues, 4 models selected
> select subtract #8.15
306 atoms, 36 residues, 3 models selected
> select subtract #8.16
1 model selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> select add #4
13618 atoms, 10529 bonds, 13618 residues, 6 models selected
> select add #5
20709 atoms, 15827 bonds, 20709 residues, 11 models selected
> select add #6
26399 atoms, 20443 bonds, 26399 residues, 16 models selected
> show sel surfaces
> select subtract #4
20011 atoms, 15387 bonds, 20011 residues, 18 models selected
> select subtract #5
12920 atoms, 10089 bonds, 12920 residues, 13 models selected
> select subtract #6
7230 atoms, 5473 bonds, 7230 residues, 8 models selected
> select subtract #2
4 models selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> select add #5
14321 atoms, 10771 bonds, 14321 residues, 6 models selected
> color (#!2,5 & sel) #f2b8aeff
[Repeated 1 time(s)]
> color (#!2,5 & sel) #f2b8aeca
> color (#!2,5 & sel) #f2b8aec5
> color (#!2,5 & sel) #f2b8aea2
> color (#!2,5 & sel) #f2b8ae92
> color (#!2,5 & sel) #f2b8ae8f
> color (#!2,5 & sel) #f2b8ae83
> color (#!2,5 & sel) #f2b8ae80
> color (#!2,5 & sel) #f2b8ae77
> color (#!2,5 & sel) #f2b8ae75
> color (#!2,5 & sel) #f2b8ae76
> color (#!2,5 & sel) #f2b8ae7a
> color (#!2,5 & sel) #f2b8ae7b
> select subtract #5
7230 atoms, 5473 bonds, 7230 residues, 9 models selected
> select subtract #2
4 models selected
> select add #6
5690 atoms, 4616 bonds, 5690 residues, 1 model selected
> select add #4
12078 atoms, 9672 bonds, 12078 residues, 5 models selected
> color (#!4,6 & sel) #c2e5cf7b
> select subtract #6
6388 atoms, 5056 bonds, 6388 residues, 8 models selected
> select subtract #4
4 models selected
> select add #5
7091 atoms, 5298 bonds, 7091 residues, 1 model selected
> select add #2
14321 atoms, 10771 bonds, 14321 residues, 6 models selected
> color (#!2,5 & sel) #efd6d17b
[Repeated 1 time(s)]
> color (#!2,5 & sel) #efd6d17c
> color (#!2,5 & sel) #efd6d17f
> select add #4
20709 atoms, 15827 bonds, 20709 residues, 11 models selected
> select subtract #2
13479 atoms, 10354 bonds, 13479 residues, 14 models selected
> select subtract #4
7091 atoms, 5298 bonds, 7091 residues, 9 models selected
> select subtract #5
4 models selected
> select add #6
5690 atoms, 4616 bonds, 5690 residues, 1 model selected
> select add #4
12078 atoms, 9672 bonds, 12078 residues, 5 models selected
> color (#!4,6 & sel) #bcc6dd7f
> select subtract #6
6388 atoms, 5056 bonds, 6388 residues, 8 models selected
> select subtract #4
4 models selected
> undo
> select subtract #6
6388 atoms, 5056 bonds, 6388 residues, 8 models selected
> select subtract #4
4 models selected
> select add #6
5690 atoms, 4616 bonds, 5690 residues, 1 model selected
> select add #4
12078 atoms, 9672 bonds, 12078 residues, 5 models selected
> color (#!4,6 & sel) #d5ebf07f
> select subtract #6
6388 atoms, 5056 bonds, 6388 residues, 8 models selected
> select subtract #4
4 models selected
> select add #8.2
550 atoms, 76 residues, 1 model selected
> select add #8.3
1073 atoms, 149 residues, 2 models selected
> select add #8.4
1615 atoms, 224 residues, 3 models selected
> select add #8.5
2157 atoms, 299 residues, 4 models selected
> select add #8.6
2707 atoms, 375 residues, 5 models selected
> select add #8.7
3249 atoms, 450 residues, 6 models selected
> select add #8.8
3791 atoms, 525 residues, 7 models selected
> select add #8.9
4341 atoms, 601 residues, 8 models selected
> select add #8.10
4891 atoms, 677 residues, 9 models selected
> select add #8.11
5425 atoms, 751 residues, 10 models selected
Alignment identifier is 1
Alignment identifier is 8/I
Alignment identifier is 2
Alignment identifier is 8/Q
> select #8/Q:2
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/Q
534 atoms, 542 bonds, 74 residues, 1 model selected
> hide sel cartoons
> select #8/Q:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/Q:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #8/J-K,M-N:2-3
60 atoms, 56 bonds, 8 residues, 1 model selected
> select #8/J-K,M-N:2-3
60 atoms, 56 bonds, 8 residues, 1 model selected
> select #8/J-K,M-N:2-3
60 atoms, 56 bonds, 8 residues, 1 model selected
> select #8/J-K,M-N
2168 atoms, 2200 bonds, 300 residues, 1 model selected
> hide sel cartoons
> select #8/J-K,M-N:58
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #8/J-K,M-N:58-61
116 atoms, 112 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #8/I:2
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/I
523 atoms, 531 bonds, 73 residues, 1 model selected
> hide sel cartoons
> select #8/I:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/I:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #8/I:2
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/I
523 atoms, 531 bonds, 73 residues, 1 model selected
> select #8/H,L,O-P:2
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #8/H,L,O-P
2200 atoms, 2232 bonds, 304 residues, 1 model selected
> hide sel cartoons
> select #8/H,L,O-P:58
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #8/H,L,O-P:58-61
116 atoms, 112 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #8/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #8/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select #8/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #8/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select #8/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> view matrix models #8,1,0,0,0.032442,0,1,0,0.0059412,0,0,1,-0.0014518
> select #8/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models #8,1,0,0,0.097325,0,1,0,0.017824,0,0,1,-0.0043555
> ui mousemode right select
> select clear
> style #2,4-6,8 ball
Changed 37546 atom styles
> select clear
> select #8/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #4/F:4727@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #4/F:4243@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #4/F:6033@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #4/F:5181@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #4/F:4730@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #4/F:6455@O
1 atom, 1 residue, 1 model selected
> select #4/F:6009@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #4/F:5165@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #4/F:4724@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
Drag select of rfxa1_outlet_hollow2.pdb_F SES surface, 630 of 3926 triangles,
5 atoms, 4 residues, 5 bonds
Drag select of rfxa1_outlet_hollow2.pdb_F SES surface, 139 of 3926 triangles,
rfxa1_outlet_hollow2.pdb_G SES surface, 258 of 7744 triangles,
rfxa1_outlet_hollow2.pdb_H SES surface, 293 of 35632 triangles, 3 residues
> select #4/F:5592@O
1 atom, 1 residue, 1 model selected
> select #4/G:548@O
1 atom, 1 residue, 1 model selected
> select #4/F:4717@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
Drag select of rfxa1_outlet_hollow2.pdb_F SES surface, 74 of 3926 triangles
Drag select of rfxa1_outlet_hollow2.pdb_F SES surface, 27 of 3926 triangles
> hide #!2,4-6,8 surfaces
> show #!2,4-6,8 surfaces
> hide #!2,4-6,8 surfaces
> select add #6
5690 atoms, 4616 bonds, 5690 residues, 2 models selected
> show sel surfaces
> select add #4
12078 atoms, 9672 bonds, 12078 residues, 6 models selected
> select add #5
19169 atoms, 14970 bonds, 19169 residues, 10 models selected
> select add #2
26399 atoms, 20443 bonds, 26399 residues, 15 models selected
> show sel surfaces
> select clear
> select add #8.17
2232 atoms, 291 residues, 1 model selected
> select add #8.12
4464 atoms, 582 residues, 2 models selected
Alignment identifier is 3
> select #8/T,Z:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/T,Z:1-108
1608 atoms, 1628 bonds, 216 residues, 1 model selected
> hide sel cartoons
> select #8/T,Z:109
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #8/T,Z:109-198
994 atoms, 1026 bonds, 2 pseudobonds, 132 residues, 2 models selected
> hide sel cartoons
> select #5/F:8194@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 603 of 31532 triangles,
2 residues
> select clear
> select #8/T:202
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/T,Z:199
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/T,Z:199-216
286 atoms, 292 bonds, 36 residues, 1 model selected
> hide sel cartoons
> select #8/T,Z:217
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #8/T,Z:217-223
98 atoms, 98 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select #8/T,Z:224-225
32 atoms, 32 bonds, 4 residues, 1 model selected
> select #8/T,Z:224-235
210 atoms, 216 bonds, 24 residues, 1 model selected
> hide sel cartoons
> select #4/I:3079@O
1 atom, 1 residue, 1 model selected
> select #4/I:3089@O
1 atom, 1 residue, 1 model selected
> select add #4
6388 atoms, 5056 bonds, 6388 residues, 2 models selected
> select subtract #4
4 models selected
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!2 models
Cell requested for row 0 is out of bounds for table with 28 rows! Resizing
table model.
> close #1
> close #3
> open
> /Users/wujingyi/Desktop/RfxATPasePDB+map_new/RfxATPase_PDB/J436_state1_synthasis_2.82A_14.82w-coot-3.pdb
Summary of feedback from opening
/Users/wujingyi/Desktop/RfxATPasePDB+map_new/RfxATPase_PDB/J436_state1_synthasis_2.82A_14.82w-coot-3.pdb
---
warning | Cannot find LINK/SSBOND residue CYS (40 )
Chain information for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
R | No description available
S W | No description available
T | No description available
U | No description available
V | No description available
X | No description available
Y | No description available
Z | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1,8 atoms
> show #!1,8 cartoons
> select add #8
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #8
16 models selected
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #1.27
36450 atoms, 36947 bonds, 2 pseudobonds, 5094 residues, 28 models selected
> select subtract #1.25
35708 atoms, 36206 bonds, 2 pseudobonds, 4945 residues, 27 models selected
> select subtract #1.24
35343 atoms, 35842 bonds, 2 pseudobonds, 4871 residues, 26 models selected
> select subtract #1.23
34585 atoms, 35085 bonds, 2 pseudobonds, 4720 residues, 25 models selected
> select subtract #1.22
33838 atoms, 34339 bonds, 2 pseudobonds, 4570 residues, 24 models selected
> select subtract #1.21
32250 atoms, 32736 bonds, 4305 residues, 22 models selected
> select subtract #1.19
31170 atoms, 31646 bonds, 4167 residues, 21 models selected
> select subtract #1.18
30643 atoms, 31111 bonds, 4094 residues, 20 models selected
> select subtract #1.17
30100 atoms, 30560 bonds, 4019 residues, 19 models selected
> select subtract #1.16
29557 atoms, 30009 bonds, 3944 residues, 18 models selected
> select subtract #1.15
29022 atoms, 29466 bonds, 3870 residues, 17 models selected
> select subtract #1.14
28487 atoms, 28923 bonds, 3796 residues, 16 models selected
> select subtract #1.13
27944 atoms, 28372 bonds, 3721 residues, 15 models selected
> select subtract #1.12
27409 atoms, 27829 bonds, 3647 residues, 14 models selected
> select subtract #1.11
26874 atoms, 27286 bonds, 3573 residues, 13 models selected
> select subtract #1.10
26358 atoms, 26762 bonds, 3501 residues, 12 models selected
> hide sel cartoons
> select subtract #1.26
25606 atoms, 26011 bonds, 3350 residues, 11 models selected
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 11 models selected
> select subtract #1
26 models selected
> select add #1.19
1080 atoms, 138 residues, 1 model selected
> hide sel cartoons
> select add #1.22
1827 atoms, 288 residues, 2 models selected
> select add #1.23
2585 atoms, 439 residues, 3 models selected
> select add #1.25
3327 atoms, 588 residues, 4 models selected
> select add #1.26
4079 atoms, 739 residues, 5 models selected
> select add #1.24
4444 atoms, 813 residues, 6 models selected
> hide sel cartoons
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 8 models selected
> select subtract #1
26 models selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> select add #1.27
3130 atoms, 543 residues, 2 models selected
> color (#!1 & sel) forest green
> select subtract #1.21
1542 atoms, 278 residues, 3 models selected
> select subtract #1.27
1 model selected
> select add #1.9
543 atoms, 75 residues, 1 model selected
> select add #1.10
1059 atoms, 147 residues, 2 models selected
> select add #1.11
1594 atoms, 221 residues, 3 models selected
> select add #1.12
2129 atoms, 295 residues, 4 models selected
> select add #1.13
2672 atoms, 370 residues, 5 models selected
> select add #1.14
3207 atoms, 444 residues, 6 models selected
> select add #1.15
3742 atoms, 518 residues, 7 models selected
> select add #1.16
4285 atoms, 593 residues, 8 models selected
> select add #1.17
4828 atoms, 668 residues, 9 models selected
> select add #1.18
5355 atoms, 741 residues, 10 models selected
> color (#!1 & sel) #f5ccdc7f
> color (#!1 & sel) #f5ccdc73
> color (#!1 & sel) #f5ccdc76
> color (#!1 & sel) #f5ccdc81
> color (#!1 & sel) #f5ccdca6
> color (#!1 & sel) #f5ccdcbb
> color (#!1 & sel) #f5ccdcff
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 12 models selected
> select subtract #1
26 models selected
Cell requested for row 0 is out of bounds for table with 34 rows! Resizing
table model.
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!8 models
> show #!1 models
> select clear
> select add #1.9
543 atoms, 75 residues, 1 model selected
> select subtract #1.9
1 model selected
> select add #1.9
543 atoms, 75 residues, 1 model selected
> show sel cartoons
> select subtract #1.9
1 model selected
> select #1/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style (#!1 & sel) stick
Changed 11 atom styles
> select clear
> hide #!1 models
> show #!8 models
> select #8/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #8
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 3 models selected
> show #!1 models
> select subtract #8
16 models selected
> hide #!8 models
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style (#!1 & sel) stick
Changed 11 atom styles
> select clear
> open "/Users/wujingyi/Desktop/RfxATPasePDB+map_new/local
> map/Fo/J546_state1_synthasis_Fo_3.52A_14.82w.mrc"
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400,
pixel 0.93, shown at level 0.041, step 2, values float32
> volume #3 step 1
> volume #3 level 0.1262
> volume #3 level 0.1343
> color zone #3 near #1 distance 5.58
> surface dust #3 size 9.3
> volume #3 level 0.1059
> ui tool show "Color Zone"
> color zone #3 near #1 distance 5.58
> volume splitbyzone #3
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
> surface dust #9.3 size 9.3
> surface dust #9.4 size 9.3
> surface dust #9.12 size 9.3
> surface dust #9.17 size 9.3
> surface dust #9.18 size 9.3
> surface dust #9.19 size 9.3
> surface dust #9.20 size 9.3
> surface dust #9.21 size 9.3
> surface dust #9.22 size 9.3
> volume #9.17 level 0.08025
> volume #9.12 color #f5ccdc80
> volume #9.17 color #228b2275
> select #8/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #8/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show #!1 atoms
> hide #!1 atoms
Drag select of 9.12 J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 , 1283
residues, 3 pseudobonds
Alignment identifier is 1/I
Alignment identifier is 1/Q
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 1/T
Alignment identifier is 1/Z
> select #1/N,M,K,J:3
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1/N,M,K,J
2140 atoms, 2172 bonds, 296 residues, 1 model selected
> hide sel cartoons
> select #1/P,O,L,H:3
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1/P,O,L,H
2172 atoms, 2204 bonds, 300 residues, 1 model selected
> hide sel cartoons
> select #1/Q:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Q
527 atoms, 535 bonds, 73 residues, 1 model selected
> hide sel cartoons
> select #1/I:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/I
516 atoms, 524 bonds, 72 residues, 1 model selected
> hide sel cartoons
> select #1/I:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/I:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
> show sel atoms
> style (#!1 & sel) stick
Changed 29 atom styles
> hide sel atoms
> select #1/Q:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/Q:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #1/P,O,L,H:57
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1/P,O,L,H:57-60
116 atoms, 112 bonds, 16 residues, 1 model selected
> select #1/P,O,L,H:58
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #1/P,O,L,H:58-61
116 atoms, 112 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #1/N,M,K,J:58
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #1/N,M,K,J:58-60
84 atoms, 80 bonds, 12 residues, 1 model selected
> select #1/N,M,K,J:58
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #1/N,M,K,J:58-61
116 atoms, 112 bonds, 16 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Q:59-60
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/Q:58-59
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/Q:58-59
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/P,O,L,H:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/P,O,L,H:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1/N,M,K,J:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/N,M,K,J:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> style #1#9.12#!9 stick
Changed 37992 atom styles
> hide #!9.12 models
> show #!9.17 models
> color zone #9.17 near #1 distance 5.58
> volume #9.17 level 0.09308
> volume #9.17 color #228b2233
> select clear
> select #1/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> style #1#!9 ball
Changed 37992 atom styles
> select clear
> select #1/P,O,L,H:3
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1/P,O,L,H
2172 atoms, 2204 bonds, 300 residues, 1 model selected
> select #1/T:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:1-219
940 atoms, 945 bonds, 2 pseudobonds, 169 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-197
787 atoms, 785 bonds, 1 pseudobond, 160 residues, 2 models selected
> hide sel cartoons
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-238
987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected
> hide sel cartoons
> select #1/T:220
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:220-240
108 atoms, 107 bonds, 21 residues, 1 model selected
> hide sel cartoons
> select #1/T:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:1-239
1040 atoms, 1045 bonds, 2 pseudobonds, 189 residues, 2 models selected
> select #1/T:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:1-240
1048 atoms, 1053 bonds, 2 pseudobonds, 190 residues, 2 models selected
> select clear
> select #1/T:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:1-240
1048 atoms, 1053 bonds, 2 pseudobonds, 190 residues, 2 models selected
> color (#!1 & sel) white
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-238
987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected
> color (#!1 & sel) white
> show sel cartoons
> select #1/T:1-2
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/T:1-240
1048 atoms, 1053 bonds, 2 pseudobonds, 190 residues, 2 models selected
> show sel cartoons
> select clear
> color zone #3 near #1 distance 5.58
> volume splitbyzone #3
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #10.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #10.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #10.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #10.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #10.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #10.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #10.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #10.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #10.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #10.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #10.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #10.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #10.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #10.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #10.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #10.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #10.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #10.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #10.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #10.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #10.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #10.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
> surface dust #10.12 size 9.3
> surface dust #10.18 size 9.3
> select #1/T:1-15
74 atoms, 73 bonds, 15 residues, 1 model selected
> select #1/T:1-240
1048 atoms, 1053 bonds, 2 pseudobonds, 190 residues, 2 models selected
> hide sel cartoons
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-238
987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected
> hide sel cartoons
> volume #10.18 color #228b222f
> volume #10.18 color #228b2220
> volume #10.18 level 0.1266
> volume #10.18 level -0.04986
> volume #10.18 level 0.1485
> volume #10.18 level 0.1716
> hide #!9 models
> hide #!10 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!1 models
> cartoon style (#!1 & sel) modeHelix tube sides 20
> show #!10 models
> hide #!10 models
> show #!9 models
> volume #10.18 color forestgreen
> volume #10.18 level 0.04628
> volume #10.18
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> cartoon style (#!1 & sel) xsection oval modeHelix default
> close #10
> close #9
> show #!3 models
> color zone #3 near #1 distance 5.58
> volume splitbyzone #3
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
> hide #!9 models
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 3 models selected
> select clear
> select #1/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/Z:259
22 atoms, 20 bonds, 2 residues, 2 models selected
> color (#!1 & sel) forest green
> select clear
> close #9
> show #!3 models
> color zone #3 near #1 distance 5.58
[Repeated 3 time(s)]
> volume splitbyzone #3
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
> volume #9.18 color #228b2236
> volume #9.12 color #f5ccdc10
> select clear
> surface dust #9.6 size 9.3
> surface dust #9.7 size 9.3
> surface dust #9.8 size 9.3
> surface dust #9.9 size 9.3
> surface dust #9.10 size 9.3
> surface dust #9.11 size 9.3
> surface dust #9.18 size 9.3
> surface dust #9.22 size 9.3
> hide #!9 models
> show #!9 models
> close #9
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> select add #1.21
3130 atoms, 543 residues, 2 models selected
> color (#!1 & sel) forest green
> select subtract #1.27
1588 atoms, 265 residues, 3 models selected
> select subtract #1.21
1 model selected
> select add #1.22
747 atoms, 150 residues, 1 model selected
> select subtract #1.22
1 model selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> select add #1.27
3130 atoms, 543 residues, 2 models selected
> show sel cartoons
> select subtract #1.27
1588 atoms, 265 residues, 3 models selected
> select subtract #1.21
1 model selected
> show #!3 models
> color zone #3 near #1 distance 5.58
> volume splitbyzone #3
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
> volume #9.17 color #228b2226
> ui mousemode right "map eraser"
> color zone #3 near #1 distance 5.46
> color zone #3 near #1 distance 1.16
Can only have one displayed volume when erasing
[Repeated 3 time(s)]
> volume erase #9.17 center 152.43,174.17,258.92 radius 19.158
> volume erase #9.17 center 153.75,161.59,282.41 radius 19.158
> volume erase #9.17 center 173.67,140.98,285.93 radius 19.158
> volume erase #9.17 center 214.92,154.35,251.25 radius 19.158
> volume erase #9.17 center 189.54,139.56,230.38 radius 19.158
> volume erase #9.17 center 161.94,132.72,255.5 radius 19.158
> volume erase #9.17 center 165.94,129.39,251.54 radius 19.158
> volume erase #9.17 center 219.48,213.42,266.64 radius 19.158
> volume erase #9.17 center 222.62,211.3,261.28 radius 19.158
> volume erase #9.17 center 201.59,143.68,253.31 radius 19.158
> volume erase #9.17 center 175.09,146.43,234.13 radius 19.158
> volume erase #9.17 center 146.96,145.6,254.29 radius 19.158
> volume erase #9.17 center 152.14,200.47,260.87 radius 19.158
> volume erase #9.17 center 190.15,234.78,248.78 radius 19.158
> volume erase #9.17 center 208.66,210.82,271.16 radius 19.158
> volume erase #9.17 center 184.43,226.41,289.75 radius 19.158
> volume erase #9.17 center 187.4,240.87,276.81 radius 19.158
> volume erase #9.17 center 151.67,225.5,267.55 radius 19.158
> volume erase #9.17 center 187.86,206.62,234.8 radius 19.158
> volume erase #9.17 center 176.45,240.53,245.58 radius 19.158
> volume erase #9.17 center 164.05,207.38,291.8 radius 19.158
> volume erase #9.17 center 174.07,217.65,283.92 radius 19.158
> volume erase #9.17 center 157.44,141.71,273.58 radius 19.158
> volume erase #9.17 center 205.82,146.87,282.2 radius 19.158
> volume erase #9.17 center 210.51,210.58,302.68 radius 19.158
> volume erase #9.17 center 172.25,216.53,237.66 radius 19.158
> volume erase #9.17 center 169.46,209.2,240.77 radius 19.158
> volume erase #9.17 center 173.94,234.22,258.62 radius 19.158
> volume erase #9.17 center 181.73,229.18,264.5 radius 19.158
> volume erase #9.17 center 169.94,155.29,236.77 radius 19.158
> volume erase #9.17 center 155.37,158.7,264.92 radius 19.158
> volume erase #9.17 center 177.66,127.42,250.24 radius 19.158
> volume erase #9.17 center 158.83,130.61,239.24 radius 19.158
> volume erase #9.17 center 212.13,147.59,256.04 radius 19.158
> volume erase #9.17 center 192.4,127.04,250.84 radius 19.158
> volume erase #9.17 center 190.29,130.33,251.54 radius 19.158
> volume erase #9.17 center 204.59,208.99,283.98 radius 19.158
> volume erase #9.17 center 187.77,212.27,256.33 radius 6.882
> volume erase #9.17 center 193.69,215,255.53 radius 6.882
> volume erase #9.17 center 194.62,211.78,255.47 radius 6.882
> volume erase #9.17 center 180.75,209.09,252.83 radius 6.882
> volume erase #9.17 center 170.21,213.47,264.81 radius 6.882
> volume erase #9.17 center 168.33,212.78,263.85 radius 6.882
> volume erase #9.17 center 168.44,204.13,263.27 radius 6.882
> volume erase #9.17 center 172.82,196.61,273.72 radius 6.882
> volume erase #9.17 center 190.83,210.71,259.96 radius 6.882
> volume erase #9.17 center 171.54,201.29,268.16 radius 6.882
> volume erase #9.17 center 174.54,211.12,257.86 radius 6.882
> volume erase #9.17 center 172,211.23,261.44 radius 6.882
> volume erase #9.17 center 182.86,208.02,253.73 radius 6.882
> volume erase #9.17 center 178.01,210.41,254.54 radius 6.882
> volume erase #9.17 center 189.64,203.09,265.12 radius 3.534
> volume erase #9.17 center 189.22,205.57,265.53 radius 3.534
> volume erase #9.17 center 188.71,205.82,265.38 radius 3.534
> volume erase #9.17 center 188.45,204.8,265.02 radius 3.534
> volume erase #9.17 center 189.33,209.68,269.7 radius 3.534
> volume erase #9.17 center 189.57,204.42,269.41 radius 3.534
> volume erase #9.17 center 187.92,203.87,268.41 radius 3.534
> volume erase #9.17 center 188.87,208.36,272.62 radius 3.534
> volume erase #9.17 center 178.66,201.46,269.96 radius 3.534
> volume erase #9.17 center 175.41,205.33,266.51 radius 3.534
> volume erase #9.17 center 175.35,202.29,266.21 radius 3.534
> volume erase #9.17 center 175.21,209.99,266.38 radius 3.534
> volume erase #9.17 center 176.57,208.71,265.3 radius 3.534
> undo
> volume erase #9.17 center 174.1,160.84,260.26 radius 3.534
> volume erase #9.17 center 173.62,150.17,257.32 radius 3.534
> volume erase #9.17 center 178.44,147.87,255.11 radius 3.534
> volume erase #9.17 center 177.46,144.05,262.45 radius 6.138
> volume erase #9.17 center 187.16,144.91,265.74 radius 6.138
> volume erase #9.17 center 178.72,143.64,266.97 radius 6.138
> volume erase #9.17 center 174.72,144.39,267.55 radius 6.138
> volume erase #9.17 center 184.24,143.74,260.01 radius 6.138
> volume erase #9.17 center 178.58,149.45,271.81 radius 6.138
> volume erase #9.17 center 188.85,148.87,268.7 radius 6.138
> volume erase #9.17 center 194.67,148.29,267.3 radius 6.138
> volume erase #9.17 center 185.16,146.15,274.14 radius 6.138
> volume erase #9.17 center 189.87,155.34,246.5 radius 6.138
> volume erase #9.17 center 185.27,153.7,249.93 radius 6.138
> volume erase #9.17 center 180.63,153.4,249.85 radius 6.138
> volume erase #9.17 center 172.1,152.35,253.37 radius 6.138
> volume erase #9.17 center 180.4,149.7,253.14 radius 6.138
> volume erase #9.17 center 182.05,147.51,256.42 radius 6.138
> volume erase #9.17 center 174.18,158.85,280.12 radius 6.138
> volume erase #9.17 center 190.24,152.7,260.54 radius 6.138
> volume erase #9.17 center 183.35,148.58,269.85 radius 6.138
> volume erase #9.17 center 168.89,153.93,268.14 radius 6.138
> volume erase #9.17 center 170.22,163.27,261.84 radius 6.138
> volume erase #9.17 center 172.78,146.62,264.18 radius 6.138
> volume erase #9.17 center 172.3,159.1,268.25 radius 6.138
> volume erase #9.17 center 176.79,165.54,279.84 radius 6.138
> volume erase #9.17 center 168.04,159.46,256.93 radius 6.138
> volume erase #9.17 center 170.91,155.78,254.37 radius 6.138
> volume erase #9.17 center 194.02,154.01,257.87 radius 6.138
> volume erase #9.17 center 195.18,156.17,260.96 radius 6.138
> volume erase #9.17 center 186.13,148.92,261.48 radius 2.046
> ui tool show "Side View"
> view
> volume erase #9.17 center 185.47,151.71,264.21 radius 2.046
> volume erase #9.17 center 184.33,153.52,266.53 radius 2.046
> volume erase #9.17 center 185.22,151.18,263.04 radius 2.046
> volume erase #9.17 center 183.72,151.59,262.72 radius 2.046
> volume erase #9.17 center 185.28,153.23,262.99 radius 2.046
> volume erase #9.17 center 184.9,155.85,263.52 radius 2.046
> volume erase #9.17 center 184.9,155.85,263.52 radius 2.604
> volume erase #9.17 center 183.67,152.73,263.6 radius 2.604
> view
> style #1#9.17#!9 stick
Changed 37992 atom styles
> open
> /Users/wujingyi/Desktop/RfxATPasePDB+map_new/RfxATPase_PDB/J436_state1_synthasis_2.82A_14.82w-coot-3.pdb
Summary of feedback from opening
/Users/wujingyi/Desktop/RfxATPasePDB+map_new/RfxATPase_PDB/J436_state1_synthasis_2.82A_14.82w-coot-3.pdb
---
warning | Cannot find LINK/SSBOND residue CYS (40 )
Chain information for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
R | No description available
S W | No description available
T | No description available
U | No description available
V | No description available
X | No description available
Y | No description available
Z | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1,11 atoms
> show #!1,11 cartoons
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #1.26
37240 atoms, 37746 bonds, 3 pseudobonds, 5221 residues, 28 models selected
> select subtract #1.25
36498 atoms, 37005 bonds, 3 pseudobonds, 5072 residues, 27 models selected
> select subtract #1.24
36133 atoms, 36641 bonds, 3 pseudobonds, 4998 residues, 26 models selected
> select subtract #1.23
35375 atoms, 35884 bonds, 3 pseudobonds, 4847 residues, 25 models selected
> select subtract #1.22
34628 atoms, 35138 bonds, 3 pseudobonds, 4697 residues, 24 models selected
> select subtract #1.20
34263 atoms, 34774 bonds, 3 pseudobonds, 4623 residues, 23 models selected
> select subtract #1.19
33183 atoms, 33684 bonds, 3 pseudobonds, 4485 residues, 22 models selected
> select subtract #1.2
29378 atoms, 29821 bonds, 3 pseudobonds, 3987 residues, 21 models selected
> select subtract #1.3
25585 atoms, 25970 bonds, 3 pseudobonds, 3491 residues, 20 models selected
> select subtract #1.4
21763 atoms, 22090 bonds, 3 pseudobonds, 2991 residues, 19 models selected
> select subtract #1.5
18169 atoms, 18433 bonds, 3 pseudobonds, 2522 residues, 18 models selected
> select subtract #1.6
14564 atoms, 14765 bonds, 3 pseudobonds, 2052 residues, 17 models selected
> select subtract #1.7
10978 atoms, 11116 bonds, 3 pseudobonds, 1584 residues, 16 models selected
> select subtract #1.8
8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 15 models selected
> hide sel cartoons
Cell requested for row 10 is out of bounds for table with 38 rows! Resizing
table model.
> hide #!11 models
> show #!11 models
> hide #!1 models
> select add #11
46688 atoms, 47303 bonds, 6 pseudobonds, 6667 residues, 16 models selected
> show sel & #!11 surfaces
> hide sel & #!11 surfaces
> select subtract #11
8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 40 models selected
> select add #11.2
12501 atoms, 8806 bonds, 3 pseudobonds, 1793 residues, 15 models selected
> select add #11.3
16294 atoms, 8806 bonds, 3 pseudobonds, 2289 residues, 16 models selected
> select add #11.4
20116 atoms, 8806 bonds, 3 pseudobonds, 2789 residues, 17 models selected
> select add #11.6
23721 atoms, 8806 bonds, 3 pseudobonds, 3259 residues, 18 models selected
> select add #11.5
27315 atoms, 8806 bonds, 3 pseudobonds, 3728 residues, 19 models selected
> select add #11.7
30901 atoms, 8806 bonds, 3 pseudobonds, 4196 residues, 20 models selected
> select add #11.8
33183 atoms, 8806 bonds, 3 pseudobonds, 4485 residues, 21 models selected
> select add #11.19
34263 atoms, 8806 bonds, 3 pseudobonds, 4623 residues, 22 models selected
> select add #11.20
34628 atoms, 8806 bonds, 3 pseudobonds, 4697 residues, 23 models selected
> select add #11.24
34993 atoms, 8806 bonds, 3 pseudobonds, 4771 residues, 24 models selected
> select add #11.26
35745 atoms, 8806 bonds, 3 pseudobonds, 4922 residues, 25 models selected
> select add #11.25
36487 atoms, 8806 bonds, 3 pseudobonds, 5071 residues, 26 models selected
> select add #11.22
37234 atoms, 8806 bonds, 3 pseudobonds, 5221 residues, 27 models selected
> select add #11.23
37992 atoms, 8806 bonds, 3 pseudobonds, 5372 residues, 28 models selected
> hide sel & #!11 cartoons
> select add #11
46688 atoms, 47303 bonds, 6 pseudobonds, 6667 residues, 30 models selected
> select subtract #11
8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 40 models selected
> select add #11.27
10238 atoms, 8806 bonds, 3 pseudobonds, 1573 residues, 15 models selected
> select add #11.21
11826 atoms, 8806 bonds, 3 pseudobonds, 1838 residues, 16 models selected
> color (#!11 & sel) forest green
> select subtract #11.21
10238 atoms, 8806 bonds, 3 pseudobonds, 1573 residues, 17 models selected
> select subtract #11.27
8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 15 models selected
> select add #11.18
9223 atoms, 8806 bonds, 3 pseudobonds, 1368 residues, 15 models selected
> select add #11.17
9766 atoms, 8806 bonds, 3 pseudobonds, 1443 residues, 16 models selected
> select add #11.16
10309 atoms, 8806 bonds, 3 pseudobonds, 1518 residues, 17 models selected
> select add #11.15
10844 atoms, 8806 bonds, 3 pseudobonds, 1592 residues, 18 models selected
> select add #11.14
11379 atoms, 8806 bonds, 3 pseudobonds, 1666 residues, 19 models selected
> select add #11.13
11922 atoms, 8806 bonds, 3 pseudobonds, 1741 residues, 20 models selected
> select add #11.12
12457 atoms, 8806 bonds, 3 pseudobonds, 1815 residues, 21 models selected
> select add #11.11
12992 atoms, 8806 bonds, 3 pseudobonds, 1889 residues, 22 models selected
> select add #11.10
13508 atoms, 8806 bonds, 3 pseudobonds, 1961 residues, 23 models selected
> select add #11.9
14051 atoms, 8806 bonds, 3 pseudobonds, 2036 residues, 24 models selected
> color (#!11 & sel) #f5ccdcff
> select add #11
46688 atoms, 47303 bonds, 6 pseudobonds, 6667 residues, 26 models selected
> select subtract #11
8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 40 models selected
> view
> color zone #3 near #1 distance 1.06
> color zone #3 near #1 distance 0.96
> color zone #3 near #1 distance 0.95
> ui mousemode right select
> select #11/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> style #11#!9 stick
Changed 37992 atom styles
Drag select of 74 residues
Drag select of 85 residues
Alignment identifier is 11/I
Alignment identifier is 11/Q
Alignment identifier is 1
Alignment identifier is 2
> select #11/I:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/I
516 atoms, 524 bonds, 72 residues, 1 model selected
> hide sel cartoons
> select #11/N,M,K,J:3
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #11/N,M,K,J
2140 atoms, 2172 bonds, 296 residues, 1 model selected
> hide sel cartoons
> select #11/P,O,L,H:3
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #11/P,O,L,H
2172 atoms, 2204 bonds, 300 residues, 1 model selected
> hide sel cartoons
> select #11/Q:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/Q
527 atoms, 535 bonds, 73 residues, 1 model selected
> hide sel cartoons
> select #11/N,M,K,J:58
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #11/N,M,K,J:58-61
116 atoms, 112 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #11/P,O,L,H:58
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #11/P,O,L,H:58-61
116 atoms, 112 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #11/Q:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/Q:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #11/I:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/I:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
> select clear
> lighting soft
> select #11/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/Q:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/I:4-39,41-73
489 atoms, 495 bonds, 69 residues, 1 model selected
> select #11/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11/P,O,L,H:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #11/P,O,L,H:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select #11/N,M,K,J:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #11/N,M,K,J:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> show #!1 models
> select add #1.2
3805 atoms, 498 residues, 1 model selected
> select add #1.3
7598 atoms, 994 residues, 2 models selected
> select add #1.4
11420 atoms, 1494 residues, 3 models selected
> select add #1.5
15014 atoms, 1963 residues, 4 models selected
> select add #1.6
18619 atoms, 2433 residues, 5 models selected
> select add #1.7
22205 atoms, 2901 residues, 6 models selected
> select add #1.8
24487 atoms, 3190 residues, 7 models selected
> select add #1.9
25030 atoms, 3265 residues, 8 models selected
> select add #1.10
25546 atoms, 3337 residues, 9 models selected
> select subtract #1.10
25030 atoms, 3265 residues, 10 models selected
> select subtract #1.9
24487 atoms, 3190 residues, 9 models selected
> hide sel cartoons
> select add #1.19
25567 atoms, 3328 residues, 8 models selected
> select add #1.20
25932 atoms, 3402 residues, 9 models selected
> select add #1.24
26297 atoms, 3476 residues, 10 models selected
> select add #1.22
27044 atoms, 3626 residues, 11 models selected
> select add #1.23
27802 atoms, 3777 residues, 12 models selected
> select add #1.25
28544 atoms, 3926 residues, 13 models selected
> select add #1.26
29296 atoms, 4077 residues, 14 models selected
> hide sel cartoons
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 16 models selected
> select subtract #1
26 models selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> show sel cartoons
> select subtract #1.21
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel cartoons
> select subtract #1.27
1 model selected
> select add #11.21
1588 atoms, 265 residues, 1 model selected
> select add #11.27
3130 atoms, 543 residues, 2 models selected
> hide sel cartoons
> select subtract #11.21
1542 atoms, 278 residues, 3 models selected
> select subtract #11.27
1 model selected
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select subtract #1
26 models selected
> color #1,11#!9 byhetero
> select clear
[Repeated 1 time(s)]
> volume #9.12 color #f5ccdc27
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> volume erase #9.12 center 184.1,172.1,227.7 radius 15.252
> volume erase #9.12 center 184.32,173.74,226.15 radius 21.39
> volume erase #9.12 center 186.52,200.84,224.47 radius 21.39
> volume erase #9.12 center 185.09,179.62,220.84 radius 21.39
> volume erase #9.12 center 170.15,177.87,222.26 radius 21.39
> volume erase #9.12 center 215.69,164.39,225.17 radius 21.39
> volume erase #9.12 center 216.27,170.95,228.22 radius 21.39
> volume erase #9.12 center 219.37,188.32,232.19 radius 21.39
> volume erase #9.12 center 221.77,198.05,232.67 radius 21.39
> volume erase #9.12 center 199.82,151.87,227.61 radius 21.39
> volume erase #9.12 center 210.63,174.67,229.21 radius 21.39
> volume erase #9.12 center 189.58,200.46,228.62 radius 21.39
> volume erase #9.12 center 201.15,199.61,227.53 radius 21.39
> volume erase #9.12 center 169.94,190.74,229.69 radius 21.39
> volume erase #9.12 center 169.7,163.35,224.36 radius 21.39
> volume erase #9.12 center 169.9,173.13,228.26 radius 21.39
> volume erase #9.12 center 170.12,179.65,296.99 radius 21.39
> volume erase #9.12 center 176.61,190.26,292.89 radius 21.39
> volume erase #9.12 center 185.4,157.68,290.36 radius 21.39
> volume erase #9.12 center 213.28,183.99,298.98 radius 21.39
> volume erase #9.12 center 213.03,159.31,289.71 radius 21.39
> volume erase #9.12 center 208.87,201.17,291.62 radius 21.39
> volume erase #9.12 center 215.87,170.23,292.11 radius 21.39
> volume erase #9.12 center 196.57,176.8,291.69 radius 21.39
> volume erase #9.12 center 191.52,210.19,292.08 radius 21.39
> volume erase #9.12 center 171.81,170.99,288.63 radius 21.39
> volume erase #9.12 center 210.68,175.67,289.23 radius 21.39
> volume erase #9.12 center 206.45,189.34,233.5 radius 21.39
> volume erase #9.12 center 209.93,175.44,233.17 radius 21.39
> volume erase #9.12 center 200.8,206.37,235.59 radius 21.39
> volume erase #9.12 center 183.1,160.4,230.21 radius 21.39
> volume erase #9.12 center 175.47,172.03,232.27 radius 21.39
> volume erase #9.12 center 160.52,176.91,233.03 radius 21.39
> volume erase #9.12 center 166.54,188.87,234.37 radius 21.39
> volume erase #9.12 center 189.24,182.31,255.42 radius 7.812
> volume erase #9.12 center 188.92,183.04,248.3 radius 7.812
> volume erase #9.12 center 187.49,182.01,258.55 radius 7.812
> volume erase #9.12 center 185.79,180.87,262.65 radius 7.812
> volume erase #9.12 center 185.95,179.3,267.44 radius 6.882
> volume erase #9.12 center 185.26,182.54,267.4 radius 6.882
> volume erase #9.12 center 189.69,183.11,267.13 radius 6.882
> volume erase #9.12 center 190.92,180.28,267.14 radius 6.882
> volume erase #9.12 center 215.04,190.21,264.25 radius 6.882
> surface dust #9.12 size 9.3
> volume erase #9.12 center 184.24,174.01,269.49 radius 6.882
> volume erase #9.12 center 191.11,173.89,268.94 radius 9.3
> volume erase #9.12 center 190.48,172.8,268.72 radius 9.3
> volume erase #9.12 center 193.88,181.19,269.01 radius 9.3
> volume erase #9.12 center 187.96,184.06,270.77 radius 9.3
> volume erase #9.12 center 185.52,183.78,269.87 radius 9.3
> volume erase #9.12 center 183.1,182.21,269.56 radius 9.3
> volume erase #9.12 center 184.72,178.47,262.38 radius 9.3
> volume erase #9.12 center 185.13,178.34,260.06 radius 9.3
> volume erase #9.12 center 188.45,179.77,258.99 radius 9.3
> volume erase #9.12 center 189.45,182.63,259.39 radius 9.3
> volume erase #9.12 center 187.75,185.93,259.34 radius 9.3
> volume erase #9.12 center 183.66,183.86,258.44 radius 9.3
> volume erase #9.12 center 184.18,178.26,255.5 radius 9.3
> volume erase #9.12 center 192.37,182.56,255.04 radius 9.3
> volume erase #9.12 center 192.09,179.03,255.86 radius 9.3
> volume erase #9.12 center 184.66,187.36,250.02 radius 9.3
> volume erase #9.12 center 177.46,188.32,248.92 radius 9.3
> volume erase #9.12 center 187.86,175.68,260.08 radius 9.3
> volume erase #9.12 center 184.25,176.71,260.31 radius 9.3
> volume erase #9.12 center 189.78,175.3,251.29 radius 9.3
> volume erase #9.12 center 193.96,181.47,255.43 radius 9.3
> volume erase #9.12 center 193.73,183.07,258.27 radius 9.3
> volume erase #9.12 center 192.98,179.02,257.36 radius 9.3
> volume erase #9.12 center 183.39,200.21,279.43 radius 9.3
> volume erase #9.12 center 172.34,194.09,277.6 radius 9.3
> volume erase #9.12 center 166.7,183.16,275.79 radius 9.3
> volume erase #9.12 center 167.25,189.29,276.18 radius 9.3
> volume erase #9.12 center 175.93,157.41,272.95 radius 9.3
> volume erase #9.12 center 172.21,159.67,272.12 radius 9.3
> volume erase #9.12 center 160.83,175.29,272.1 radius 9.3
> volume erase #9.12 center 197.05,158.92,273.59 radius 9.3
> volume erase #9.12 center 185.44,160.03,273.73 radius 9.3
> volume erase #9.12 center 203.92,166.03,275.21 radius 9.3
> volume erase #9.12 center 206.96,192,276.94 radius 9.3
> volume erase #9.12 center 193.11,199.4,277.69 radius 9.3
> volume erase #9.12 center 181.19,180.13,268.05 radius 9.3
> volume erase #9.12 center 187.06,185.68,265.92 radius 9.3
> volume erase #9.12 center 183.64,184.63,262.57 radius 9.3
> volume erase #9.12 center 154.78,187.08,258.92 radius 9.3
> volume erase #9.12 center 209.28,182.52,275.57 radius 9.3
> volume erase #9.12 center 211.12,177.72,275.43 radius 9.3
> volume erase #9.12 center 211.62,173.18,272.77 radius 9.3
> volume erase #9.12 center 201.18,199.48,275.42 radius 9.3
> volume erase #9.12 center 190.27,185.12,264.27 radius 9.3
> volume erase #9.12 center 190.37,185.81,264.28 radius 9.3
> volume erase #9.12 center 192.76,183.8,261.73 radius 9.3
> volume erase #9.12 center 211.01,157.81,252.3 radius 9.3
> volume erase #9.12 center 197.77,162.56,247.3 radius 6.138
> volume erase #9.12 center 194.95,174.09,254.2 radius 6.138
> volume erase #9.12 center 194.54,175.08,258.85 radius 6.138
> volume erase #9.12 center 198.16,180.12,259.16 radius 6.138
> volume erase #9.12 center 178.51,176.9,258 radius 6.138
> volume erase #9.12 center 186.02,194.42,251.21 radius 6.138
> volume erase #9.12 center 180.91,201.48,247.92 radius 6.138
> volume erase #9.12 center 177.32,202.11,251.5 radius 6.138
> volume erase #9.12 center 189.36,204.86,251.93 radius 6.138
> volume erase #9.12 center 196.64,165.41,246.98 radius 6.138
> volume erase #9.12 center 202.11,164.05,248.42 radius 6.138
> volume erase #9.12 center 188.59,163.81,247.75 radius 6.138
> volume erase #9.12 center 206.74,177.37,271.52 radius 6.138
> volume erase #9.12 center 207.27,177.56,269.78 radius 6.138
> volume erase #9.12 center 212.56,177.76,269.99 radius 6.138
> volume erase #9.12 center 192.22,190.68,265.26 radius 6.138
> volume erase #9.12 center 203.15,185.1,272.41 radius 6.138
> volume erase #9.12 center 209.61,188.74,255.54 radius 3.348
> volume erase #9.12 center 209.12,176.58,253.99 radius 3.348
> volume erase #9.12 center 205.76,167.23,266.32 radius 3.348
> volume erase #9.12 center 182.43,162.7,250.28 radius 3.348
> volume erase #9.12 center 168.7,180.89,253.17 radius 3.348
> volume erase #9.12 center 165.82,183.19,255.02 radius 3.348
> volume erase #9.12 center 165.69,179.65,253.86 radius 3.348
> volume erase #9.12 center 167.47,164.1,254.65 radius 3.348
> volume erase #9.12 center 168.13,173.05,255.06 radius 1.488
> volume erase #9.12 center 166.62,188.47,256.38 radius 2.232
> volume erase #9.12 center 175.28,197.9,257.61 radius 2.232
> volume erase #9.12 center 175.57,201.08,256.18 radius 2.232
> volume erase #9.12 center 181.09,195.37,272.08 radius 2.232
> volume erase #9.12 center 179.61,196.92,272.58 radius 3.534
> volume erase #9.12 center 169.64,185.02,266.02 radius 2.046
> volume erase #9.12 center 169.92,183.65,267.55 radius 2.046
> volume erase #9.12 center 169.14,184.16,265.41 radius 2.046
> volume erase #9.12 center 171.46,184.85,262.93 radius 2.046
> volume erase #9.12 center 172.44,183.01,263.15 radius 2.046
> volume erase #9.12 center 185.11,197.53,267.64 radius 2.976
> volume erase #9.12 center 198.09,194.54,267.16 radius 2.976
> volume erase #9.12 center 197.15,195.09,267.25 radius 2.976
> volume erase #9.12 center 202.82,187.35,263.76 radius 2.418
> volume erase #9.12 center 202.99,187.65,265.52 radius 2.418
> volume erase #9.12 center 205.72,188.36,266.97 radius 2.418
> volume erase #9.12 center 199.49,168.29,264.78 radius 2.418
> volume erase #9.12 center 189.36,162.93,264.17 radius 2.418
> volume erase #9.12 center 179.94,167.12,262.62 radius 2.418
> volume erase #9.12 center 179.73,165.96,264.92 radius 2.418
> volume erase #9.12 center 172.3,172.9,264.8 radius 2.418
> volume erase #9.12 center 175.74,193.26,267.56 radius 2.418
> volume erase #9.12 center 188.92,163.79,260.56 radius 1.302
> volume erase #9.12 center 188.44,166,260.96 radius 1.302
> volume erase #9.12 center 191.97,158.18,263.11 radius 1.302
> volume erase #9.12 center 193.63,158.15,263.19 radius 1.302
> volume erase #9.12 center 192.76,159.15,264 radius 1.302
> volume erase #9.12 center 198.51,168.88,254.85 radius 1.302
> volume erase #9.12 center 199.71,169.88,255.91 radius 1.302
> volume erase #9.12 center 199.71,169.88,255.91 radius 1.86
> volume erase #9.12 center 204.17,175.8,261.63 radius 1.86
> volume erase #9.12 center 172.2,195.24,256.4 radius 1.86
> volume erase #9.12 center 171.3,193.77,255.96 radius 1.86
> volume erase #9.12 center 200.87,163.58,255.5 radius 1.86
> volume #9.12 level 0.083
> volume erase #9.12 center 207.93,193.98,255.12 radius 4.65
> volume erase #9.12 center 209.68,201.98,257.22 radius 4.65
> volume erase #9.12 center 214.6,177.35,254.25 radius 4.65
> volume erase #9.12 center 216.87,182.4,258.95 radius 4.65
> volume erase #9.12 center 215.86,171.68,257.39 radius 6.696
> volume erase #9.12 center 206.05,204.49,262.94 radius 6.696
> volume erase #9.12 center 193.24,191.28,250.88 radius 6.696
> volume erase #9.12 center 157.95,174.2,259.6 radius 6.696
> volume erase #9.12 center 159.18,169.52,259.77 radius 6.696
> volume erase #9.12 center 186.01,189.41,261.1 radius 6.696
> volume erase #9.12 center 178.73,183.27,253.83 radius 6.696
> volume erase #9.12 center 211.88,182.74,252.48 radius 6.696
> volume erase #9.12 center 207.36,194.07,251.61 radius 6.696
> volume erase #9.12 center 206.13,164.9,251.38 radius 6.696
> volume erase #9.12 center 207.78,170.34,248.51 radius 6.696
> volume erase #9.12 center 201.27,202.03,253.51 radius 6.696
> volume erase #9.12 center 195,199.31,250.4 radius 6.696
> volume erase #9.12 center 194.47,204.1,253.32 radius 6.696
> volume erase #9.12 center 182.23,202.2,252.09 radius 6.696
> volume erase #9.12 center 169.22,199.88,254.89 radius 6.696
> volume erase #9.12 center 161.93,196.55,257.12 radius 6.696
> volume erase #9.12 center 176.91,206.8,258.12 radius 6.696
> volume erase #9.12 center 173.29,184.41,255.72 radius 2.79
> volume erase #9.12 center 172.18,184.39,256.72 radius 2.79
> volume erase #9.12 center 171.92,185.05,257.24 radius 2.79
> volume erase #9.12 center 169.01,174.26,254.74 radius 2.79
> volume erase #9.12 center 172.08,175.63,261.58 radius 1.488
> volume erase #9.12 center 171.52,175.58,262.8 radius 1.488
> volume erase #9.12 center 196.67,195.6,258.92 radius 1.488
> volume erase #9.12 center 197.62,194.73,262.63 radius 1.488
> volume erase #9.12 center 188.36,203.39,269.5 radius 1.488
> volume erase #9.12 center 188.66,202.09,268.26 radius 1.488
> volume erase #9.12 center 192.04,201.52,269.55 radius 1.488
> volume erase #9.12 center 192.04,201.52,269.55 radius 2.232
> volume erase #9.12 center 194.45,203.49,268.33 radius 2.232
> volume erase #9.12 center 197.18,202.52,267.91 radius 2.232
> volume erase #9.12 center 191.54,203.42,267.86 radius 2.232
> volume erase #9.12 center 207.73,193.75,268.03 radius 2.232
> volume erase #9.12 center 207.6,191.7,266.66 radius 2.232
> volume erase #9.12 center 205.54,195.6,268.01 radius 2.232
> volume erase #9.12 center 209.14,193.95,265.53 radius 2.232
> volume erase #9.12 center 196.62,194.57,264.82 radius 2.232
> volume erase #9.12 center 196.85,191.74,263.62 radius 2.232
> volume erase #9.12 center 186.31,196.72,263.71 radius 2.232
> volume erase #9.12 center 185.88,198.13,264.72 radius 2.232
> volume erase #9.12 center 184.84,195.57,265.65 radius 2.232
> volume erase #9.12 center 172.16,183.66,264.03 radius 2.232
> volume erase #9.12 center 171.76,182.85,263.81 radius 2.232
> volume erase #9.12 center 170.72,184.39,264.98 radius 2.232
> volume erase #9.12 center 171.49,182.88,266.59 radius 2.232
> volume erase #9.12 center 179.15,166.74,261.29 radius 2.232
> volume erase #9.12 center 178.87,164.06,263.52 radius 2.232
> volume erase #9.12 center 198.17,157.98,262.84 radius 2.232
> volume erase #9.12 center 196.37,157.87,264.09 radius 2.232
> volume erase #9.12 center 194.34,158.92,264.5 radius 2.232
> volume erase #9.12 center 195.72,158.08,263.56 radius 2.232
> volume erase #9.12 center 201.58,168.23,265.11 radius 2.232
> volume erase #9.12 center 204.06,178.3,265.26 radius 2.232
> volume erase #9.12 center 207.2,171.8,253.33 radius 2.232
> volume erase #9.12 center 182.09,156.89,255.37 radius 2.232
> volume erase #9.12 center 179.67,158.49,264.13 radius 2.79
> volume erase #9.12 center 199.48,167.75,261.41 radius 1.302
> volume erase #9.12 center 199.29,166.63,262.29 radius 1.302
> volume erase #9.12 center 197.13,168.94,260.81 radius 1.302
> volume erase #9.12 center 196.97,168.35,255.11 radius 1.302
> volume erase #9.12 center 189.83,160.27,254.03 radius 1.302
> volume erase #9.12 center 176.49,163.63,254.58 radius 1.302
> volume erase #9.12 center 173.91,163.42,253.82 radius 1.302
> volume erase #9.12 center 188.4,164.13,260.27 radius 1.302
> volume erase #9.12 center 188.45,164.32,260.22 radius 1.302
> volume erase #9.12 center 187.98,163.39,260.8 radius 1.302
> volume erase #9.12 center 187.93,163.16,262.27 radius 1.302
> volume erase #9.12 center 203.58,186.48,261.77 radius 1.302
> volume erase #9.12 center 188.6,202.12,258.59 radius 1.302
> volume erase #9.12 center 188.13,201.53,258.4 radius 1.302
> volume erase #9.12 center 187.85,202.17,258.04 radius 1.302
> volume erase #9.12 center 196.63,197.98,266.59 radius 1.302
> volume erase #9.12 center 195,201.99,265.96 radius 1.302
> volume erase #9.12 center 195.26,201.96,266.98 radius 2.046
> volume erase #9.12 center 194.1,202.28,266.88 radius 2.046
> volume erase #9.12 center 195.01,201.77,266.73 radius 2.046
> volume erase #9.12 center 169.05,194.15,266.61 radius 2.046
> volume erase #9.12 center 164.62,180.47,265.09 radius 2.046
> volume erase #9.12 center 168.71,180.39,267.54 radius 2.046
> volume erase #9.12 center 169.25,189.34,267.22 radius 2.046
> volume erase #9.12 center 171.83,193.4,267.25 radius 2.046
> volume erase #9.12 center 174.32,199.59,267.49 radius 2.046
> volume erase #9.12 center 204.58,185.48,263.24 radius 2.046
> volume erase #9.12 center 209.04,174.47,254.29 radius 2.046
> volume erase #9.12 center 208.15,174.41,256.03 radius 2.046
> volume erase #9.12 center 209.2,172.04,254.9 radius 2.046
> volume erase #9.12 center 203.32,171.82,253.03 radius 2.046
> volume erase #9.12 center 197.09,167.61,261.64 radius 2.046
> volume erase #9.12 center 190.05,165.29,260.95 radius 2.046
> volume erase #9.12 center 166.94,175.41,255.61 radius 2.046
> volume erase #9.12 center 164.43,178.66,257.44 radius 2.046
> volume erase #9.12 center 165.27,178.75,256.96 radius 2.046
> volume erase #9.12 center 167.95,178.15,254.46 radius 2.046
> volume erase #9.12 center 168.71,191.92,257.08 radius 2.046
> volume erase #9.12 center 171.92,192.05,255.22 radius 2.046
> volume erase #9.12 center 167.56,193.6,258.06 radius 2.046
> volume erase #9.12 center 168.48,192.7,259.22 radius 2.046
> volume erase #9.12 center 167.16,189.2,259.01 radius 2.046
> volume erase #9.12 center 177.73,189.97,265.54 radius 2.046
> volume erase #9.12 center 164.83,176.17,256.01 radius 2.046
> volume erase #9.12 center 187.19,159.39,253.32 radius 2.046
> volume erase #9.12 center 187.76,160.93,254.39 radius 2.046
> volume erase #9.12 center 200.75,161.43,255.11 radius 2.046
> volume erase #9.12 center 199.8,173.83,256.52 radius 2.046
> volume erase #9.12 center 199.88,169.15,256.4 radius 2.046
> volume erase #9.12 center 177.57,193.36,263.08 radius 2.046
> volume erase #9.12 center 177.52,194.14,264.2 radius 2.046
> volume erase #9.12 center 176.39,198.61,270.06 radius 2.046
> volume erase #9.12 center 177.48,199.24,269.15 radius 2.046
> volume erase #9.12 center 180.56,198.81,269.71 radius 2.046
> volume erase #9.12 center 181.64,201.92,267.75 radius 2.046
> volume erase #9.12 center 178.32,201.57,267.94 radius 2.046
> volume erase #9.12 center 179.92,199.74,268.99 radius 2.046
> volume erase #9.12 center 177.91,198.42,268.97 radius 2.046
> volume erase #9.12 center 182.72,200.9,268.03 radius 2.046
> volume erase #9.12 center 168.77,192.56,267.85 radius 2.046
> volume erase #9.12 center 169.88,167,266.26 radius 2.046
> volume erase #9.12 center 168.87,166.02,263.63 radius 2.046
> volume erase #9.12 center 174.56,164.55,254.84 radius 2.046
> volume erase #9.12 center 170.27,169.04,253.83 radius 2.046
> volume erase #9.12 center 171.39,171.99,254.18 radius 2.046
> volume erase #9.12 center 169.11,170.84,254.99 radius 2.046
> volume erase #9.12 center 198.75,191.53,258.17 radius 2.046
> volume erase #9.12 center 200.35,189.69,258.05 radius 2.046
> volume erase #9.12 center 175.1,200.1,259.4 radius 2.046
> volume erase #9.12 center 169.59,167,255.02 radius 2.046
> volume erase #9.12 center 172.21,166.28,254.44 radius 2.046
> volume erase #9.12 center 173.12,169.18,253.77 radius 2.046
> volume erase #9.12 center 175.59,165.3,256.26 radius 1.116
> volume erase #9.12 center 210.55,180.34,264.99 radius 1.116
> volume erase #9.12 center 209.31,182.15,266.22 radius 1.116
> volume erase #9.12 center 174.21,188.44,257.58 radius 1.116
> volume erase #9.12 center 175.04,189.6,257.47 radius 1.116
> volume erase #9.12 center 174.68,188.31,258.97 radius 1.116
> volume erase #9.12 center 182.49,194.98,257.93 radius 1.302
> volume erase #9.12 center 180.89,194.59,257.99 radius 1.302
> volume erase #9.12 center 172.82,189.41,255.87 radius 1.302
> volume erase #9.12 center 179.86,200.18,258.51 radius 1.302
> volume erase #9.12 center 203.52,198.12,258.69 radius 2.604
> volume erase #9.12 center 205.7,196.86,257.2 radius 2.604
> volume erase #9.12 center 199.73,199.1,257.84 radius 2.604
> volume erase #9.12 center 202.23,196.65,254.86 radius 2.604
> volume erase #9.12 center 214.39,181.65,261.94 radius 2.604
> volume erase #9.12 center 201.63,169.64,266.87 radius 2.604
> volume erase #9.12 center 203.44,176.56,264.28 radius 2.604
> volume erase #9.12 center 199.65,173.13,256.57 radius 2.604
> volume erase #9.12 center 207.41,195.15,266.81 radius 2.604
> volume erase #9.12 center 197.6,194.56,263.23 radius 2.046
> volume erase #9.12 center 196.63,192.06,264.06 radius 2.046
> volume erase #9.12 center 208.53,168.55,255.65 radius 2.046
> volume erase #9.12 center 199.24,167.43,264.15 radius 2.046
> volume erase #9.12 center 202.29,179.83,262.7 radius 2.046
> volume erase #9.12 center 202.59,180.06,265.14 radius 2.046
> volume erase #9.12 center 204.66,164.48,264.21 radius 2.046
> volume erase #9.12 center 207.54,188.07,257.39 radius 2.046
> volume erase #9.12 center 190.2,164.16,264.62 radius 2.046
> volume erase #9.12 center 190.78,162.66,264.21 radius 2.046
> volume erase #9.12 center 191.04,164.57,264.48 radius 2.046
> volume erase #9.12 center 191.74,162.88,264.01 radius 2.046
> volume erase #9.12 center 169.31,168.78,265.58 radius 2.046
> volume erase #9.12 center 178.43,165.86,264.01 radius 2.046
> volume erase #9.12 center 168.09,175.4,256.5 radius 2.046
> volume erase #9.12 center 187.52,197.18,263.46 radius 2.046
> volume erase #9.12 center 195.2,196.96,266.89 radius 2.046
> volume erase #9.12 center 173.38,180.8,256.98 radius 2.046
> volume erase #9.12 center 173.04,177,262.32 radius 2.046
> volume erase #9.12 center 202.13,183.82,257.15 radius 2.046
> volume erase #9.12 center 202.59,183.01,257.41 radius 2.046
> volume erase #9.12 center 201.81,183.26,259.26 radius 2.046
> volume erase #9.12 center 202.47,188.32,266.44 radius 2.046
> volume erase #9.12 center 202.54,188.53,264.11 radius 2.046
> volume erase #9.12 center 199.27,197.29,257.92 radius 2.046
> volume erase #9.12 center 199.08,196.93,257.18 radius 2.046
> volume erase #9.12 center 198.56,194.64,257.17 radius 2.046
> volume erase #9.12 center 200.41,197.94,258.49 radius 2.046
> volume erase #9.12 center 200.78,197.63,257.26 radius 2.046
> volume erase #9.12 center 171.11,186.58,262.63 radius 1.302
> volume erase #9.12 center 172.53,186.62,263.26 radius 1.302
> volume erase #9.12 center 167.28,181.59,265.98 radius 1.302
> volume erase #9.12 center 204.71,190.74,266.51 radius 1.302
> volume erase #9.12 center 205.21,192.8,266.78 radius 1.302
> volume erase #9.12 center 175.11,193.67,265.78 radius 1.302
> volume erase #9.12 center 174.65,191.1,268.05 radius 1.302
> volume erase #9.12 center 194.48,167.68,256 radius 1.302
> volume erase #9.12 center 194.93,165.18,252.98 radius 1.302
> volume erase #9.12 center 199.68,169.25,258.87 radius 1.302
> volume erase #9.12 center 199.8,168.54,259.04 radius 1.302
> volume erase #9.12 center 182.85,198.53,265.9 radius 1.302
> volume erase #9.12 center 184.13,197.25,266.1 radius 1.302
> volume erase #9.12 center 183.16,197.67,265.33 radius 1.302
> volume erase #9.12 center 178.4,168.3,263.12 radius 1.302
> volume erase #9.12 center 177.59,167.43,260.27 radius 1.302
> view
[Repeated 1 time(s)]
> save /Users/wujingyi/Desktop/figure/figure4/state1_Fo侧视atom+map.cxs
> includeMaps true
——— End of log from Tue Mar 18 21:19:53 2025 ———
opened ChimeraX session
> ui tool show "Model Panel"
> hide #!9 models
> select add #11.27
1542 atoms, 278 residues, 1 model selected
> select add #11.21
3130 atoms, 543 residues, 2 models selected
Alignment identifier is 11/T
Alignment identifier is 11/Z
> select #11/T:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/T:1-108
536 atoms, 535 bonds, 1 pseudobond, 99 residues, 2 models selected
> hide sel cartoons
> select #11/T:135-136
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #11/T:135-240
323 atoms, 321 bonds, 1 pseudobond, 65 residues, 2 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> select subtract #11.21
1 model selected
> select add #11.21
1588 atoms, 265 residues, 1 model selected
> select subtract #11.21
1 model selected
> hide #!11 models
> show #!11 models
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> select add #1.21
3130 atoms, 543 residues, 2 models selected
Alignment identifier is 1/T
Alignment identifier is 1/Z
> select #1/T:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:1-88
436 atoms, 435 bonds, 1 pseudobond, 79 residues, 2 models selected
> hide sel cartoons
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-88
431 atoms, 430 bonds, 88 residues, 1 model selected
> hide sel cartoons
> select #1/T:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:89-107
95 atoms, 94 bonds, 19 residues, 1 model selected
> select #1/T:29-109
404 atoms, 403 bonds, 1 pseudobond, 72 residues, 2 models selected
> select #1/T:29-113
424 atoms, 423 bonds, 1 pseudobond, 76 residues, 2 models selected
> select #1/T:29-110
409 atoms, 408 bonds, 1 pseudobond, 73 residues, 2 models selected
> select #1/T:110
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:110-239
499 atoms, 504 bonds, 1 pseudobond, 89 residues, 2 models selected
> hide sel cartoons
> select add #1.27
2041 atoms, 504 bonds, 1 pseudobond, 367 residues, 3 models selected
> select subtract #1.21
1542 atoms, 278 residues, 3 models selected
> hide sel cartoons
> ui mousemode right select
> select clear
> save /Users/wujingyi/Desktop/figure/figure4/state1_Fo俯视atom+mapT细节1.png
> width 1660 height 1243 supersample 3 transparentBackground true
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel cartoons
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-58
284 atoms, 283 bonds, 58 residues, 1 model selected
> hide sel cartoons
> select #1/Z:79
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:79-238
604 atoms, 602 bonds, 1 pseudobond, 123 residues, 2 models selected
> hide sel cartoons
> select #1/Z:59
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:59-88
147 atoms, 146 bonds, 30 residues, 1 model selected
> hide sel cartoons
> select #1/Z:89-90
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/Z:89-111
115 atoms, 114 bonds, 23 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Z:257
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #11.27
1553 atoms, 10 bonds, 279 residues, 3 models selected
> hide sel atoms
> select subtract #11.27
11 atoms, 10 bonds, 1 residue, 3 models selected
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save /Users/wujingyi/Desktop/figure/figure4/state1_Fo俯视atom+mapZ细节1.png
> width 1660 height 1243 supersample 3 transparentBackground true
[Repeated 1 time(s)]
> ui tool show Distances
> select #11/J:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #11/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #11/J:59@CA
1 atom, 1 residue, 1 model selected
> select add #11/I:59@CA
2 atoms, 2 residues, 2 models selected
> distance #11/J:59@CA #11/I:59@CA
Distance between J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #11/J GLU 59 CA
and /I GLU 59 CA: 12.159Å
> save /Users/wujingyi/Desktop/figure/figure4/state1_Fo俯视atom+mapZ细节1.cxs
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> show #!6 models
> select add #5
7093 atoms, 5298 bonds, 7093 residues, 4 models selected
> select subtract #5
2 atoms, 2 residues, 7 models selected
> select add #5
7093 atoms, 5298 bonds, 7093 residues, 4 models selected
> color (#!5,11 & sel) #ffa07aff
[Repeated 1 time(s)]
> color (#!5,11 & sel) #ffa07af8
> color (#!5,11 & sel) #ffa07af6
> color (#!5,11 & sel) #ffa07adf
> color (#!5,11 & sel) #ffa07ad2
> color (#!5,11 & sel) #ffa07ab5
> color (#!5,11 & sel) #ffa07aa5
> color (#!5,11 & sel) #ffa07a8b
> color (#!5,11 & sel) #ffa07a84
> color (#!5,11 & sel) #ffa07a7e
[Repeated 3 time(s)]
> color (#!5,11 & sel) #ffa07a80
[Repeated 1 time(s)]
> color (#!5,11 & sel) #ff9f7a80
> color (#!5,11 & sel) #ff9d7a80
> color (#!5,11 & sel) #ff9c7a80
[Repeated 1 time(s)]
> color (#!5,11 & sel) #ff9b7a80
> color (#!5,11 & sel) #ff9a7a80
> color (#!5,11 & sel) #ff9b7a80
> color (#!5,11 & sel) #ff9c7a80
> color (#!5,11 & sel) #ff9d7a80
> color (#!5,11 & sel) #ff9e7a80
[Repeated 1 time(s)]
> color (#!5,11 & sel) #f5bc9780
> color (#!5,11 & sel) #f5bc9680
> color (#!5,11 & sel) #f5bb9680
> color (#!5,11 & sel) #f5b89380
> color (#!5,11 & sel) #f5b59280
> color (#!5,11 & sel) #f5b39180
> color (#!5,11 & sel) #f5b29080
> color (#!5,11 & sel) #f5b19080
> color (#!5,11 & sel) #f5a78c80
> color (#!5,11 & sel) #f5a48c80
> color (#!5,11 & sel) #f5a38c80
> color (#!5,11 & sel) #f59e8f80
> color (#!5,11 & sel) #f5999180
> color (#!5,11 & sel) #f5999280
[Repeated 1 time(s)]
> color (#!5,11 & sel) #f59b9280
> color (#!5,11 & sel) #f59f9180
> color (#!5,11 & sel) #f5a28f80
> color (#!5,11 & sel) #f5a58c80
[Repeated 2 time(s)]
> color (#!5,11 & sel) #f5a98980
> color (#!5,11 & sel) #f5af8680
> color (#!5,11 & sel) #f5b08480
[Repeated 1 time(s)]
> color (#!5,11 & sel) #f5b28580
[Repeated 1 time(s)]
> color (#!5,11 & sel) #f5b58680
> color (#!5,11 & sel) #f5bc8880
> color (#!5,11 & sel) #f5c08880
[Repeated 1 time(s)]
> color (#!5,11 & sel) #f5b77780
> color (#!5,11 & sel) #f5af6680
[Repeated 2 time(s)]
> color (#!5,11 & sel) #f5b46680
> color (#!5,11 & sel) #f5bb6480
> color (#!5,11 & sel) #f5be6380
[Repeated 1 time(s)]
> color (#!5,11 & sel) #f5bf6380
> color (#!5,11 & sel) #f5b95580
> color (#!5,11 & sel) #f5b74d80
> color (#!5,11 & sel) #f5b74c80
> color (#!5,11 & sel) #f5b74d80
> color (#!5,11 & sel) #f5b84e80
> color (#!5,11 & sel) #f5bc4f80
> color (#!5,11 & sel) #f5c24f80
> color (#!5,11 & sel) #f5c34e80
> select subtract #5
2 atoms, 2 residues, 7 models selected
> select add #5
7093 atoms, 5298 bonds, 7093 residues, 4 models selected
> select subtract #5
2 atoms, 2 residues, 7 models selected
> color #5 #f1b56380
> color #5 #f1ab4d80
> color #5 #f1bf5380
> color #5 #f1bb6480
> color #5 #f1c14b80
> color #5 #f1c94480
> color #5 #f1bf4180
> color #5 #e9b93f80
> color #6 #ff40ffff
> color #6 #00fdffff
> color #6 #00fdff88
[Repeated 1 time(s)]
> color #6 #00fdff87
> color #6 #00fdff80
> color #6 #00fdff60
> color #6 #64dade60
> color #6 #62d6da60
> color #6 #64bada60
> color #6 #72dad960
> color #6 #71d4da60
> color #6 #6cc7da60
> color #6 #66bccd60
> color #6 #6aafcd60
> color #6 #639ecd60
> color #6 #63a1cd60
> color #6 #3aaccd60
> color #6 #39cdc060
> color #6 #59cdc060
> color #6 #56c0cd60
> color #6 #50b3bf60
> select add #1.21
1590 atoms, 267 residues, 4 models selected
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> undo
[Repeated 2 time(s)]
> select clear
Drag select of 11 atoms, 10 bonds
> hide sel atoms
> select #11/J:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #11/J:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #11/J:60
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #11/I:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #11/I:60
13 atoms, 11 bonds, 2 residues, 2 models selected
> select add #11/I:58
20 atoms, 17 bonds, 3 residues, 2 models selected
> hide sel cartoons
> select #11/H:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #11/H:61
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #11/H:60
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add #11/H:59
29 atoms, 25 bonds, 4 residues, 2 models selected
> select subtract #11/H:59
20 atoms, 17 bonds, 3 residues, 2 models selected
> hide sel cartoons
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/Q:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #11/Q:60
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #11/Q:61
20 atoms, 17 bonds, 3 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select clear
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> select #11/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #11/J:59
18 atoms, 16 bonds, 2 residues, 2 models selected
> color (#!11 & sel) #50b3bf61
[Repeated 1 time(s)]
> color (#!11 & sel) #f5ccdc61
> color (#!11 & sel) #f5ccdc63
> color (#!11 & sel) #f5ccdcf9
> color (#!11 & sel) #f5ccdcff
> select clear
Drag select of 1 residues
> select add #11/I:59
18 atoms, 8 bonds, 2 residues, 2 models selected
> select clear
> ~distance #11/J:59@CA #11/I:59@CA
> select clear
> select #11/J:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #11/I:59
18 atoms, 16 bonds, 2 residues, 2 models selected
> color (#!11 & sel) byhetero
> select clear
Drag select of 24 atoms, 16 residues, 20 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 9 atoms, 8 residues, 8 bonds
> hide sel atoms
> hide sel cartoons
> select #1/Z:111
5 atoms, 4 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 1/Z
Alignment identifier is 1/Z
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-238
987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected
> show sel cartoons
> ui tool show "Side View"
> select clear
[Repeated 1 time(s)]
> color #5 #f6b93f80
> color #5 #f6a33f80
> color #5 #f6a73f80
> select #6/B:9615@O
1 atom, 1 residue, 1 model selected
> select subtract #6.2
1 model selected
> select add #6.2
2066 atoms, 2066 residues, 1 model selected
> select subtract #6.2
1 model selected
> color #6.3 #50b3bf73
> select #1/Z:33
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:32
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:32-33
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/Z:31
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:31-39
45 atoms, 44 bonds, 9 residues, 1 model selected
> select #1/Z:23
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/Z:23-45
112 atoms, 111 bonds, 23 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/Z:228
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:228
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:291@O
1 atom, 1 residue, 1 model selected
> select add #6.3
386 atoms, 386 residues, 2 models selected
> select subtract #6.3
1 atom, 1 residue, 3 models selected
> select add #6.2
2067 atoms, 2067 residues, 2 models selected
> select subtract #6.2
1 atom, 1 residue, 3 models selected
> select add #6.1
3239 atoms, 3239 residues, 3 models selected
> select subtract #6.1
1 model selected
> select #6/A:2100@O
1 atom, 1 residue, 1 model selected
> select add #6.1.1
1 atom, 1 residue, 3 models selected
> select subtract #6.1.1
1 atom, 1 residue, 2 models selected
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 8730 of 31532 triangles
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 7934 of 31532 triangles
> select #6/A:279@O
1 atom, 1 residue, 1 model selected
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 2470 of 31532 triangles
> select #6/A:189@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:279@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:382@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:286@O
1 atom, 1 residue, 1 model selected
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 2328 of 31532 triangles
> hide #!1,5-6,11 surfaces
> show #!1,5-6,11 surfaces
> hide #!1,5-6,11 surfaces
> select add #6
5690 atoms, 4616 bonds, 5690 residues, 3 models selected
> select subtract #6
3 models selected
> select add #6.1
3239 atoms, 3239 residues, 3 models selected
> select add #6.2
5305 atoms, 5305 residues, 4 models selected
> select add #6.3
5690 atoms, 5690 residues, 5 models selected
> show sel surfaces
> select clear
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 2577 of 31532 triangles
> select #6/A:279@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:210@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:189@O
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select add #6.3
386 atoms, 386 residues, 2 models selected
> select add #6.1.1
386 atoms, 386 residues, 4 models selected
> select subtract #6.3
1 atom, 1 residue, 4 models selected
> select subtract #6.1.1
1 atom, 1 residue, 2 models selected
> select add #6.1.1
1 atom, 1 residue, 3 models selected
> select subtract #6.1.1
1 atom, 1 residue, 2 models selected
> select add #6.1.1
1 atom, 1 residue, 3 models selected
> hide sel surfaces
> select subtract #6.1.1
1 atom, 1 residue, 2 models selected
> select add #6.1.1
1 atom, 1 residue, 3 models selected
> select #6/A:662@O
1 atom, 1 residue, 1 model selected
> select add #6.2
2067 atoms, 2067 residues, 2 models selected
> select subtract #6.2
1 atom, 1 residue, 3 models selected
> select add #6.3
386 atoms, 386 residues, 2 models selected
> select subtract #6.3
1 atom, 1 residue, 3 models selected
> select #6/A:521@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:191@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 1148 of 31532 triangles
> select #6/A:537@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:286@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:190@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 2809 of 31532 triangles
> select #6/A:417@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:321@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:382@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:282@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:193@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:662@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:280@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:291@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:241@O
1 atom, 1 residue, 1 model selected
> select #6/A:295@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:386@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:202@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:194@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:199@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:281@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:664@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:474@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:424@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:445@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:555@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:729@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:547@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:133@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:131@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:128@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:206@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:129@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:659@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:763@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:737@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
[Repeated 1 time(s)]
> select #6/A:508@O
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel surfaces
> select #6/A:516@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:349@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:139@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:562@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:648@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:751@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:633@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:660@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:513@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:242@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:365@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:769@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:352@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 30 of 31532 triangles
> select clear
[Repeated 1 time(s)]
> select #6/A:490@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:241@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:222@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:427@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:468@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:609@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:499@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:224@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:135@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:339@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:207@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:203@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:200@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:196@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:392@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:209@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:213@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:520@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:852@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:519@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 49 of 31532 triangles
> select clear
[Repeated 2 time(s)]
> select #6/A:854@O
1 atom, 1 residue, 1 model selected
> select #6/A:197@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:931@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:851@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:932@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:948@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:958@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:782@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:680@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:876@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:663@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:569@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:528@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:538@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:312@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
[Repeated 1 time(s)]
> select #6/A:408@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:303@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:296@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:322@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:130@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:211@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:201@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:216@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:220@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:536@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:527@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:623@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:554@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:443@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:974@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
[Repeated 1 time(s)]
> select #6/A:745@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:761@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:735@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:815@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:967@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
[Repeated 2 time(s)]
> select #6/A:968@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:788@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #6/A:741@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:600@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:384@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:283@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:581@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
[Repeated 1 time(s)]
> select #6/A:829@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:750@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #6/A:2118@O
1 atom, 1 residue, 1 model selected
> select add #6.1
3239 atoms, 3239 residues, 4 models selected
> select subtract #6.1
1 model selected
> select add #6.1.1
1 model selected
> select subtract #6.1.1
Nothing selected
> select add #6.1.2
1 model selected
> select subtract #6.1.2
Nothing selected
> select add #6.2
2066 atoms, 2066 residues, 2 models selected
> select subtract #6.2
1 model selected
> select add #6.2
2066 atoms, 2066 residues, 2 models selected
> select subtract #6.2
1 model selected
> select add #6.3
385 atoms, 385 residues, 2 models selected
> select subtract #6.3
1 model selected
> hide #!5 models
> show #!5 models
> select add #5
7091 atoms, 5298 bonds, 7091 residues, 1 model selected
> show sel surfaces
> select clear
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> lighting soft
> select clear
> select #6/A:2013@O
1 atom, 1 residue, 1 model selected
> select clear
> color #6 #508ebf60
> color #6 #50abbf60
> color #6 #50a7bf60
> color #6 #b9bec860
> color #6 #b8bfc860
> color #6 #b7bfc860
> color #6 #b6bfc860
> color #6 #c89e9d60
> color #6 #8bc8a060
> color #6 #76c8b460
> color #6 #74c0c860
> color #6 #63b2c860
> color #6 #5bb4c860
> color #6 #6cb1c860
> color #6 #76c2c860
> color #6 #6cc0c860
> color #6 #69c2c860
> color #6 #6cc4c860
> color #6 #6cc4c868
> color #6 #65b8bc68
> color #6 #65b8bc69
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.png"
> width 1660 height 1151 supersample 3 transparentBackground true
> color #5 #f6a73fad
> color #5 #f6a73f99
> color #5 #efd85899
> color #5 #efc36299
> color #5 #efbd7799
> color #5 #efb96c99
> ui tool show "Color Actions"
> color sandy brown
> undo
> color #5 #ecc08499
> color #5 #ecbc8099
> color #6 #65b8bca8
> color #6 #65b8bcb3
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.png"
> width 1660 height 1151 supersample 3 transparentBackground true
> select #1/Z:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:89-94
30 atoms, 29 bonds, 6 residues, 1 model selected
> select #1/Z:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:89-107
95 atoms, 94 bonds, 19 residues, 1 model selected
> color (#!1 & sel) #008f00ff
[Repeated 1 time(s)]
> color (#!1 & sel) #008f00f2
> color (#!1 & sel) #008f00dd
> color (#!1 & sel) #008f00da
> color (#!1 & sel) #008f00ca
> color (#!1 & sel) #008f00ba
> color (#!1 & sel) #008f00b7
> color (#!1 & sel) #008f00af
> color (#!1 & sel) #008f00a6
> color (#!1 & sel) #008f00c1
> color (#!1 & sel) #008f00d2
> color (#!1 & sel) #008f00d3
> color (#!1 & sel) #008f00de
> color (#!1 & sel) #008f00ff
> select clear
> select #1/Z:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:89-107
95 atoms, 94 bonds, 19 residues, 1 model selected
> hide sel cartoons
> select #1/Z:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:89-110
110 atoms, 109 bonds, 22 residues, 1 model selected
> hide sel cartoons
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.png"
> width 1660 height 1151 supersample 3 transparentBackground true
> select #1/Z:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:89-108
100 atoms, 99 bonds, 20 residues, 1 model selected
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.cxs"
> includeMaps true
> select #1/Z:221
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:221-224
18 atoms, 17 bonds, 4 residues, 1 model selected
> select #1/Z:199
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:199-204
30 atoms, 29 bonds, 6 residues, 1 model selected
> select #1/Z:239-240
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/Z:239-315
555 atoms, 564 bonds, 77 residues, 1 model selected
> hide sel cartoons
> hide #!6 models
> hide #!5 models
> hide #!11 models
> hide sel atoms
> select clear
> select #1/Z:89
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:89-111
115 atoms, 114 bonds, 23 residues, 1 model selected
> show sel cartoons
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA
> exH6H7.png" width 1660 height 1151 supersample 3 transparentBackground true
> select #1/Z:239-240
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/Z:239-315
555 atoms, 564 bonds, 77 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/Z:238
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-238
987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected
> hide sel cartoons
> show #!6 models
> show #!5 models
> select
> #1/Z:2-22,46-49,59-78,89-107,112-133,195-197,199-218,221-232,239-274,281-314
1117 atoms, 1117 bonds, 191 residues, 1 model selected
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!11 models
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA H6H7.png"
> width 1660 height 1151 supersample 3 transparentBackground true
> select #1/Z:202
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:202
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:187
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:187
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add #11.12
535 atoms, 74 residues, 1 model selected
> show sel atoms
> select add #1.21
2123 atoms, 339 residues, 3 models selected
> select subtract #11.12
1588 atoms, 265 residues, 3 models selected
> hide sel atoms
> undo
[Repeated 3 time(s)]
> select subtract #11.12
1 model selected
Cell requested for row 0 is out of bounds for table with 64 rows! Resizing
table model.
> hide #!1 models
> select add #11.15
535 atoms, 74 residues, 1 model selected
> select subtract #11.15
1 model selected
> select add #11.12
535 atoms, 74 residues, 1 model selected
> show sel atoms
> select subtract #11.12
1 model selected
> select add #11
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> select subtract #11
26 models selected
> undo
[Repeated 3 time(s)]
> select subtract #11.12
1 model selected
> select add #11.12
535 atoms, 74 residues, 1 model selected
> show sel cartoons
Alignment identifier is 11/K
> select #11/K:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/K:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> show sel atoms
> select #11/K:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/K:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add #11.12
535 atoms, 74 residues, 1 model selected
> hide sel cartoons
> select clear
> select #11/K:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/K:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
> select clear
> select #11/K:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/K:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!11 & sel) byhetero
> select clear
> select #11/K:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/K:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/K:60
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/K:60-61
13 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #11/K:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/K:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> select add #5
7091 atoms, 5298 bonds, 7091 residues, 4 models selected
> select add #6
12781 atoms, 9914 bonds, 12781 residues, 9 models selected
> select clear
> select #5/F:8194@O
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #1/Z:298
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #11/K:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #11/K:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> color #6 #65b8bcbe
[Repeated 1 time(s)]
> color #6 #65b8bcbf
> color #5 #ecbc80ae
> color #5 #ecbc80bf
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA H6H7.png"
> width 1660 height 1151 supersample 3 transparentBackground true
> select #1/Z:1-2
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/Z
1542 atoms, 1550 bonds, 1 pseudobond, 278 residues, 2 models selected
> show sel cartoons
> select clear
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-238
987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected
> hide sel cartoons
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA H6H7.png"
> width 1660 height 1151 supersample 3 transparentBackground true
> select #1/Z:239-241
15 atoms, 14 bonds, 3 residues, 1 model selected
> select #1/Z:239-315
555 atoms, 564 bonds, 77 residues, 1 model selected
> select #1/Z:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:1-238
987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected
> show sel cartoons
> select #1/Z:239
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:239-315
555 atoms, 564 bonds, 77 residues, 1 model selected
> hide sel cartoons
> hide #!5 models
> hide #!6 models
> hide #!11 models
> hide sel atoms
> select clear
> select #1/Z:35
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:35
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:35-44
48 atoms, 47 bonds, 10 residues, 1 model selected
> select #1/Z:23
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/Z:23-35
64 atoms, 63 bonds, 13 residues, 1 model selected
> select #1/Z:24-25
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/Z:24-35
60 atoms, 59 bonds, 12 residues, 1 model selected
> hide sel cartoons
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA
> exH6H7.png" width 1660 height 1151 supersample 3 transparentBackground true
> select #1/Z:227
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/Z:228
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/Z:1-7
35 atoms, 34 bonds, 7 residues, 1 model selected
> select #1/Z
1542 atoms, 1550 bonds, 1 pseudobond, 278 residues, 2 models selected
> show sel cartoons
> select clear
> show #!5 models
> show #!6 models
> show #!11 models
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.cxs"
> includeMaps true
——— End of log from Thu Mar 27 15:32:10 2025 ———
opened ChimeraX session
> ui tool show "Model Panel"
> hide #!6 models
> hide #!5 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!1 models
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> show sel cartoons
> select subtract #1.21
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel cartoons
> ui tool show "Side View"
> ui mousemode right select
Drag select of 10 atoms, 8 bonds
> hide sel atoms
Drag select of 30 atoms, 6 residues, 25 bonds
> hide sel atoms
> hide sel cartoons
> select add #11
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 7 models selected
> select subtract #11
26 models selected
> select add #11.9
543 atoms, 75 residues, 1 model selected
> select add #11.10
1059 atoms, 147 residues, 2 models selected
> select add #11.11
1594 atoms, 221 residues, 3 models selected
> select add #11.13
2137 atoms, 296 residues, 4 models selected
> select add #11.12
2672 atoms, 370 residues, 5 models selected
> show sel cartoons
> hide sel cartoons
> select subtract #11.9
2129 atoms, 295 residues, 6 models selected
> select subtract #11.10
1613 atoms, 223 residues, 5 models selected
> select subtract #11.11
1078 atoms, 149 residues, 4 models selected
> select subtract #11.12
543 atoms, 75 residues, 3 models selected
> select subtract #11.13
1 model selected
> select add #11.14
535 atoms, 74 residues, 1 model selected
> select add #11.15
1070 atoms, 148 residues, 2 models selected
> select add #11.16
1613 atoms, 223 residues, 3 models selected
> select add #11.17
2156 atoms, 298 residues, 4 models selected
> select add #11.18
2683 atoms, 371 residues, 5 models selected
> show sel cartoons
Alignment identifier is 11/Q
Alignment identifier is 1
Alignment identifier is 2
> select clear
> select #11/N,M:3
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #11/N,M
1070 atoms, 1086 bonds, 148 residues, 1 model selected
> hide sel cartoons
> select #11/N,M:58
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #11/N,M:58-61
58 atoms, 56 bonds, 8 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> select #11/P,O:58
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #11/P,O:58-60
42 atoms, 40 bonds, 6 residues, 1 model selected
> select #11/P,O:3
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #11/P,O
1086 atoms, 1102 bonds, 150 residues, 1 model selected
> hide sel cartoons
> select #11/P,O:58
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #11/P,O:58-61
58 atoms, 56 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #11/Q:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/Q
527 atoms, 535 bonds, 73 residues, 1 model selected
> hide sel cartoons
> select #11/Q:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/Q:58-61
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel cartoons
> select clear
Drag select of 13 residues
> hide sel cartoons
Drag select of 9 residues
> hide sel cartoons
> select clear
Drag select of 7 residues
> show sel cartoons
> ~hbonds
Alignment identifier is 1/T
> select #1/T:241
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/T:241-250
78 atoms, 78 bonds, 10 residues, 1 model selected
> show sel cartoons
> select clear
> show #!4 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!8 models
> hide #!1 models
> hide #!11 models
> show #!2 models
> show #!4 models
> ui tool show Matchmaker
> matchmaker #1/T to #8/T pairing ss
Parameters
---
Chain pairing | ss
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 RfxATP_state_1_Fo-4-coot-0.pdb, chain T (#8) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#1), sequence
alignment score = 1188.2
RMSD between 144 pruned atom pairs is 1.326 angstroms; (across all 265 pairs:
3.573)
> matchmaker #1/T to #8/T pairing ss
Parameters
---
Chain pairing | ss
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 RfxATP_state_1_Fo-4-coot-0.pdb, chain T (#8) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#1), sequence
alignment score = 1188.2
RMSD between 144 pruned atom pairs is 1.326 angstroms; (across all 265 pairs:
3.573)
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!8 models
> select add #1.18
527 atoms, 73 residues, 1 model selected
> select add #1.17
1070 atoms, 148 residues, 2 models selected
> select add #1.16
1613 atoms, 223 residues, 3 models selected
> select add #1.15
2148 atoms, 297 residues, 4 models selected
> select add #1.14
2683 atoms, 371 residues, 5 models selected
> show sel cartoons
Alignment identifier is 1/Q
Alignment identifier is 1
Alignment identifier is 2
> hide sel cartoons
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Q:59-60
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1/P,O:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/P,O:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel cartoons
> select #1/N,M:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/N,M:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel cartoons
> select clear
> cartoon style #1-2,4 xsection oval modeHelix default
> select clear
> undo
> cartoon style #1-2,4 modeHelix tube sides 20
> select clear
> hide #!4 models
> show #!11 models
> ui tool show Matchmaker
> matchmaker #11/T to #8/T pairing ss
Parameters
---
Chain pairing | ss
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 RfxATP_state_1_Fo-4-coot-0.pdb, chain T (#8) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#11), sequence
alignment score = 1188.2
RMSD between 144 pruned atom pairs is 1.326 angstroms; (across all 265 pairs:
3.573)
> matchmaker #11/T to #8/T pairing ss
Parameters
---
Chain pairing | ss
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 RfxATP_state_1_Fo-4-coot-0.pdb, chain T (#8) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#11), sequence
alignment score = 1188.2
RMSD between 144 pruned atom pairs is 1.326 angstroms; (across all 265 pairs:
3.573)
> select add #11
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> select subtract #11.2
34187 atoms, 34634 bonds, 3 pseudobonds, 4874 residues, 28 models selected
> select subtract #11.3
30394 atoms, 30783 bonds, 3 pseudobonds, 4378 residues, 27 models selected
> select subtract #11.4
26572 atoms, 26903 bonds, 3 pseudobonds, 3878 residues, 26 models selected
> select subtract #11.5
22978 atoms, 23246 bonds, 3 pseudobonds, 3409 residues, 25 models selected
> select subtract #11.7
19392 atoms, 19597 bonds, 3 pseudobonds, 2941 residues, 24 models selected
> select subtract #11.6
15787 atoms, 15929 bonds, 3 pseudobonds, 2471 residues, 23 models selected
> select subtract #11.8
13505 atoms, 13619 bonds, 3 pseudobonds, 2182 residues, 22 models selected
> select subtract #11.19
12425 atoms, 12529 bonds, 3 pseudobonds, 2044 residues, 21 models selected
> select subtract #11.20
12060 atoms, 12165 bonds, 3 pseudobonds, 1970 residues, 20 models selected
> select subtract #11.21
10472 atoms, 10562 bonds, 1 pseudobond, 1705 residues, 19 models selected
> select subtract #11.22
9725 atoms, 9816 bonds, 1 pseudobond, 1555 residues, 18 models selected
> select subtract #11.23
8967 atoms, 9059 bonds, 1 pseudobond, 1404 residues, 17 models selected
> select subtract #11.24
8602 atoms, 8695 bonds, 1 pseudobond, 1330 residues, 16 models selected
> select subtract #11.25
7860 atoms, 7954 bonds, 1 pseudobond, 1181 residues, 15 models selected
> select subtract #11.27
6318 atoms, 6404 bonds, 903 residues, 13 models selected
> select subtract #11.26
5566 atoms, 5653 bonds, 752 residues, 12 models selected
> show sel cartoons
Alignment identifier is 11/I
Alignment identifier is 11/Q
Alignment identifier is 1
Alignment identifier is 2
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 4 residues
> select clear
> select #1/N:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/O:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/P:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show #!4 models
> select #11/N,M,K,J:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #11/N,M,K,J:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #11/P,O,L,H:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #11/P,O,L,H:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
Drag select of 5 residues
> hide sel cartoons
Drag select of 1 residues
> select clear
> undo
Drag select of 1 residues
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/Q:59-60
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/Q:59-60
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #4/F:4727@O
1 atom, 1 residue, 1 model selected
> select add #4.4
1328 atoms, 1328 residues, 2 models selected
> select subtract #4.4
1 atom, 1 residue, 3 models selected
> select subtract #4.1
1 model selected
> select add #4.1
230 atoms, 230 residues, 1 model selected
> hide sel surfaces
> select clear
> select #1/T:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add #1.9
543 atoms, 75 residues, 1 model selected
> select add #1.10
1059 atoms, 147 residues, 2 models selected
> select add #1.11
1594 atoms, 221 residues, 3 models selected
> select add #1.12
2129 atoms, 295 residues, 4 models selected
> select add #1.13
2672 atoms, 370 residues, 5 models selected
> select subtract #1.10
2156 atoms, 298 residues, 6 models selected
> select subtract #1.9
1613 atoms, 223 residues, 5 models selected
> select subtract #1.11
1078 atoms, 149 residues, 4 models selected
> select subtract #1.12
543 atoms, 75 residues, 3 models selected
> select subtract #1.13
1 model selected
> select add #1.18
527 atoms, 73 residues, 1 model selected
> select add #1.17
1070 atoms, 148 residues, 2 models selected
> select add #1.16
1613 atoms, 223 residues, 3 models selected
> select add #1.15
2148 atoms, 297 residues, 4 models selected
> select add #1.14
2683 atoms, 371 residues, 5 models selected
> show sel cartoons
> select clear
> hide #!1-2,4,11 cartoons
> undo
> select add #1.18
527 atoms, 73 residues, 1 model selected
> select add #1.17
1070 atoms, 148 residues, 2 models selected
> select add #1.16
1613 atoms, 223 residues, 3 models selected
> select add #1.15
2148 atoms, 297 residues, 4 models selected
> select add #1.14
2683 atoms, 371 residues, 5 models selected
> hide sel cartoons
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 7 models selected
> select subtract #1
26 models selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> select subtract #2
4 models selected
> color #2 #efd6d180
> color #2 #efd6d1be
> color #2 #ecbc80be
> color #4 #65b8bc7f
> color #4 #65b8bcc4
> color #4 #65b8bcc0
> select clear
> select #11/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #11/P:59
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add #11/O:59
27 atoms, 24 bonds, 3 residues, 3 models selected
> select add #11/N:59
36 atoms, 32 bonds, 4 residues, 4 models selected
> select add #11/M:59
45 atoms, 40 bonds, 5 residues, 5 models selected
> show sel atoms
> select clear
> select #1/T:27
5 atoms, 4 bonds, 1 residue, 1 model selected
Alignment identifier is 1/T
> select #1/T:27
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:27-58
133 atoms, 131 bonds, 1 pseudobond, 23 residues, 2 models selected
> hide sel cartoons
> select clear
> select #1/T:148
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:135-136
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/T:135-190
72 atoms, 70 bonds, 1 pseudobond, 15 residues, 2 models selected
> hide sel cartoons
> select clear
> select #4/I:483@O
1 atom, 1 residue, 1 model selected
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a1hollow+AA 整体.png"
> width 1660 height 1174 supersample 3 transparentBackground true
> save "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a1hollow+AA 整体.cxs"
> hide #!2 models
> hide #!4 models
> hide #!11 models
> coulombic #!1
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 85
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S PRO 86
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 87
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 88
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 90
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 91
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 92
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 93
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 95
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 96
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 97
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 98
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S PRO 99
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 100
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 101
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 102
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 103
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 104
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 105
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 106
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 107
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 108
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 109
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LYS 110
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 112
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S TYR 113
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S PRO 115
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASP 116
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 117
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 118
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 119
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 120
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S PHE 121
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 122
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 123
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASP 124
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 125
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 126
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 127
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 128
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 131
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 132
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 133
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 134
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 135
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASP 137
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 138
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 139
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 140
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASP 141
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 142
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 143
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 144
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 145
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 146
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 147
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S MET 148
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 151
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 152
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 153
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASN 154
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S MET 155
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S MET 156
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 157
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T MET 1
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 2
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 3
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 4
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 5
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 6
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 7
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 8
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 9
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 11
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 12
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 13
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 15
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 17
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 18
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 19
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 20
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 21
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 22
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 24
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 25
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 26
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 27
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LYS 28
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 29
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T HIS 30
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 31
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 32
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 33
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 55
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 56
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 57
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 58
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 59
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 60
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 61
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 62
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 63
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 64
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 65
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 66
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 67
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 68
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 70
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 71
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 72
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 73
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 75
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 76
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 89
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLN 90
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 91
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 92
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 93
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLU 94
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 95
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T MET 96
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 97
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLU 98
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 100
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 101
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 102
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 103
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLN 105
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 106
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 107
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASP 108
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 109
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 110
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 111
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 112
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LYS 114
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 135
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 136
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 138
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 140
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 141
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 143
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T CYS 144
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 145
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 146
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 147
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 190
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 191
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 192
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 193
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 195
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 196
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASP 198
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 199
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 200
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 201
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 202
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 203
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TRP 205
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 207
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 208
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 209
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 210
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 212
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 213
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLN 214
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 215
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 216
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 218
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLN 219
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 221
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 223
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 225
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 226
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 227
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LYS 228
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 229
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 230
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 231
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 232
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 233
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLU 234
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 236
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 271
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 272
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 273
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T MET 274
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 276
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 277
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 278
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 279
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 280
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 281
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 282
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 283
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 285
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 286
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 287
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 11
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 12
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 14
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 15
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 16
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 17
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 18
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 19
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U PHE 20
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 21
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 22
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U TRP 23
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 24
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 25
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 26
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 27
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U PHE 28
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 29
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U TYR 30
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 31
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U PRO 32
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 33
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 34
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 35
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U MET 36
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 37
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 38
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 39
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 40
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 41
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 42
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 43
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 44
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 45
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 46
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 48
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 49
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 50
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 52
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 53
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 54
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 55
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 56
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 57
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 58
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 60
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 62
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 63
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 64
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U TYR 65
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 66
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 68
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 69
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 71
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 73
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 74
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 75
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U SER 78
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 79
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 80
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 82
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 84
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 85
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 86
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 88
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 90
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 93
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 94
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 95
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 97
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U HIS 99
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 100
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 101
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 103
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 104
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 105
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 106
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U SER 107
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 108
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 109
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 110
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 112
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 114
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 115
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 116
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 117
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 118
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 119
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U MET 120
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 121
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 123
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 124
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 125
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 126
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 127
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U MET 128
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 130
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 131
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 132
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 133
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 134
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 135
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 137
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 138
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 139
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 140
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 141
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 143
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 144
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 145
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 147
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U HIS 148
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 149
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 150
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 151
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 152
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 153
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 154
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U SER 155
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 156
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 158
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 159
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V TRP 8
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 10
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 11
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 12
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 14
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 15
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 16
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 17
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 18
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 19
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V PHE 20
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 21
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 22
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V TRP 23
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 24
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 25
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 26
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 27
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V PHE 28
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 29
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V TYR 30
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 31
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V PRO 32
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 33
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 34
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 35
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V MET 36
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 37
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 38
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 39
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 40
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 41
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 42
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 43
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 44
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 45
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 46
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 48
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 49
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 50
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 52
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 53
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 54
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 55
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 56
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 57
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 58
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 60
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 62
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 63
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 64
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V TYR 65
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 66
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 68
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 69
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 71
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 73
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 74
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 75
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V SER 78
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 79
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 80
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 82
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 84
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 85
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 86
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 88
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 90
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 93
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 94
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 95
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 97
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V HIS 99
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 100
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 101
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 103
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 104
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 105
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 106
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V SER 107
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 108
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 109
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 110
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 112
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 114
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 115
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 116
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 117
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 118
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 119
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V MET 120
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 121
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 123
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 124
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 125
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 126
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 127
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V MET 128
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 130
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 131
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 132
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 133
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 134
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 135
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 137
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 138
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 139
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 140
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 141
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 143
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 144
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 145
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 147
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V HIS 148
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 149
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 150
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 151
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 152
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 153
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 154
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V SER 155
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 156
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 85
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W PRO 86
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 87
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 88
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 90
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 91
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 92
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 93
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 95
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 96
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 97
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 98
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W PRO 99
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 100
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 101
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 102
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 103
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 104
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 105
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 106
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 107
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 108
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 109
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LYS 110
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 112
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W TYR 113
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W PRO 115
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASP 116
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 117
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 118
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 119
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 120
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W PHE 121
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 122
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 123
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASP 124
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 125
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 126
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 127
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 128
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 131
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 132
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 133
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 134
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 135
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASP 137
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 138
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 139
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 140
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASP 141
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 142
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 143
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 144
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 145
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 146
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 147
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W MET 148
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 151
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 152
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 153
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASN 154
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W MET 155
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W MET 156
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 157
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 12
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 14
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 15
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 16
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 17
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 18
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 19
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X PHE 20
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 21
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 22
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X TRP 23
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 24
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 25
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 26
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 27
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X PHE 28
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 29
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X TYR 30
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 31
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X PRO 32
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 33
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 34
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 35
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X MET 36
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 37
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 38
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 39
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 40
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 41
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 42
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 43
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 44
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 45
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 46
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 48
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 49
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 50
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 52
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 53
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 54
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 55
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 56
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 57
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 58
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 60
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 62
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 63
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 64
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X TYR 65
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 66
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 68
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 69
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 71
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 73
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 74
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 75
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X SER 78
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 79
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 80
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 82
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 84
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 85
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 86
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 88
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 90
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 93
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 94
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 95
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 97
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X HIS 99
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 100
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 101
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 103
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 104
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 105
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 106
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X SER 107
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 108
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 109
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 110
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 112
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 114
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 115
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 116
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 117
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 118
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 119
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X MET 120
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 121
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 123
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 124
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 125
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 126
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 127
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X MET 128
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 130
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 131
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 132
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 133
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 134
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 135
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 137
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 138
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 139
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 140
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 141
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 143
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 144
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 145
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 147
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X HIS 148
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 149
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 150
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 151
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 152
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 153
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 154
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X SER 155
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 156
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 158
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 159
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y TRP 8
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 10
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 11
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 12
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 14
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 15
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 16
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 17
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 18
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 19
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y PHE 20
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 21
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 22
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y TRP 23
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 24
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 25
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 26
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 27
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y PHE 28
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 29
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y TYR 30
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 31
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y PRO 32
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 33
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 34
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 35
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y MET 36
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 37
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 38
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 39
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 40
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 41
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 42
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 43
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 44
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 45
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 46
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 48
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 49
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 50
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 52
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 53
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 54
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 55
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 56
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 57
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 58
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 60
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 62
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 63
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 64
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y TYR 65
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 66
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 68
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 69
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 71
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 73
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 74
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 75
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y SER 78
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 79
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 80
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 82
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 84
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 85
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 86
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 88
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 90
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 93
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 94
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 95
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 97
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y HIS 99
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 100
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 101
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 103
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 104
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 105
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 106
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y SER 107
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 108
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 109
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 110
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 112
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 114
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 115
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 116
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 117
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 118
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 119
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y MET 120
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 121
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 123
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 124
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 125
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 126
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 127
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y MET 128
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 130
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 131
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 132
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 133
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 134
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 135
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 137
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 138
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 139
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 140
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 141
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 143
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 144
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 145
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 147
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y HIS 148
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 149
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 150
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 151
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 152
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 153
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 154
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y SER 155
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 156
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 158
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 1
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 2
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 3
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 4
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 5
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 6
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 7
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 8
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 9
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 11
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 12
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 13
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 15
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 17
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 18
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 19
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 20
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 21
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 22
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 24
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 25
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 26
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 27
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LYS 28
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 29
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z HIS 30
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 31
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 32
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 33
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 36
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 37
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 38
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 39
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z CYS 40
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 41
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 45
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 47
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 48
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 49
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 50
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z CYS 51
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 53
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 55
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 56
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 57
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 58
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 59
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 60
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 61
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 62
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 63
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 64
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 65
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 66
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 67
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 68
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 70
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 71
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 72
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 73
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 75
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 76
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 79
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 80
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 82
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 83
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 84
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 85
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 86
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 87
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 89
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 90
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 91
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 92
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 93
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 94
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 95
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 96
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 97
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 98
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 100
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 101
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 102
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 103
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 105
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 106
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 107
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASP 108
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 109
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 110
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 111
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 112
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LYS 114
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 115
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 116
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 117
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 118
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z CYS 119
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 121
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 123
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 124
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 125
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 126
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 127
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 128
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 129
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 130
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 131
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 132
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 134
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 135
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 136
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 138
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 140
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 141
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 143
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z CYS 144
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 145
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 146
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 147
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 186
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 187
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 188
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 189
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 190
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 191
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 192
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 193
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 195
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 196
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASP 198
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 199
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 200
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 201
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 202
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 203
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TRP 205
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 207
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 208
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 209
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 210
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 212
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 213
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 214
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 215
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 216
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 218
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 219
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 221
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 223
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 225
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 226
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 227
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LYS 228
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 229
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 230
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 231
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 232
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 233
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 234
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 236
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 237
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 240
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 241
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 274
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 276
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 277
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 278
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 279
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 280
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 281
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 282
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 283
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 285
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 286
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 287
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_A SES
surface #1.2: minimum, -18.27, mean -1.83, maximum 13.91
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_B SES
surface #1.3: minimum, -15.47, mean -1.37, maximum 13.82
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_C SES
surface #1.4: minimum, -16.31, mean -1.63, maximum 13.40
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_D SES
surface #1.5: minimum, -28.87, mean -2.68, maximum 10.52
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_E SES
surface #1.6: minimum, -20.09, mean -2.56, maximum 8.70
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_F SES
surface #1.7: minimum, -18.01, mean -2.95, maximum 8.98
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_G SES
surface #1.8: minimum, -16.97, mean 1.81, maximum 17.95
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_H SES
surface #1.9: minimum, -10.11, mean -0.93, maximum 7.53
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_I SES
surface #1.10: minimum, -10.05, mean -0.85, maximum 6.44
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_J SES
surface #1.11: minimum, -12.46, mean -0.37, maximum 8.45
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_K SES
surface #1.12: minimum, -11.92, mean -0.41, maximum 9.98
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_L SES
surface #1.13: minimum, -10.16, mean -0.92, maximum 7.70
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_M SES
surface #1.14: minimum, -9.92, mean -0.18, maximum 9.75
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_N SES
surface #1.15: minimum, -10.12, mean -0.53, maximum 8.00
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_O SES
surface #1.16: minimum, -10.15, mean -0.67, maximum 9.21
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_P SES
surface #1.17: minimum, -11.20, mean -1.02, maximum 7.64
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Q SES
surface #1.18: minimum, -10.56, mean -0.41, maximum 7.82
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_R SES
surface #1.19: minimum, -19.83, mean -2.00, maximum 12.65
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_S SES
surface #1.20: minimum, -13.38, mean -0.26, maximum 7.63
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_T SES
surface #1.21: minimum, -18.46, mean -0.85, maximum 9.62
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_U SES
surface #1.22: minimum, -7.30, mean -1.52, maximum 9.63
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_V SES
surface #1.23: minimum, -9.18, mean -1.53, maximum 10.50
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_W SES
surface #1.24: minimum, -13.86, mean -0.26, maximum 7.70
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_X SES
surface #1.25: minimum, -8.05, mean -1.46, maximum 9.60
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Y SES
surface #1.26: minimum, -8.08, mean -1.63, maximum 9.55
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Z SES
surface #1.27: minimum, -13.95, mean -1.49, maximum 9.76
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> select subtract #1.21
36404 atoms, 36894 bonds, 1 pseudobond, 5107 residues, 28 models selected
> hide sel surfaces
> hide sel cartoons
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 27 models selected
> select subtract #1
26 models selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting flat
> lighting full
> select clear
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:249
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:249
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:234
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:234
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:290
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select subtract #1.21
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel surfaces
Alignment identifier is 1/Z
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:265-266
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/Z:265-270
44 atoms, 44 bonds, 6 residues, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268-269
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> color #1.21 #65b8bcff
> select add #1.21
1597 atoms, 8 bonds, 266 residues, 2 models selected
> coulombic sel
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_T SES
surface #1.21: minimum, -18.46, mean -0.85, maximum 9.62
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Z SES
surface #1.27: minimum, -13.95, mean -1.49, maximum 9.76
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #1.21
9 atoms, 8 bonds, 1 residue, 3 models selected
> select add #1.25
751 atoms, 8 bonds, 150 residues, 2 models selected
> select subtract #1.25
9 atoms, 8 bonds, 1 residue, 3 models selected
> select subtract #1.27
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel surfaces
> select clear
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting flat
> lighting full
> lighting shadows false
> lighting soft
> view
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save /Users/wujingyi/Desktop/figure/figure4/state1_a1电势.png width 1660
> height 1174 supersample 3 transparentBackground true
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> hide sel surfaces
> hide sel atoms
> select clear
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel surfaces
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel surfaces
> select subtract #1.27
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!1 atoms
> hide #!1 cartoons
> show #!1 surfaces
> undo
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> select subtract #1.27
1 model selected
> select add #1.1
3 pseudobonds, 1 model selected
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> select subtract #1.27
36450 atoms, 36947 bonds, 2 pseudobonds, 5094 residues, 28 models selected
> hide sel surfaces
> select clear
Drag select of 5 atoms, 12 residues, 5 bonds
> hide sel atoms
> select clear
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> show sel surfaces
> select #1/Z:234@CB
1 atom, 1 residue, 1 model selected
> select clear
> save /Users/wujingyi/Desktop/figure/figure4/state1_a2电势.png width 1660
> height 1174 supersample 3 transparentBackground true
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> select subtract #1.27
1 model selected
> select add #1.9
543 atoms, 75 residues, 1 model selected
> select add #1.10
1059 atoms, 147 residues, 2 models selected
> select add #1.11
1594 atoms, 221 residues, 3 models selected
> select add #1.12
2129 atoms, 295 residues, 4 models selected
> select add #1.14
2664 atoms, 369 residues, 5 models selected
> select add #1.13
3207 atoms, 444 residues, 6 models selected
> select add #1.15
3742 atoms, 518 residues, 7 models selected
> select add #1.16
4285 atoms, 593 residues, 8 models selected
> select add #1.17
4828 atoms, 668 residues, 9 models selected
> select add #1.18
5355 atoms, 741 residues, 10 models selected
> show sel surfaces
> select clear
> view
> save /Users/wujingyi/Desktop/figure/figure4/state1_c-ring电势.png width 1660
> height 1174 supersample 3 transparentBackground true
> save /Users/wujingyi/Desktop/figure/figure4/state1_c-ring电势图.cxs
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> select subtract #1.27
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel surfaces
> select add #1.26
2294 atoms, 429 residues, 2 models selected
> select subtract #1.27
752 atoms, 151 residues, 3 models selected
> select subtract #1.26
1 model selected
> select add #1.20
365 atoms, 74 residues, 1 model selected
> select add #1.19
1445 atoms, 212 residues, 2 models selected
> select subtract #1.20
1080 atoms, 138 residues, 3 models selected
> select subtract #1.19
1 model selected
> select add #1.19
1080 atoms, 138 residues, 1 model selected
> select subtract #1.19
1 model selected
> select add #1.18
527 atoms, 73 residues, 1 model selected
> select add #1.17
1070 atoms, 148 residues, 2 models selected
> select add #1.16
1613 atoms, 223 residues, 3 models selected
> select add #1.15
2148 atoms, 297 residues, 4 models selected
> select add #1.14
2683 atoms, 371 residues, 5 models selected
> select add #1.13
3226 atoms, 446 residues, 6 models selected
> select add #1.12
3761 atoms, 520 residues, 7 models selected
> select add #1.11
4296 atoms, 594 residues, 8 models selected
> select add #1.10
4812 atoms, 666 residues, 9 models selected
> select add #1.9
5355 atoms, 741 residues, 10 models selected
> hide sel surfaces
> select #1/Z:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:274@CB
1 atom, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:274@CB
1 atom, 1 residue, 1 model selected
> select #1/Z:276@O
1 atom, 1 residue, 1 model selected
> select #1/Z:263@O
1 atom, 1 residue, 1 model selected
> select subtract #1.27
1 model selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> show sel surfaces
> select clear
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!1 models
> show #!11 models
> hide #!11 models
> hide #!1 models
> show #!1 models
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select subtract #1
26 models selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> select add #1.27
3130 atoms, 543 residues, 2 models selected
> color (#!1 & sel) forest green
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 4 models selected
> select subtract #1
26 models selected
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> select subtract #1.21
36404 atoms, 36894 bonds, 1 pseudobond, 5107 residues, 28 models selected
> select subtract #1.27
34862 atoms, 35344 bonds, 4829 residues, 26 models selected
> hide sel cartoons
> select clear
> show #!11 models
> select add #11.21
1588 atoms, 265 residues, 1 model selected
> select add #11.27
3130 atoms, 543 residues, 2 models selected
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #11/Z to #1/T pairing ss
Parameters
---
Chain pairing | ss
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 J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#1) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain Z (#11), sequence
alignment score = 1208.4
RMSD between 157 pruned atom pairs is 1.357 angstroms; (across all 265 pairs:
3.245)
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel cartoons
> select add #11.21
3130 atoms, 543 residues, 3 models selected
> hide sel cartoons
> ui mousemode right select
Drag select of 30 atoms, 5 residues, 25 bonds
> hide sel atoms
> hide sel cartoons
> cartoon style (#!11 & sel) modeHelix tube sides 20
> select clear
> select add #11.27
1542 atoms, 278 residues, 1 model selected
> color (#!11 & sel) light gray
> select clear
> select add #11.21
1588 atoms, 265 residues, 1 model selected
> select subtract #11.21
1 model selected
> select add #11.27
1542 atoms, 278 residues, 1 model selected
Alignment identifier is 11/Z
> select add #1.21
3130 atoms, 543 residues, 3 models selected
Alignment identifier is 1/T
Destroying pre-existing alignment with identifier 11/Z
Alignment identifier is 11/Z
> select clear
> select #11/Z:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/Z:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select #1/T:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select subtract #1.21
1 model selected
Cell requested for row 0 is out of bounds for table with 37 rows! Resizing
table model.
> hide #!1 models
> hide #!11 models
> show #!8 models
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RfxATP_state_1_Fo-4-coot-2.pdb"
Chain information for RfxATP_state_1_Fo-4-coot-2.pdb #10
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RfxATP_state_1_Fo-4-coot-2.pdb"
Chain information for RfxATP_state_1_Fo-4-coot-2.pdb #12
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!8 models
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select add #12
22294 atoms, 22730 bonds, 4 pseudobonds, 2962 residues, 20 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 34 models selected
> select add #10.2
11697 atoms, 11365 bonds, 2 pseudobonds, 1557 residues, 19 models selected
> select add #10.3
12220 atoms, 11365 bonds, 2 pseudobonds, 1630 residues, 20 models selected
> select add #10.4
12762 atoms, 11365 bonds, 2 pseudobonds, 1705 residues, 21 models selected
> select add #10.5
13304 atoms, 11365 bonds, 2 pseudobonds, 1780 residues, 22 models selected
> select add #10.6
13854 atoms, 11365 bonds, 2 pseudobonds, 1856 residues, 23 models selected
> select add #10.7
14396 atoms, 11365 bonds, 2 pseudobonds, 1931 residues, 24 models selected
> select add #10.8
14938 atoms, 11365 bonds, 2 pseudobonds, 2006 residues, 25 models selected
> select add #10.9
15488 atoms, 11365 bonds, 2 pseudobonds, 2082 residues, 26 models selected
> select add #10.10
16038 atoms, 11365 bonds, 2 pseudobonds, 2158 residues, 27 models selected
> select add #10.11
16572 atoms, 11365 bonds, 2 pseudobonds, 2232 residues, 28 models selected
> select subtract #12
5425 atoms, 751 residues, 27 models selected
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected
> select subtract #10
16 models selected
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #10.17
4464 atoms, 582 residues, 2 models selected
> color (#!10 & sel) forest green
> hide sel atoms
> show sel cartoons
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 4 models selected
> select subtract #10
16 models selected
> select add #12.12
2232 atoms, 291 residues, 1 model selected
> select add #12.17
4464 atoms, 582 residues, 2 models selected
> color (#!12 & sel) light gray
> hide sel atoms
> show sel cartoons
> select subtract #12.17
2232 atoms, 291 residues, 3 models selected
> select subtract #12.12
1 model selected
> select add #12
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> select subtract #12.17
8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected
> select subtract #12.12
6683 atoms, 6791 bonds, 899 residues, 16 models selected
> hide sel cartoons
> hide sel atoms
> select add #12
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 16 models selected
> select subtract #12
16 models selected
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> select subtract #10.12
8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected
> select subtract #10.17
6683 atoms, 6791 bonds, 899 residues, 16 models selected
> hide sel atoms
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 16 models selected
> select subtract #10
16 models selected
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #10.17
4464 atoms, 582 residues, 2 models selected
> show sel cartoons
> select clear
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> select add #10.12
4464 atoms, 582 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> select clear
> show #!10,12 cartoons
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> select clear
> undo
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> select subtract #12.17
1 model selected
> select add #12.12
2232 atoms, 291 residues, 1 model selected
> hide sel cartoons
> select subtract #12.12
1 model selected
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> select subtract #10.17
1 model selected
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> select subtract #10.17
1 model selected
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> hide sel cartoons
> select subtract #10.17
1 model selected
> ui tool show Matchmaker
> matchmaker #12/Z to #10/T pairing ss
Parameters
---
Chain pairing | ss
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 RfxATP_state_1_Fo-4-coot-2.pdb, chain T (#10) with
RfxATP_state_1_Fo-4-coot-2.pdb, chain Z (#12), sequence alignment score =
1380.4
RMSD between 187 pruned atom pairs is 1.074 angstroms; (across all 291 pairs:
2.932)
> matchmaker #12/Z to #10/T pairing ss
Parameters
---
Chain pairing | ss
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 RfxATP_state_1_Fo-4-coot-2.pdb, chain T (#10) with
RfxATP_state_1_Fo-4-coot-2.pdb, chain Z (#12), sequence alignment score =
1380.4
RMSD between 187 pruned atom pairs is 1.074 angstroms; (across all 291 pairs:
2.932)
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #12.17
4464 atoms, 582 residues, 3 models selected
Alignment identifier is 1
> select #10/T:30 #12/Z:30
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #10/T:30 #12/Z:30
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [30] RMSD: 0.804
> show sel atoms
> select #10/T:130 #12/Z:130
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #10/T:130 #12/Z:130
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [130] RMSD: 0.879
> show sel atoms
> select #10/T:140 #12/Z:140
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #10/T:140 #12/Z:140
12 atoms, 10 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [140] RMSD: 3.423
> show sel atoms
> select #10/T:187 #12/Z:187
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #10/T:187 #12/Z:187
14 atoms, 12 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [163] RMSD: 2.893
> show sel atoms
> select #10/T:263 #12/Z:263
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #10/T:263 #12/Z:263
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [239] RMSD: 0.744
> select #10/T:263,268 #12/Z:263,268
34 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region chains T,Z [239] + 1 other block RMSD: 0.813
> show sel atoms
> select #10/T:259 #12/Z:259
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #10/T:259 #12/Z:259
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [235] RMSD: 0.890
> show sel atoms
> select #10/T:252 #12/Z:252
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #10/T:252 #12/Z:252
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [228] RMSD: 0.342
> show sel atoms
> select #10/T:2-22,59-78,88-108,116-133,199-220,224-230,237-278,282-314
> #12/Z:2-22,59-78,88-108,116-133,199-220,224-230,237-278,282-314
2874 atoms, 2928 bonds, 368 residues, 2 models selected
> select #10/T:248 #12/Z:248
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #10/T:248-249 #12/Z:248-249
30 atoms, 28 bonds, 4 residues, 2 models selected
1 [ID: 1] region chains T,Z [224-225] RMSD: 0.828
> show sel atoms
> select #10/T:245 #12/Z:245
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #10/T:245 #12/Z:245
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [221] RMSD: 1.184
> show sel atoms
> select #10/T:228 #12/Z:228
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #10/T:228 #12/Z:228
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [204] RMSD: 2.971
> show sel atoms
> select clear
> style #10,12 stick
Changed 22294 atom styles
> select clear
> cartoon style #10,12 modeHelix tube sides 20
> select clear
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light yellow
> color sel lemon chiffon
> color sel light goldenrod yellow
> color sel old lace
> color sel light yellow
> color sel ivory
> color sel light yellow
> color sel lemon chiffon
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png" width 1660
> height 1174 supersample 3 transparentBackground true
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> select clear
> select add #12
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> hide sel cartoons
> show #!1 models
> hide #!1 models
> select add #10.12
13379 atoms, 11365 bonds, 2 pseudobonds, 1772 residues, 19 models selected
> hide sel cartoons
> select clear
> color #10,12 byhetero
> select clear
> ui mousemode right select
> select clear
Drag select of 2 atoms, 1 bonds
Drag select of 1 atoms, 1 bonds
> ui tool show "Color Actions"
> color sel lemon chiffon
> select clear
> select #12/Z:245@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:245@N
2 atoms, 1 bond, 1 residue, 2 models selected
> color sel lemon chiffon
> select clear
> select add #12/Z:249@N
1 atom, 1 bond, 1 residue, 1 model selected
> select subtract #12/Z:249@N
1 model selected
> select add #12/Z:249@N
1 atom, 1 residue, 1 model selected
> select add #12/Z:249@O
2 atoms, 1 bond, 1 residue, 2 models selected
> color sel lemon chiffon
> select clear
> select add #10/T:248@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:248@O
2 atoms, 2 residues, 3 models selected
> color sel lemon chiffon
> select clear
> select #12/Z:252@O
1 atom, 1 residue, 1 model selected
> select subtract #12/Z:252@O
Nothing selected
> select add #12/Z:252@N
1 atom, 1 residue, 1 model selected
> select add #12/Z:252@O
2 atoms, 1 residue, 1 model selected
> color sel lemon chiffon
> select clear
> select #12/Z:259@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:259@N
2 atoms, 1 bond, 1 residue, 2 models selected
> color sel lemon chiffon
> select clear
> select #12/Z:263@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:263@N
2 atoms, 1 bond, 1 residue, 2 models selected
> color sel lemon chiffon
> select clear
> select #12/Z:130@O
1 atom, 1 residue, 1 model selected
> select add #10/T:130@O
2 atoms, 1 bond, 2 residues, 2 models selected
> select subtract #10/T:130@O
1 atom, 1 bond, 1 residue, 2 models selected
> select add #12/Z:130@N
2 atoms, 1 bond, 1 residue, 1 model selected
> select subtract #12/Z:130@N
1 atom, 1 bond, 1 residue, 1 model selected
Drag select of 1 atoms
> color sel lemon chiffon
> select clear
Drag select of 1 atoms, 1 bonds
Drag select of 1 atoms
> color sel lemon chiffon
> select clear
> select add #12/Z:268@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:268@N
2 atoms, 1 bond, 1 residue, 1 model selected
> color sel lemon chiffon
> select clear
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lemon chiffon
> select subtract #10.12
1 model selected
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> color (#!12 & sel) forest green
> select clear
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> select add #10.12
4464 atoms, 582 residues, 3 models selected
> show sel cartoons
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png" width 1660
> height 1174 supersample 3 transparentBackground true
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #12.17
4464 atoms, 582 residues, 3 models selected
> hide sel cartoons
> select clear
> ui mousemode right select
> select #10/T:290 #12/Z:290
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #10/T:290 #12/Z:290
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [266] RMSD: 1.278
> show sel atoms
> select clear
> ui mousemode right select
Drag select of 6 atoms, 4 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 3 atoms, 2 bonds
> color (#!10 & sel) byhetero
> select clear
Drag select of 2 atoms, 1 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 1 atoms
> color (#!10 & sel) byhetero
> select clear
Drag select of 5 atoms, 4 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 8 atoms, 7 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 1 atoms
> color (#!10 & sel) byhetero
> select clear
Drag select of 3 atoms, 2 bonds
> select subtract #10/T:140@C
2 atoms, 1 bond, 1 residue, 3 models selected
> color (#!12 & sel) byhetero
> select clear
Drag select of 3 atoms, 2 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 7 atoms, 7 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 1 atoms
> color sel byhetero
> select clear
> select #10/T:248@OG
1 atom, 1 residue, 1 model selected
> select add #12/Z:248@OG
2 atoms, 2 residues, 3 models selected
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 6 atoms, 5 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 1 atoms
> color (#!10,12 & sel) byhetero
> select clear
> select add #12/Z:187@OG1
1 atom, 1 residue, 1 model selected
Drag select of 34 atoms, 32 bonds
> color (#!10,12 & sel) byhetero
> select clear
> select #12/Z:30@N
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms
> select clear
> select #12/Z:30@N
1 atom, 1 residue, 1 model selected
> color (#!12 & sel) forest green
> select clear
Drag select of 1 atoms
> select add #10/T:30@N
2 atoms, 1 residue, 2 models selected
> ui tool show "Color Actions"
> color sel lemon chiffon
> select clear
> select #12/Z:30@O
1 atom, 1 residue, 1 model selected
> color sel forest green
> select clear
Drag select of 1 atoms, 2 bonds
> color sel lemon chiffon
> select clear
Drag select of 1 atoms
> color sel forest green
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加AA .png" width
> 1660 height 1174 supersample 3 transparentBackground true
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加AA .png" width
> 1660 height 1591 supersample 3 transparentBackground true
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #12.17
4464 atoms, 582 residues, 3 models selected
> show sel cartoons
> ui mousemode right select
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png" width 1660
> height 1591 supersample 3 transparentBackground true
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .cxs"
> open
> /Users/wujingyi/Desktop/rfxATPase_PDB/J437_state1_hydrolysis_2.94A_7.88w-coot-3.pdb
Chain information for J437_state1_hydrolysis_2.94A_7.88w-coot-3.pdb #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H J K L M N O P | No description available
I Q | No description available
R | No description available
S W | No description available
T | No description available
U X | No description available
V | No description available
Y | No description available
Z | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!10,12-13 atoms
> show #!10,12-13 cartoons
Cell requested for row 11 is out of bounds for table with 47 rows! Resizing
table model.
> hide #!12 models
> hide #!10 models
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #13
26 models selected
> select add #13.2
3805 atoms, 498 residues, 1 model selected
> select add #13.3
7598 atoms, 994 residues, 2 models selected
> select add #13.4
11420 atoms, 1494 residues, 3 models selected
> color (#!13 & sel) #0099ccff
> select subtract #13.2
7615 atoms, 996 residues, 4 models selected
> select subtract #13.3
3822 atoms, 500 residues, 3 models selected
> select subtract #13.4
1 model selected
> select add #13.5
3597 atoms, 469 residues, 1 model selected
> select add #13.6
7202 atoms, 939 residues, 2 models selected
> select add #13.7
10788 atoms, 1407 residues, 3 models selected
> color (#!13 & sel) #e9d49bff
> select subtract #13.5
7191 atoms, 938 residues, 4 models selected
> select subtract #13.6
3586 atoms, 468 residues, 3 models selected
> select subtract #13.7
1 model selected
> select add #13.8
2282 atoms, 289 residues, 1 model selected
> color (#!13 & sel) #002befff
> color (#!13 & sel) #2befc8ff
> select subtract #13.8
1 model selected
> select add #13.9
535 atoms, 74 residues, 1 model selected
> select add #13.10
1062 atoms, 147 residues, 2 models selected
> select add #13.11
1597 atoms, 221 residues, 3 models selected
> select add #13.12
2132 atoms, 295 residues, 4 models selected
> select add #13.13
2667 atoms, 369 residues, 5 models selected
> select add #13.14
3202 atoms, 443 residues, 6 models selected
> select add #13.15
3737 atoms, 517 residues, 7 models selected
> select add #13.16
4272 atoms, 591 residues, 8 models selected
> select add #13.17
4807 atoms, 665 residues, 9 models selected
> select add #13.18
5334 atoms, 738 residues, 10 models selected
> color (#!13 & sel) #f5ccdcff
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected
> select subtract #13
26 models selected
> select add #13.21
1588 atoms, 265 residues, 1 model selected
> select add #13.27
3130 atoms, 543 residues, 2 models selected
> color (#!13 & sel) forest green
> select clear
> select add #13.22
747 atoms, 150 residues, 1 model selected
> select add #13.26
1959 atoms, 301 residues, 2 models selected
> select subtract #13.26
747 atoms, 150 residues, 3 models selected
> select add #13.25
1812 atoms, 300 residues, 2 models selected
> color (#!13 & sel) #c5c5ecff
> select clear
> select add #13.23
764 atoms, 152 residues, 1 model selected
> select add #13.26
1976 atoms, 303 residues, 2 models selected
> color (#!13 & sel) #9e7bbaff
> select clear
> select add #13.20
365 atoms, 74 residues, 1 model selected
> select subtract #13.20
1 model selected
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected
> select subtract #13.2
34773 atoms, 35235 bonds, 3 pseudobonds, 4851 residues, 28 models selected
> select add #13.2
38578 atoms, 35235 bonds, 3 pseudobonds, 5349 residues, 27 models selected
> select subtract #13.9
38043 atoms, 34692 bonds, 3 pseudobonds, 5275 residues, 28 models selected
> select subtract #13.10
37516 atoms, 34157 bonds, 3 pseudobonds, 5202 residues, 27 models selected
> select subtract #13.12
36981 atoms, 33614 bonds, 3 pseudobonds, 5128 residues, 26 models selected
> select subtract #13.11
36446 atoms, 33071 bonds, 3 pseudobonds, 5054 residues, 25 models selected
> select subtract #13.13
35911 atoms, 32528 bonds, 3 pseudobonds, 4980 residues, 24 models selected
> select subtract #13.14
35376 atoms, 31985 bonds, 3 pseudobonds, 4906 residues, 23 models selected
> select subtract #13.15
34841 atoms, 31442 bonds, 3 pseudobonds, 4832 residues, 22 models selected
> select subtract #13.16
34306 atoms, 30899 bonds, 3 pseudobonds, 4758 residues, 21 models selected
> select subtract #13.17
33771 atoms, 30356 bonds, 3 pseudobonds, 4684 residues, 20 models selected
> select subtract #13.18
33244 atoms, 29821 bonds, 3 pseudobonds, 4611 residues, 19 models selected
> select subtract #13.21
31656 atoms, 28218 bonds, 1 pseudobond, 4346 residues, 18 models selected
> select subtract #13.27
30114 atoms, 26668 bonds, 4068 residues, 16 models selected
> hide sel cartoons
> select clear
> select add #13.21
1588 atoms, 265 residues, 1 model selected
> select add #13.27
3130 atoms, 543 residues, 2 models selected
> color (#!13 & sel) dark gray
> select clear
> select add #13.9
535 atoms, 74 residues, 1 model selected
> select add #13.10
1062 atoms, 147 residues, 2 models selected
> select add #13.11
1597 atoms, 221 residues, 3 models selected
> select add #13.12
2132 atoms, 295 residues, 4 models selected
> select add #13.13
2667 atoms, 369 residues, 5 models selected
> select add #13.14
3202 atoms, 443 residues, 6 models selected
> select add #13.15
3737 atoms, 517 residues, 7 models selected
> select add #13.16
4272 atoms, 591 residues, 8 models selected
> select add #13.17
4807 atoms, 665 residues, 9 models selected
> select add #13.18
5334 atoms, 738 residues, 10 models selected
> hide sel cartoons
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected
> select subtract #13
26 models selected
> select add #13.21
1588 atoms, 265 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> cartoon style (#!13 & sel) modeHelix tube sides 20
> select clear
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected
> select subtract #13
26 models selected
> select add #13.21
1588 atoms, 265 residues, 1 model selected
> select add #13.27
3130 atoms, 543 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> color sel lavender
> color sel light steel blue
> select clear
> color light steel blue
> undo
> select #13/Z:241
5 atoms, 4 bonds, 1 residue, 1 model selected
> color #13.27 #b0bed1ff
> color #13.27 #b8c6daff
> undo
> select subtract #13.27
1 model selected
> select add #13.27
1542 atoms, 278 residues, 1 model selected
> color (#!13 & sel) #b8c6daff
> color (#!13 & sel) #b4c2d5ff
> color (#!13 & sel) #b0bed1ff
> color (#!13 & sel) #b0bdd0ff
> color (#!13 & sel) #b0bed0ff
> color (#!13 & sel) #adbbcdff
> color (#!13 & sel) #abb9cbff
> color (#!13 & sel) #aab7c9ff
> color (#!13 & sel) #abb8caff
> color (#!13 & sel) #adbaccff
> color (#!13 & sel) #adbacdff
> color (#!13 & sel) #afbdd0ff
> color (#!13 & sel) #afbdd5ff
> color (#!13 & sel) #afbdd9ff
> color (#!13 & sel) #afbddbff
> color (#!13 & sel) #afbde0ff
> color (#!13 & sel) #afbddfff
> color (#!13 & sel) #afbdddff
> color (#!13 & sel) #afbddbff
> color (#!13 & sel) #afbdd9ff
> color (#!13 & sel) #afbdd5ff
> color (#!13 & sel) #afbdd3ff
> color (#!13 & sel) #afbdd2ff
> color (#!13 & sel) #a9bdd2ff
> color (#!13 & sel) #a3bdd2ff
> color (#!13 & sel) #a5bdd2ff
> color (#!13 & sel) #abbdd2ff
> color (#!13 & sel) #afbdd2ff
> color (#!13 & sel) #aebdd2ff
> color (#!13 & sel) #abbdd2ff
> color (#!13 & sel) #abb9d2ff
> color (#!13 & sel) #abb6d2ff
> color (#!13 & sel) #abb5d2ff
> color (#!13 & sel) #abb7d2ff
> color (#!13 & sel) #abb9d2ff
> color (#!13 & sel) #abbad2ff
> color (#!13 & sel) #abbbd2ff
> color (#!13 & sel) #abbdd2ff
> select subtract #13.27
1 model selected
> select add #13.27
1542 atoms, 278 residues, 1 model selected
> color (#!13 & sel) #abbdd2ff
> color (#!13 & sel) #abbdd5ff
> color (#!13 & sel) #abbdd8ff
> color (#!13 & sel) #abbdddff
> color (#!13 & sel) #abbde3ff
> color (#!13 & sel) #abbde9ff
> color (#!13 & sel) #abbdeeff
> color (#!13 & sel) #abbdecff
> color (#!13 & sel) #abbdebff
> color (#!13 & sel) #abbde1ff
> color (#!13 & sel) #abbdd4ff
> color (#!13 & sel) #abbdd3ff
> color (#!13 & sel) #abbdd2ff
> color (#!13 & sel) #abbdd7ff
> select subtract #13.27
1 model selected
> select clear
> select #13/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style (#!13 & sel) stick
Changed 11 atom styles
> select clear
> select add #13.10
527 atoms, 73 residues, 1 model selected
> select add #13.11
1062 atoms, 147 residues, 2 models selected
> select add #13.12
1597 atoms, 221 residues, 3 models selected
> select add #13.13
2132 atoms, 295 residues, 4 models selected
> select add #13.14
2667 atoms, 369 residues, 5 models selected
> select add #13.15
3202 atoms, 443 residues, 6 models selected
> select add #13.16
3737 atoms, 517 residues, 7 models selected
> select add #13.17
4272 atoms, 591 residues, 8 models selected
> select add #13.18
4799 atoms, 664 residues, 9 models selected
Alignment identifier is 2
Alignment identifier is 3
> select #13/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #13/I,Q:59-60
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #13/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #13/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel cartoons
> style (#!13 & sel) stick
Changed 18 atom styles
> select clear
> select #13/P,O,N,L-M,K,J:59
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #13/P,O,N,L-M,K,J:59
63 atoms, 56 bonds, 7 residues, 1 model selected
> show sel atoms
> style (#!13 & sel) stick
Changed 63 atom styles
> select clear
> select #10/T:290 #12/Z:290
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #10/T:290 #12/Z:290
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [266] RMSD: 1.278
> show #!5-6,13 atoms
> hide #!5-6,13 atoms
> undo
Drag select of 4 atoms, 5 bonds
> select clear
> select add #13.9
535 atoms, 74 residues, 1 model selected
> select subtract #13.9
1 model selected
> select add #13.10
527 atoms, 73 residues, 1 model selected
> select subtract #13.10
1 model selected
> select add #13.9
535 atoms, 74 residues, 1 model selected
Alignment identifier is 13/H
> select #13/H:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #13/H:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style (#!13 & sel) stick
Changed 9 atom styles
> select clear
> open
> /Users/wujingyi/Desktop/rfxATPase_PDB/J437_state1_hydrolysis_2.94A_7.88w-coot-4.pdb
Chain information for J437_state1_hydrolysis_2.94A_7.88w-coot-4.pdb #14
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H J K L M N O P | No description available
I Q | No description available
R | No description available
S W | No description available
T | No description available
U X | No description available
V | No description available
Y | No description available
Z | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!5-6,13-14 atoms
> select add #14
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #14.2
34773 atoms, 35235 bonds, 3 pseudobonds, 4851 residues, 28 models selected
> select subtract #14.3
30980 atoms, 31384 bonds, 3 pseudobonds, 4355 residues, 27 models selected
> select subtract #14.4
27158 atoms, 27504 bonds, 3 pseudobonds, 3855 residues, 26 models selected
> select subtract #14.5
23561 atoms, 23844 bonds, 3 pseudobonds, 3386 residues, 25 models selected
> select subtract #14.6
19956 atoms, 20176 bonds, 3 pseudobonds, 2916 residues, 24 models selected
> select subtract #14.7
16370 atoms, 16527 bonds, 3 pseudobonds, 2448 residues, 23 models selected
> select subtract #14.8
14088 atoms, 14217 bonds, 3 pseudobonds, 2159 residues, 22 models selected
> select subtract #14.27
12546 atoms, 12667 bonds, 2 pseudobonds, 1881 residues, 21 models selected
> select subtract #14.26
11334 atoms, 11445 bonds, 2 pseudobonds, 1730 residues, 20 models selected
> select subtract #14.25
10269 atoms, 10378 bonds, 2 pseudobonds, 1580 residues, 19 models selected
> select subtract #14.24
9904 atoms, 10014 bonds, 2 pseudobonds, 1506 residues, 18 models selected
> select subtract #14.23
9140 atoms, 9251 bonds, 2 pseudobonds, 1354 residues, 17 models selected
> select subtract #14.22
8393 atoms, 8505 bonds, 2 pseudobonds, 1204 residues, 16 models selected
> select subtract #14.21
6805 atoms, 6902 bonds, 939 residues, 14 models selected
> select subtract #14.20
6440 atoms, 6538 bonds, 865 residues, 13 models selected
> select subtract #14.19
5548 atoms, 5636 bonds, 748 residues, 12 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> color (#!14 & sel) #f5ccdcff
Cell requested for row 13 is out of bounds for table with 41 rows! Resizing
table model.
> select add #14
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected
> select subtract #14
26 models selected
> hide #!13 models
> hide #!6 models
> hide #!5 models
Drag select of 738 residues
Alignment identifier is 1
Alignment identifier is 4
> show #!13 models
> show #!5 models
> show #!6 models
> select #14/P,O,N,L-M,K,J,H:76
64 atoms, 56 bonds, 8 residues, 1 model selected
> select #14/P,O,N,L-M,K,J,H
4280 atoms, 4344 bonds, 592 residues, 1 model selected
> hide sel cartoons
> select #14/P,O,N,L-M,K,J,H:59
72 atoms, 64 bonds, 8 residues, 1 model selected
> select #14/P,O,N,L-M,K,J,H:59
72 atoms, 64 bonds, 8 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select #14/I,Q:75
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #14/I,Q
1054 atoms, 1070 bonds, 146 residues, 1 model selected
> hide sel cartoons
> select #14/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #14/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select clear
> style #5-6,13-14 ball
Changed 89937 atom styles
> style #5-6,13-14 stick
Changed 89937 atom styles
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX63CH/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4 (23E214)
Kernel Version: Darwin 23.4.0
Time since boot: 46天3小时39分钟
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Redmi 27 NU:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Resolution: 3024 x 1964
UI Looks like: 1512 x 982 @ 120.00Hz
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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