![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Last modified 10 months ago
#16912 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-15.3.1-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00007ff845e54b00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 124)
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{
"uptime" : 290000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 2505,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-02-19 18:18:15.4572 +0100",
"codeSigningMonitor" : 0,
"incident" : "231ED2CF-99B5-403D-8668-519FD58E7943",
"pid" : 75013,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-14 09:31:11.6702 +0100",
"procStartAbsTime" : 66153584356873,
"procExitAbsTime" : 291786984527627,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"2EF1C7E5-CB47-546C-881F-28C6D02FF09B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "250318AF-B0C7-4CAC-6AA5-6AB535BC3FE0",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "D229F5D1-CD0F-4BBF-AC24-9EED06C2FB64",
"wakeTime" : 34567,
"bridgeVersion" : {"build":"22P3051","train":"9.3"},
"sleepWakeUUID" : "88E596E4-3C7C-4126-B1C3-02914CA9166A",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4403867648\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1067db000-1067df000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":75013},
"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\nVM - (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\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4403867648\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1067db000-1067df000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
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"size" : 4841443,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3002358,
"uuid" : "0d3fd4c1-55be-30b9-aa97-225609c52278",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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"base" : 140703176241152,
"size" : 572544,
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"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"sharedCache" : {
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=4.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 3880K 1 \nCG image 1812K 103 \nCG raster data 8K 1 \nColorSync 272K 33 \nCoreAnimation 4176K 258 \nCoreGraphics 24K 5 \nCoreImage 20K 1 \nCoreServices 620K 2 \nCoreUI image data 5184K 55 \nFoundation 32K 2 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 3.4G 3043 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 164K 41 \nStack 193.8M 42 \nStack Guard 56.0M 1 \nVM_ALLOCATE 371.2M 446 \nVM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 47.1M 1200 \n__DATA_CONST 118.3M 1040 \n__DATA_DIRTY 2599K 348 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 224.9M 227 \n__OBJC_RO 76.9M 1 \n__OBJC_RW 2375K 2 \n__TEXT 1.5G 1209 \n__TPRO_CONST 272K 2 \ndyld private memory 296K 3 \nmapped file 594.5M 105 \nowned unmapped memory 121.9M 1 \nshared memory 3552K 38 \n=========== ======= ======= \nTOTAL 6.9G 8245 \nTOTAL, minus reserved VM space 6.7G 8245 \n",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J763_class_00_00082_volume.mrc
Opened cryosparc_P70_J763_class_00_00082_volume.mrc as #1, grid size
128,128,128, pixel 2.38, shown at level 0.175, step 1, values float32
> volume #1 level 0.2605
> volume #1 level 0.3148
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J776_008_volume_map.mrc
Opened cryosparc_P70_J776_008_volume_map.mrc as #2, grid size 300,300,300,
pixel 1.02, shown at level 0.035, step 2, values float32
> volume #2 level 0.07536
> lighting soft
> volume #2 level 0.08421
> volume #2 step 1
> volume #2 level 0.1129
> volume #2 level 0.1262
> volume #2 level 0.1384
> volume #2 level 0.1446
> volume #2 level 0.1794
> volume #2 level 0.1139
> volume #2 level 0.08728
> volume #2 level 0.1016
> volume #2 level 0.1067
> view
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/trimer_fit.pdb
Summary of feedback from opening
/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/trimer_fit.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 57 GLU A 61 1 5
Start residue of secondary structure not found: HELIX 2 2 ASN A 68 GLN A 74 1
7
Start residue of secondary structure not found: HELIX 3 3 PRO A 77 VAL A 81 1
5
Start residue of secondary structure not found: HELIX 4 4 VAL A 95 VAL A 107 1
13
Start residue of secondary structure not found: HELIX 5 5 ALA A 114 LYS A 123
1 10
15 messages similar to the above omitted
End residue of secondary structure not found: HELIX 21 21 LEU A 269 LYS A 281
1 13
Start residue of secondary structure not found: HELIX 22 22 GLU A 288 ALA A
298 1 11
Start residue of secondary structure not found: HELIX 23 23 CYS A 299 HIS A
304 1 6
Start residue of secondary structure not found: HELIX 24 24 SER A 307 THR A
320 1 14
Start residue of secondary structure not found: HELIX 25 25 ILE A 325 ILE A
334 1 10
Start residue of secondary structure not found: HELIX 26 26 ALA A 335 GLN A
337 1 3
12 messages similar to the above omitted
End residue of secondary structure not found: HELIX 39 39 LYS A 461 GLU A 478
1 18
Start residue of secondary structure not found: HELIX 40 40 THR A 489 ASN A
508 1 20
Start residue of secondary structure not found: HELIX 41 41 PRO A 511 LEU A
524 1 14
Start residue of secondary structure not found: HELIX 42 42 PRO A 527 TYR A
529 1 3
Start residue of secondary structure not found: HELIX 43 43 PRO A 563 VAL A
567 1 5
Start residue of secondary structure not found: HELIX 44 44 ASP A 581 LYS A
589 1 9
3 messages similar to the above omitted
End residue of secondary structure not found: HELIX 48 48 LEU A 697 LYS A 699
1 3
Start residue of secondary structure not found: HELIX 49 49 ARG A 702 THR A
715 1 14
Start residue of secondary structure not found: SHEET 1 1 1 LYS A 531 HIS A
533 0
Start residue of secondary structure not found: SHEET 2 2 1 ASP A 543 LEU A
548 0
Start residue of secondary structure not found: SHEET 3 3 1 MET A 649 PHE A
655 0
Start residue of secondary structure not found: SHEET 4 4 1 TYR A 684 LEU A
689 0
Chain information for trimer_fit.pdb
---
Chain | Description
3.1/A 3.2/A | No description available
3.3/A | No description available
3.1/D 3.2/D | No description available
Computing secondary structure
> ui tool show "Fit in Map"
> fitmap #3.1 inMap #1
Fit molecule trimer_fit.pdb (#3.1) to map
cryosparc_P70_J763_class_00_00082_volume.mrc (#1) using 5927 atoms
average map value = 0.2425, steps = 76
shifted from previous position = 13.2
rotated from previous position = 6.09 degrees
atoms outside contour = 3784, contour level = 0.31483
Position of trimer_fit.pdb (#3.1) relative to
cryosparc_P70_J763_class_00_00082_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.99729341 -0.03122240 -0.06656593 20.29814582
0.02602687 0.99664965 -0.07753762 4.67634168
0.06876383 0.07559526 0.99476474 -8.89332490
Axis 0.72154427 -0.63765804 0.26975191
Axis point 0.00000000 159.68100316 129.60582224
Rotation angle (degrees) 6.09139195
Shift along axis 9.26511246
> undo
> color bychain
> color byhetero
> rainbow
> color bypolymer
> close #3
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_J398-a-b-
> c-coot-2.pdb
Chain information for F5_J398-a-b-c-coot-2.pdb #3
---
Chain | Description
A | No description available
B D | No description available
> dssp
Computing secondary structure
> fitmap #3 inMap #2
Fit molecule F5_J398-a-b-c-coot-2.pdb (#3) to map
cryosparc_P70_J776_008_volume_map.mrc (#2) using 14247 atoms
average map value = 0.0697, steps = 280
shifted from previous position = 29.6
rotated from previous position = 24.7 degrees
atoms outside contour = 10794, contour level = 0.10672
Position of F5_J398-a-b-c-coot-2.pdb (#3) relative to
cryosparc_P70_J776_008_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.91950048 -0.02894727 0.39202159 -16.20378507
-0.02973498 0.98930541 0.14279575 7.59306784
-0.39196262 -0.14295752 0.90880606 90.62617398
Axis -0.34244997 0.93953559 -0.00094400
Axis point 213.96298040 0.00000000 74.26561963
Rotation angle (degrees) 24.65913573
Shift along axis 12.59739178
> volume #2 level 0.1141
> volume #2 style image
> volume #2 style mesh
> volume #2 color #b2ffb2
> volume #2 color #b2b2b2
> fitmap #3 inMap #2
Fit molecule F5_J398-a-b-c-coot-2.pdb (#3) to map
cryosparc_P70_J776_008_volume_map.mrc (#2) using 14247 atoms
average map value = 0.0697, steps = 44
shifted from previous position = 0.00302
rotated from previous position = 0.00442 degrees
atoms outside contour = 11056, contour level = 0.11406
Position of F5_J398-a-b-c-coot-2.pdb (#3) relative to
cryosparc_P70_J776_008_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.91951988 -0.02897443 0.39197406 -16.19473512
-0.02972343 0.98929715 0.14285540 7.58294791
-0.39191798 -0.14300920 0.90881718 90.62514911
Axis -0.34260330 0.93947974 -0.00089766
Axis point 213.98966670 0.00000000 74.24704270
Rotation angle (degrees) 24.65760691
Shift along axis 12.59104458
> vop flip #2
Opened cryosparc_P70_J776_008_volume_map.mrc z flip as #4, grid size
300,300,300, pixel 1.02, shown at step 1, values float32
> fitmap #3 inMap #4
Fit molecule F5_J398-a-b-c-coot-2.pdb (#3) to map
cryosparc_P70_J776_008_volume_map.mrc z flip (#4) using 14247 atoms
average map value = 0.1845, steps = 200
shifted from previous position = 13.4
rotated from previous position = 27.6 degrees
atoms outside contour = 3938, contour level = 0.11406
Position of F5_J398-a-b-c-coot-2.pdb (#3) relative to
cryosparc_P70_J776_008_volume_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99791802 0.01362056 -0.06304054 30.27766207
-0.01170048 0.99945932 0.03072745 19.39173545
0.06342498 -0.02992587 0.99753783 18.21130773
Axis -0.42556129 -0.88731878 -0.17765971
Axis point -183.63233517 0.00000000 261.37578417
Rotation angle (degrees) 4.08651778
Shift along axis -33.32706757
> lighting soft
> lighting full
> lighting soft
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> volume #4 style surface
> volume #4 level 0.08727
> volume #4 level 0.1016
> volume #4 level 0.106
> volume #4 level 0.1221
> volume #4 style mesh
> show atoms
> color byhetero
> color bychain
> color byhetero
> volume #4 level 0.1132
> volume #4 level 0.09888
> select ~sel & ##selected
Nothing selected
> select #1/c:658
Nothing selected
> select #1/D:658
Nothing selected
> select #2/D:658
Nothing selected
> select #3/D:658
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> volume #4 level 0.08012
> volume #4 level 0.1105
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J789_007_volume_map_sharp.mrc
Opened cryosparc_P70_J789_007_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.02, shown at level 0.0525, step 2, values float32
> hide #!4-5 target m
> show #!2 target m
> hide #!3 target m
> select ~sel & ##selected
Nothing selected
> show #!1 target m
> hide #!2 target m
> show #!5 target m
> hide #!1 target m
> vop flip #5
Opened cryosparc_P70_J789_007_volume_map_sharp.mrc z flip as #6, grid size
300,300,300, pixel 1.02, shown at step 1, values float32
> volume #6 level 0.1861
> volume #6 level 0.2177
> volume #6 level 0.2845
> view
> dust
Unknown command: dust
> hide dust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide dust #5 size 3
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide dust #6 size 3
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide dust size 3 #6
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide dust size 3
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide dust size 3
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide dust 3
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide dust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Hide Dust"
> surface dust #6 size 4.25
> surface dust #6 size 3.98
> surface dust #6 size 3.34
> surface dust #6 size 3.12
> surface dust #6 size 1.61
> surface dust #6 size 1.65
> surface dust #6 size 1.79
> surface dust #6 size 1.81
> surface dust #6 size 1.92
> show #!3 models
> fitmap #3 inMap #6
Fit molecule F5_J398-a-b-c-coot-2.pdb (#3) to map
cryosparc_P70_J789_007_volume_map_sharp.mrc z flip (#6) using 14247 atoms
average map value = 0.3002, steps = 68
shifted from previous position = 0.281
rotated from previous position = 0.403 degrees
atoms outside contour = 7732, contour level = 0.28448
Position of F5_J398-a-b-c-coot-2.pdb (#3) relative to
cryosparc_P70_J789_007_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.99800334 0.01982428 -0.05996949 29.21625211
-0.01805840 0.99939136 0.02984637 20.09234886
0.06052468 -0.02870382 0.99775390 18.40245480
Axis -0.42056030 -0.86549782 -0.27210761
Axis point -138.88910089 0.00000000 248.57023415
Rotation angle (degrees) 3.99157283
Shift along axis -34.68452807
> volume #6 style mesh
> volume #6 level 0.2448
> volume #6 style surface
> volume #6 level 0.2117
> surface dust #6 size 1.85
> surface dust #6 size 1.72
> volume #6 level 0.1786
> volume #6 level 0.2084
> volume #6 level 0.2415
> volume #6 level 0.1786
> surface dust #6 size 1.85
> surface dust #6 size 2.24
> surface dust #6 size 2.27
> surface dust #6 size 4.13
> surface dust #6 size 6.91
> surface dust #6 size 6.83
> view
> surface dust #6 size 8.99
> view
> color bychain
> hide #!3 models
> show #!3 models
> view
> volume #6 color #b2b2b2
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/cryosparc_P70_789_007_volume_map_sharp.mrc
> models #6
> close #6
> close
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs
> format session
Opened cryosparc_P43_J469_008_volume_map.mrc as #2, grid size 288,288,288,
pixel 0.902, shown at level 0.0497, step 1, values float32
Opened cryosparc_P43_J469_008_volume_map_sharp.mrc as #3, grid size
288,288,288, pixel 0.902, shown at level 0.171, step 1, values float32
> set bgColor #ffffff00
opened ChimeraX session
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/FAST42apo_dimer/F2_coot1-P43_J469-coot-1.pdb
Chain information for F2_coot1-P43_J469-coot-1.pdb #4
---
Chain | Description
A | No description available
B | No description available
> show #!1 models
> hide #!1 models
> hide #!2 models
> select #1/A
4349 atoms, 4435 bonds, 540 residues, 1 model selected
> select #4/B
4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected
> hide sel cartoons
> show #!2 models
> select #4/A
4349 atoms, 4435 bonds, 540 residues, 1 model selected
> ui tool show "Color Actions"
> hide #!2 models
> select add #2
4349 atoms, 4435 bonds, 540 residues, 3 models selected
> show #!1 models
> hide #!1 models
> select add #4
8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 4 models selected
> select subtract #4
2 models selected
> select subtract #2
Nothing selected
> show #!1 models
> hide #1.1 models
> hide #!4 models
> show #!4 models
> color #4 #48d6d2ff
> hide #!1 models
> 4/a:457-527
Unknown command: 4/a:457-527
> select #4/a:457-527
572 atoms, 585 bonds, 71 residues, 1 model selected
> select #4/a:453-527
605 atoms, 618 bonds, 75 residues, 1 model selected
> select #4/a:453-549
780 atoms, 795 bonds, 97 residues, 1 model selected
> Sel #4/a:572-618
Unknown command: Sel #4/a:572-618
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> select #1/a:576-695
948 atoms, 967 bonds, 120 residues, 1 model selected
> select #4/a:576-695
948 atoms, 967 bonds, 120 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ef8a62ff
> graphics silhouettes false
> graphics silhouettes true
> select clear
> select #4/a:453-549
780 atoms, 795 bonds, 97 residues, 1 model selected
> color sel #2166acff
> select clear
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> select #4/a:457–527
Expected an objects specifier or a keyword
> select #4/a:457–527
Expected an objects specifier or a keyword
> select #4/a:457-527
572 atoms, 585 bonds, 71 residues, 1 model selected
> select clear
> select #4/a:447-307
Nothing selected
> select #4/a:307-407
808 atoms, 819 bonds, 101 residues, 1 model selected
> color sel #d1e5f0ff
> color sel #d1e5f0a8
> color sel #d1e5f0a7
> color sel #d1e5f0a8
> select clear
> color #4 #67a9cfa8
> undo
> select #4/a:307-407
808 atoms, 819 bonds, 101 residues, 1 model selected
> select clear
> select #4/a:307-407
808 atoms, 819 bonds, 101 residues, 1 model selected
> color #4 #67a9cfff
> undo
> select #4/a:307-407
808 atoms, 819 bonds, 101 residues, 1 model selected
> color #4 #67a9cfff
> select clear
> undo
> select clear
> select #4/a:307-407
808 atoms, 819 bonds, 101 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #67a9cfff
> select clear
> color #4 #b2d6d2ff
> color #4 #b2b2d2ff
> color #4 #b2b2b2ff
> select #4/a:307-407
808 atoms, 819 bonds, 101 residues, 1 model selected
> color #4 #67a9cfff
> select #4/a:307-407
808 atoms, 819 bonds, 101 residues, 1 model selected
> color sel #02a9cfff
> select clear
> color #4 gray
> color #4 dim gray
> lighting soft
> lighting simple
> color #4 red
> color #4 dim gray
> color #4 light gray
> lighting soft
> select clear
> select #4/a:636-692
453 atoms, 462 bonds, 57 residues, 1 model selected
> select #4/a:576-692
921 atoms, 939 bonds, 117 residues, 1 model selected
> color sel #ef8a62ff
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> select #4/a:457-527
572 atoms, 585 bonds, 71 residues, 1 model selected
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J815_class_00_00084_volume_sharp.mrc
Opened cryosparc_P70_J815_class_00_00084_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.03, shown at level 0.0975, step 1, values float32
> volume #5 level 0.2989
> volume #5 level 0.45
> hide #!4 models
> volume #5 level 0.537
> close #5
> show #!4 models
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> 636-692
Unknown command: 636-692
> select #4/a:572-618,636-692
828 atoms, 845 bonds, 104 residues, 1 model selected
> select #4/a:457–527
Expected an objects specifier or a keyword
> select #4/a:457-527
572 atoms, 585 bonds, 71 residues, 1 model selected
> color sel #2166acff
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> color sel #d1e5f0ff
> select clear
> color #4 #57e5f0ff
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> color cornflower blue
> undo
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #4/a:457-531
601 atoms, 614 bonds, 75 residues, 1 model selected
> color sel #57e5f0ff
> color sel #2166acff
> select clear
> select #4/a:636-692
453 atoms, 462 bonds, 57 residues, 1 model selected
> select #4/a:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> color sel #ef8a62ff
> select clear
> select #4/a:453-531
634 atoms, 647 bonds, 79 residues, 1 model selected
> color sel #2166acff
> select clear
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> select #4/a:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> color sel light gray
> select clear
> select #4/a:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> select #4/a:619-695
604 atoms, 615 bonds, 77 residues, 1 model selected
> color sel light gray
> select clear
> select #4/a:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> color #4 #ef8a62ff
> undo
> color sel #ef8a62ff
> select clear
> view
> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP.jpg" width 1163 height 850 supersample 4
> view
> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP-1.jpg" width 1163 height 890 supersample 4
> view
> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP.jpg" width 1163 height 890 supersample 4
> turn y 180
> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP-1.jpg" width 1163 height 890 supersample 4
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J817_012_volume_map.mrc
Opened cryosparc_P70_J817_012_volume_map.mrc as #5, grid size 256,256,256,
pixel 1.02, shown at level 0.0212, step 1, values float32
> volume #5 level 0.1332
> hide #!4 models
> view
> volume #5 level 0.2064
> volume #5 level 0.235
> select add #5
2 models selected
> close #5
> show #!4 models
> view
> coulombic #!4
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for F2_coot1-P43_J469-coot-1.pdb_A SES surface #4.2: minimum,
-17.17, mean -0.89, maximum 15.16
Coulombic values for F2_coot1-P43_J469-coot-1.pdb_B SES surface #4.3: minimum,
-17.76, mean -0.82, maximum 17.84
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!4 surfaces
> select #1/B
4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected
> hide #!4 surfaces
> show #!4 surfaces
> select #1/B
4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected
> select #1/A#4/A
8698 atoms, 8870 bonds, 1080 residues, 2 models selected
> hide sel & #!4 surfaces
> hide sel & #!4 cartoons
> hide sel & #!4 surfaces
> select clear
> hide #!4 surfaces
> show #!4 cartoons
> select #4/a:453-531
634 atoms, 647 bonds, 79 residues, 1 model selected
> select #4/b:453-531
634 atoms, 647 bonds, 79 residues, 1 model selected
> color (#!4 & sel) #2166acff
> select clear
> select #4/a:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> select #4/b:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> color (#!4 & sel) #d1e5f0ff
> select clear
> select #4/b:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> color (#!4 & sel) #67a9cfff
> select clear
> select ~sel & ##selected
Nothing selected
> select #4/a:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> select #4/b:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> select #4/a:636-695
480 atoms, 490 bonds, 60 residues, 1 model selected
> select #4/a:453-531
634 atoms, 647 bonds, 79 residues, 1 model selected
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> select clear
> view
> dssp
Computing secondary structure
> select clear
> select #4/A:631
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/A:632
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #4/A:633
28 atoms, 25 bonds, 3 residues, 2 models selected
> select add #4/A:634
35 atoms, 31 bonds, 4 residues, 2 models selected
> select add #4/A:635
40 atoms, 35 bonds, 5 residues, 2 models selected
> color (#!4 & sel) #de825bff
> select clear
> select #4/a:453-530
628 atoms, 641 bonds, 78 residues, 1 model selected
> select #4/a:453-531
634 atoms, 647 bonds, 79 residues, 1 model selected
> select #4/b:453-531
634 atoms, 647 bonds, 79 residues, 1 model selected
> select clear
> Sel #4/a:572-618
Unknown command: Sel #4/a:572-618
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> select #4/b:572-618
369 atoms, 377 bonds, 46 residues, 1 model selected
> color (#!4 & sel) #d1e5f0ff
> color (#!4 & sel) #67a9cfff
> select #4/a:576-695
948 atoms, 967 bonds, 120 residues, 1 model selected
> select clear
> select #4/a:576-631
436 atoms, 444 bonds, 56 residues, 1 model selected
> select #4/a:636-692
453 atoms, 462 bonds, 57 residues, 1 model selected
> select #4/a:636-693
461 atoms, 470 bonds, 58 residues, 1 model selected
> select #4/a:631-693
501 atoms, 510 bonds, 63 residues, 1 model selected
> color (#!4 & sel) #ef8a62ff
> select #4/b:631-693
501 atoms, 510 bonds, 63 residues, 1 model selected
> color (#!4 & sel) #ef8a62ff
> select clear
> select #4/B:694
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/B:695
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #4/B:694
19 atoms, 18 bonds, 2 residues, 2 models selected
> color (#!4 & sel) #ef8a62ff
> select clear
> dssp
Computing secondary structure
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/FAST2_domains.cxs
> select #1/A#4/A
8698 atoms, 8870 bonds, 1080 residues, 2 models selected
> hide sel & #!4 cartoons
> show sel & #!4 cartoons
> select clear
> select #1/B#4/B
8562 atoms, 8728 bonds, 2 pseudobonds, 1062 residues, 4 models selected
> hide sel & #!4 cartoons
> view sel
No displayed objects specified.
> view sel
No displayed objects specified.
> ui tool show "Model Panel"
> show target m
> hide #!3 models
> hide #!2 models
> hide #!1 models
> select add #4
12911 atoms, 13163 bonds, 2 pseudobonds, 1602 residues, 5 models selected
> select subtract #4
4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 4 models selected
> select add #1
8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 2 models selected
> select subtract #1
Nothing selected
> view
> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP.jpg" width 493 height 890 supersample 4
> turn y 180
> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP-1.jpg" width 493 height 890 supersample 4
> view
> select ~sel & ##selected
Nothing selected
> turn y -180
> view
> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP.jpg" width 1163 height 890 supersample 4
> turn y 180
> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2-FAST1-2
> and RAP-1.jpg" width 1163 height 890 supersample 4
> select #4/B
4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected
> show sel cartoons
> select clear
> select add #4
8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 2 models selected
> show sel surfaces
> color zone #4 near #4
> color zone #4 near #4 distance 5
> select clear
> hide #!4 surfaces
> cofr frontCenter
> view
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_a.jpg
> width 1163 height 890 supersample 4
> select #4/b:631-693
501 atoms, 510 bonds, 63 residues, 1 model selected
> select #4/a:576-695
948 atoms, 967 bonds, 120 residues, 1 model selected
> select #4/b:453-531
634 atoms, 647 bonds, 79 residues, 1 model selected
> select #4/a:631-693
501 atoms, 510 bonds, 63 residues, 1 model selected
> select #4/a:572-618
375 atoms, 383 bonds, 47 residues, 1 model selected
> color (#!4 & sel) cornflower blue
> select #4/b:572-618
369 atoms, 377 bonds, 46 residues, 1 model selected
> color (#!4 & sel) cornflower blue
> select clear
> select #1/A#4/A
8698 atoms, 8870 bonds, 1080 residues, 2 models selected
> hide sel & #!4 cartoons
> show sel & #!4 cartoons
> select clear
> view
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_a.jpg
> width 1163 height 890 supersample 4
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_volumes_all_clusters/J809_cluster_000.mrc
Opened J809_cluster_000.mrc as #5, grid size 300,300,300, pixel 1.02, shown at
level 0.0596, step 2, values float32
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_volumes_all_clusters/J809_cluster_001.mrc
Opened J809_cluster_001.mrc as #6, grid size 300,300,300, pixel 1.02, shown at
level 0.0582, step 2, values float32
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_volumes_all_clusters/J809_cluster_002.mrc
Opened J809_cluster_002.mrc as #7, grid size 300,300,300, pixel 1.02, shown at
level 0.0649, step 2, values float32
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_volumes_all_clusters/J809_cluster_003.mrc
Opened J809_cluster_003.mrc as #8, grid size 300,300,300, pixel 1.02, shown at
level 0.0633, step 2, values float32
> hide #!4 models
> view
> tile
4 models tiled
> volume #5 level 0.06618
> volume #5 level 0.06
> volume #5 level 0.05
> volume #5 level 0.04
> volume #5 level 0.07
> volume #6 level 0.07
> volume #7 level 0.07
> volume #8 level 0.07
> volume #8 step 1
> volume #8 level 0.08901
> volume #7 level 0.08
> volume #6 level 0.08
> volume #5 level 0.08
> volume #7 step 1
> volume #6 step 1
> volume #5 step 1
> volume #8 level 0.08
> volume #8 level 0.09
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J829_007_volume_map.mrc
Opened cryosparc_P70_J829_007_volume_map.mrc as #9, grid size 300,300,300,
pixel 1.02, shown at level 0.0408, step 2, values float32
> volume #9 level 0.1205
> volume #9 step 1
> view
> volume #9 level 0.1291
> lighting soft
> volume #9 level 0.1452
> volume #9 level 0.1893
> volume #9 level 0.1538
> volume #9 level 0.1344
> volume #9 level 0.1237
> volume #9 level 0.1269
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J830_006_volume_map.mrc
Opened cryosparc_P70_J830_006_volume_map.mrc as #10, grid size 300,300,300,
pixel 1.02, shown at level 0.0408, step 2, values float32
> volume #10 level 0.1067
> volume #10 step 1
> volume #10 level 0.1219
> volume #10 level 0.1435
> volume #10 level 0.1327
> volume #10 level 0.1716
> volume #10 level 0.1964
> volume #10 level 0.15
> volume #10 level 0.1273
> volume #10 level 0.1186
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J830_006_volume_map_sharp.mrc
Opened cryosparc_P70_J830_006_volume_map_sharp.mrc as #11, grid size
300,300,300, pixel 1.02, shown at level 0.0568, step 2, values float32
> volume #11 level 0.1375
> volume #11 step 1
> volume #11 level 0.1478
> ui tool show "Hide Dust"
> surface dust #11 size 2.46
> surface dust #11 size 1.91
> surface dust #11 size 1.85
> surface dust #11 size 2.22
> surface dust #11 size 2.19
> surface dust #11 size 3.05
> surface dust #11 size 3
> surface dust #11 size 2.15
> surface dust #11 size 2.12
> surface dust #11 size 2.42
> surface dust #11 size 2.38
> volume #11 level 0.1811
> volume #11 level 0.1759
> volume #11 level 0.158
> volume #11 level 0.2323
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J834__localfilter.mrc
Opened cryosparc_P70_J834__localfilter.mrc as #12, grid size 300,300,300,
pixel 1.02, shown at level 0.0288, step 2, values float32
> volume #12 level 0.09152
> volume #12 step 1
> volume #12 level 0.1165
> volume #12 level 0.1415
> volume #12 level 0.1165
> volume #12 level 0.2916
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J833__localfilter.mrc
Opened cryosparc_P70_J833__localfilter.mrc as #13, grid size 300,300,300,
pixel 1.02, shown at level 0.0468, step 2, values float32
> volume #13 level 0.1035
> volume #13 level 0.09125
> volume #12 level 0.154
> volume #10 level 0.1284
> volume #9 level 0.1409
> volume #9 level 0.1258
> lighting soft
> volume #9 level 0.1431
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_cluster_000.mrc
Opened cryosparc_P70_J809_cluster_000.mrc as #14, grid size 300,300,300, pixel
1.02, shown at level 0.0629, step 2, values float32
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J809_cluster_001.mrc
Opened cryosparc_P70_J809_cluster_001.mrc as #15, grid size 300,300,300, pixel
1.02, shown at level 0.0599, step 2, values float32
> hide #!9 models
> tile
2 models tiled
> volume #14 step 1
> volume #15 step 1
> volume #15 level 0.07876
> volume #14 level 0.0851
> volume #15 level 0.08935
> volume #15 level 0.08
> volume #14 level 0.085
> volume #14 level 0.08
> close #14
> close #13
> close #15
> view
> lighting soft
> volume #10 level 0.1511
> volume #9 level 0.1291
> view
> show #!1 models
> view
> select ~sel & ##selected
Nothing selected
> turn y -180
> turn y 180
> turn z 180
> turn z -180
> turn x -180
> turn y 180
> turn z 180
> turn z 90
> turn y 90
> turn y 270
> turn z 270
> turn y -270
> turn y 270
> select ~sel & ##selected
Nothing selected
> turn y 270
> turn y 90
> turn y \- 90
Expected a number or a keyword
> turn y -90
> turn y 45
> turn y -45
> turn y -80
> turn y 80
> turn y -80
> turn y 30
> turn y -30
> turn z 30
> turn z -30
> turn y -30
> turn y 30
> turn y 45
> turn y -45
> turn y 45
> turn y -45
> turn x -45
> turn x 45
> turn x 4
> turn x 45
> turn x 40
> turn y 40
> turn x 40
> turn x -60
> turn x -67
> turn x -80
> turn x 80
> turn x 90
> turn x -90
> turn x 90
> turn x 270
> select
> #1/a:196,443,492,247,290,287,283,319,320,356,658,601,194,198,281,282,412,447,449,488,532,535
182 atoms, 165 bonds, 22 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select
> #1/b:194,281,356,412,447,449,488,532,534,196,193,416,415,443,247,287,290,319,356,603,658,535
185 atoms, 170 bonds, 21 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> view
> select clear
> hide #!1 atoms
> select #1/a:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/b:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/B:196
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #107c01 dashes 5 showDist true restrict cross intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
Finding intermodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 F2_coot1-P43_J469-coot-1.pdb
4 F2_coot1-P43_J469-coot-1.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 N F2_coot1-P43_J469-coot-1.pdb #4/A ARG 194 O no hydrogen 2.431 N/A
F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 OG F2_coot1-P43_J469-coot-1.pdb #4/A LYS 193 O no hydrogen 3.293 N/A
F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 OG F2_coot1-P43_J469-coot-1.pdb #4/A ARG 194 O no hydrogen 3.195 N/A
F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 OG F2_coot1-P43_J469-coot-1.pdb #4/B SER 196 OG no hydrogen 0.000 N/A
F2_coot1-P43_J469-coot-1.pdb #4/B SER 196 OG F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 OG no hydrogen 0.000 N/A
F2_coot1-P43_J469-coot-1.pdb #4/B LYS 200 N F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 O no hydrogen 2.547 N/A
6 hydrogen bonds found
1 strict hydrogen bonds found
> hbonds sel color #107c01 dashes 5 showDist true restrict cross intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
Finding intermodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 F2_coot1-P43_J469-coot-1.pdb
4 F2_coot1-P43_J469-coot-1.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
F2_coot1-P43_J469-coot-1.pdb #4/B SER 196 OG F2_coot1-P43_J469-coot-1.pdb #1/A LYS 193 O no hydrogen 3.293 N/A
F2_coot1-P43_J469-coot-1.pdb #4/B SER 196 OG F2_coot1-P43_J469-coot-1.pdb #1/A ARG 194 O no hydrogen 3.195 N/A
2 hydrogen bonds found
0 strict hydrogen bonds found
> hide #!13 models
> hide #13.1 models
> show #13.1 models
> select add #13
3 atoms, 8 pseudobonds, 3 residues, 5 models selected
> color #13 #000b00ff models
> select clear
> select #1/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/A:194
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel overlapCutoff -0.3 resSeparation 5 intraMol false
> ignoreHiddenModels true select true showDist true reveal true
8 contacts
> hide #14.1 models
> close #14
> select clear
> select #1/B:196
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:194@O
1 atom, 1 residue, 1 model selected
> select add #1/B:196@N
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/A:194@O #1/B:196@N
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 194 O and /B SER 196 N:
2.43Å
> distance style symbol false
> distance style symbol true
> distance style symbol false
> distance style symbol true
> hide #14.1 models
> select clear
> select #1/B:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:196
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/B:194@O
1 atom, 1 residue, 1 model selected
> select add #1/A:196@N
2 atoms, 2 residues, 1 model selected
> distance #1/B:194@O #1/A:196@N
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ARG 194 O and /A SER 196 N:
2.45Å
> select #1/B:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/B:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/b:198,194,196
25 atoms, 22 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/B:198@OD2
1 atom, 1 residue, 1 model selected
> select add #1/A:193@NZ
2 atoms, 2 residues, 1 model selected
> distance #1/B:198@OD2 #1/A:193@NZ
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 198 OD2 and /A LYS 193
NZ: 3.80Å
> select #1/b:198,194,196
25 atoms, 22 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #1/a:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> view
> select #1/a:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/b:198,194,196
25 atoms, 22 bonds, 3 residues, 1 model selected
> select #1/b:198,194,196
25 atoms, 22 bonds, 3 residues, 1 model selected
> select #1/a:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/b:198,194,196
25 atoms, 22 bonds, 3 residues, 1 model selected
> select #1/a:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/b:198,194,196 sel #1/a:193,194,196
Expected a keyword
> select #1/b:198,194,196, sel #1/a:193,194,196
51 atoms, 46 bonds, 3 pseudobonds, 6 residues, 2 models selected
> select clear
> view
> select #1/b:198,194,196, sel #1/a:193,194,196
51 atoms, 46 bonds, 3 pseudobonds, 6 residues, 2 models selected
> view sel
> select clear
> view
> select #1/b:198,194,196, sel #1/a:193,194,196
51 atoms, 46 bonds, 3 pseudobonds, 6 residues, 2 models selected
> ui tool show "Side View"
> view sel
> view
> view sel
> view
> view sel
> select clear
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/fkd2-coot1_real_space_refined_002-coot-2.pdb
Chain information for fkd2-coot1_real_space_refined_002-coot-2.pdb #15
---
Chain | Description
A | No description available
B | No description available
> matchmaker #15 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker F2_coot1-P43_J469-coot-1.pdb, chain A (#1) with
fkd2-coot1_real_space_refined_002-coot-2.pdb, chain A (#15), sequence
alignment score = 2772.6
RMSD between 531 pruned atom pairs is 0.151 angstroms; (across all 534 pairs:
0.311)
> hide #!1 models
> select #15/b:198,194,196, sel #1/a:193,194,196
51 atoms, 46 bonds, 6 residues, 2 models selected
> select #15/b:198,194,196, sel #1/a:193,194,196
51 atoms, 46 bonds, 6 residues, 2 models selected
> show sel & #!15 atoms
> select #15/b:198,194,196,sel #1/a:193,194,196
51 atoms, 46 bonds, 6 residues, 2 models selected
> select #15/b:198,194,196 sel #1/a:193,194,196
Expected a keyword
> select #15/b:198,194,196
25 atoms, 22 bonds, 3 residues, 1 model selected
> select #1/a:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> select #15/b:198,194,196
25 atoms, 22 bonds, 3 residues, 1 model selected
> select #15/a:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> select #15/b:198,194,196,sel #15/a:193,194,196
51 atoms, 46 bonds, 6 residues, 1 model selected
> show sel atoms
> select #15/b:198,194,196,sel #15/a:193,194,196,198
59 atoms, 53 bonds, 7 residues, 1 model selected
> show sel atoms
> select #15/b:198,194,196,193,sel #15/a:193,194,196,198
68 atoms, 62 bonds, 8 residues, 1 model selected
> show sel atoms
> close #15
Cell requested for row 12 is out of bounds for table with 16 rows! Resizing
table model.
> close #13
> show #!1 models
> view
> select #15/b:198,194,196,193,sel #15/a:193,194,196,198
Nothing selected
> select #15/b:198,194,196,193,sel #15/a:193,194,196,198
Nothing selected
> select #1/b:198,194,196, sel #1/a:193,194,196,198
59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected
> view sel
> view
> view sel
> view
> view sel
> select ~sel & ##selected
8571 atoms, 8746 bonds, 1 pseudobond, 1064 residues, 2 models selected
> select up
8583 atoms, 8746 bonds, 1 pseudobond, 1071 residues, 2 models selected
> select up
8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 2 models selected
> select up
8630 atoms, 8799 bonds, 1 pseudobond, 1071 residues, 2 models selected
> select up
17260 atoms, 17598 bonds, 4 pseudobonds, 2142 residues, 24 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select up
17260 atoms, 17598 bonds, 5 pseudobonds, 2142 residues, 27 models selected
> select clear
> turn x 90
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> turn x -90
> view
> turn x -90
> turn x 90
> turn x -90
> select #1/b:198,194,196, sel #1/a:193,194,196,198
59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected
> view sel
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-4-a.jpg
> width 1163 height 890 supersample 4
> select #1/b:198,194,196, sel #1/a:193,194,196,198
59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected
> hide sel atoms
> color #14 #950000ff models
> color #14 #700000ff models
> color #14 #c00000ff models
> color #14 #c0b100ff models
> color #14 #c0db00ff models
> color #14 #c0fe00ff models
> color #14 #2ffe00ff models
> color #14 #19fe00ff models
> color #14 #0afe00ff models
> select clear
> color #14 #f543e2ff models
> color #14 #ae11f5ff models
> color #14 #9417f5ff models
> select #1/b:198,194,196, sel #1/a:193,194,196,198
59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected
> show sel atoms
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-4-b.jpg
> width 1163 height 890 supersample 4
> select #1/b:198,194,196, sel #1/a:193,194,196,198
59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 2 models selected
> hide sel atoms
> hide #!14 models
> select add #14
59 atoms, 53 bonds, 3 pseudobonds, 7 residues, 3 models selected
> select subtract #14
59 atoms, 53 bonds, 7 residues, 1 model selected
> select clear
> view
> select #1/a:443,492,412,447,449,488
47 atoms, 41 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> select #1/a:443,492,412,447,449,488,319
56 atoms, 49 bonds, 7 residues, 1 model selected
> select #1/b:247
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/b:247
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/a:247
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #1/a:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/b:194,281,356,247,287,290,315
66 atoms, 60 bonds, 7 residues, 1 model selected
> show sel atoms
> select #1/b:281,356,247,287,290,315
55 atoms, 50 bonds, 6 residues, 1 model selected
> select #1/B:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!1 models
> select add #5
2 models selected
> select add #6
4 models selected
> select add #7
6 models selected
> view sel
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> select clear
> hide #!8 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!9 models
> view
> volume #9 level 0.1388
> volume #9 level 0.1291
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J789_007_volume_map_sharp.mrc
Opened cryosparc_P70_J789_007_volume_map_sharp.mrc as #13, grid size
300,300,300, pixel 1.02, shown at level 0.0525, step 2, values float32
> volume #13 level 0.1758
> volume #13 step 1
> volume #13 level 0.2048
> ui tool show "Hide Dust"
> surface dust #13 size 1.91
> surface dust #13 size 2.01
> surface dust #13 size 2.72
> volume #13 level 0.1
> volume #13 level 0.04
> volume #13 level 0.09
> volume #13 level 0.1
> volume #13 level 0.2
> volume #13 level 0.3
> volume #13 level 0.25
> set bgColor white
> hide #!13 models
> show #!13 models
> show #!9 models
> hide #!13 models
> view
> hide #!9 models
> show #!14 models
> hide #!14 models
> show #!13 models
> show #!9 models
> hide #!13 models
> volume #9 level 0.1183
> hide #!9 models
> show #!13 models
> hide #!13 models
> show #!13 models
> volume #13 level 0.221
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J880_009_volume_map_sharp.mrc
Opened cryosparc_P70_J880_009_volume_map_sharp.mrc as #15, grid size
300,300,300, pixel 1.02, shown at level 0.0511, step 2, values float32
> volume #15 level 0.1518
> volume #15 step 1
> volume #15 level 0.2062
> volume #15 level 0.2533
> surface dust #15 size 6.09
> view
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!1 models
> hide #!1 atoms
> select #1/b:488,449
13 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/b:488,449,447,412,356,320,319,283,290,287,247
89 atoms, 80 bonds, 11 residues, 1 model selected
> select #1/b:488,449,447,412,356,320,319,283,290,287,247,492
96 atoms, 86 bonds, 12 residues, 1 model selected
> select #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443
107 atoms, 96 bonds, 13 residues, 1 model selected
> show sel atoms
> select clear
> select #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443
107 atoms, 96 bonds, 13 residues, 1 model selected
> color sel byhetero
> select clear
> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319
121 atoms, 110 bonds, 14 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319
121 atoms, 110 bonds, 14 residues, 1 model selected
> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319 sel
> #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443
Expected a keyword
> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319, sel
> #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443
228 atoms, 206 bonds, 27 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict both overlapCutoff -0.3 resSeparation 5 intraMol false
> ignoreHiddenModels true select true showDist true reveal true
34 contacts
> show #!15 models
> hide #!15 models
> show #14.1 models
> hide #14.1 models
> hide #!14 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #!4 models
> hide #4.2 models
> hide #4.3 models
> select add #1
8630 atoms, 8799 bonds, 38 pseudobonds, 1071 residues, 5 models selected
> select subtract #1
Nothing selected
> hide #!1.2 models
> show #!1.2 models
> hide #1.2.1 models
> close #1.2
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319, sel
> #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443
228 atoms, 206 bonds, 27 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #107c01 dashes 5 showDist true restrict both intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
Finding intermodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 F2_coot1-P43_J469-coot-1.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> hide #1.2 models
> show #1.2 models
> select subtract #1.2
Nothing selected
> select add #1.2
Nothing selected
> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319, sel
> #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443
228 atoms, 206 bonds, 27 residues, 1 model selected
> ui tool show Distances
> ui tool show H-Bonds
> hbonds sel color #107c01 dashes 5 showDist true restrict both intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
Finding intermodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 F2_coot1-P43_J469-coot-1.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> hbonds sel color #107c01 dashes 5 showDist true restrict both intraModel
> false twoColors true slopColor #008000 intraRes false select true reveal
> true retainCurrent true log true
Atom specifier selects no atoms
> select #1/A:412@OD2
1 atom, 1 residue, 1 model selected
> select #1/B:247@ND2
1 atom, 1 residue, 1 model selected
> select add #1/A:412@OD2
2 atoms, 2 residues, 1 model selected
> distance #1/B:247@ND2 #1/A:412@OD2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASN 247 ND2 and /A ASP 412
OD2: 2.65Å
> show #!14 models
> select clear
> select #1/B:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/A:415@NZ
1 atom, 1 residue, 1 model selected
> select add #1/B:281@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/A:415@NZ #1/B:281@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 415 NZ and /B GLU 281
OE2: 3.35Å
> select clear
> select #1/B:281@OE1
1 atom, 1 residue, 1 model selected
> select add #1/A:443@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/B:281@OE1 #1/A:443@NH1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B GLU 281 OE1 and /A ARG 443
NH1: 6.43Å
> select #1/B:290@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:447@OD1
2 atoms, 2 residues, 1 model selected
> distance #1/B:290@NH1 #1/A:447@OD1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ARG 290 NH1 and /A ASP 447
OD1: 3.71Å
> select clear
> select #1/B:319@NZ
1 atom, 1 residue, 1 model selected
> select add #1/A:449@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/B:319@NZ #1/A:449@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B LYS 319 NZ and /A GLU 449
OE2: 5.49Å
> select clear
> select #1/A:449@OE2
1 atom, 1 residue, 1 model selected
> select #1/B:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:449@OE2
9 atoms, 7 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #1/B:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/B:320@N
1 atom, 1 residue, 1 model selected
> select add #1/A:449@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/B:320@N #1/A:449@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 320 N and /A GLU 449
OE2: 3.62Å
> select clear
> show sel cartoons
> select clear
> select #1/B:287
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/B:287@ND1
1 atom, 1 residue, 1 model selected
> select add #1/B:320@OD1
2 atoms, 2 residues, 1 model selected
> distance #1/B:287@ND1 #1/B:320@OD1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B HIS 287 ND1 and ASP 320
OD1: 6.32Å
> select #1/B:287@CA
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #1/A:492
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/A:492@OG1
1 atom, 1 residue, 1 model selected
> select clear
> select #1/B:356@OD1
1 atom, 1 residue, 1 model selected
> select add #1/A:305
10 atoms, 8 bonds, 2 residues, 1 model selected
> select clear
> select #1/A:492@OG1
1 atom, 1 residue, 1 model selected
> select add #1/B:356@OD1
2 atoms, 2 residues, 1 model selected
> distance #1/A:492@OG1 #1/B:356@OD1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A THR 492 OG1 and /B ASN 356
OD1: 4.30Å
> select clear
Drag select of 13 residues, 2 pseudobonds
> select clear
> select #1/B:283
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select
> #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319,492,532,290
136 atoms, 123 bonds, 16 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/A:416@CG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:416
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:488
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:488
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:488
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:415@CE
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:488@O
1 atom, 1 residue, 1 model selected
> select add #1/B:356@ND2
2 atoms, 2 residues, 1 model selected
> distance #1/A:488@O #1/B:356@ND2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLY 488 O and /B ASN 356
ND2: 3.58Å
> select clear
> show sel cartoons
> select clear
> select #1/B:412@OD2
1 atom, 1 residue, 1 model selected
> select add #1/A:247@ND2
2 atoms, 2 residues, 1 model selected
> distance #1/B:412@OD2 #1/A:247@ND2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 412 OD2 and /A ASN 247
ND2: 3.51Å
> select #1/A:281@OE2
1 atom, 1 residue, 1 model selected
> select add #1/B:443@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/A:281@OE2 #1/B:443@NH1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLU 281 OE2 and /B ARG 443
NH1: 3.24Å
> select #1/B:287
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select add #1/B:412@OD1
1 atom, 1 residue, 1 model selected
> select add #1/A:281@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/B:412@OD1 #1/A:281@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 412 OD1 and /A GLU 281
OE2: 6.46Å
> select #1/A:283
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select clear
> select #1/A:290@NH1
1 atom, 1 residue, 1 model selected
> select #1/B:379
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:290@NH1
1 atom, 1 residue, 1 model selected
> select add #1/B:447@OD2
2 atoms, 2 residues, 1 model selected
> distance #1/A:290@NH1 #1/B:447@OD2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 290 NH1 and /B ASP 447
OD2: 3.70Å
> select clear
> select #1/B:447@OD1
1 atom, 1 residue, 1 model selected
> select add #1/A:287@ND1
2 atoms, 2 residues, 1 model selected
> distance #1/B:447@OD1 #1/A:287@ND1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 447 OD1 and /A HIS 287
ND1: 3.10Å
> select clear
> select #1/A:319@NZ
1 atom, 1 residue, 1 model selected
> select add #1/B:449@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/A:319@NZ #1/B:449@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 319 NZ and /B GLU 449
OE2: 3.22Å
> select #1/B:492@OG1
1 atom, 1 residue, 1 model selected
> select add #1/A:356@ND2
2 atoms, 2 residues, 1 model selected
> distance #1/B:492@OG1 #1/A:356@ND2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B THR 492 OG1 and /A ASN 356
ND2: 4.51Å
> select clear
> view
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J882_class_00_00027_volume.mrc
Opened cryosparc_P70_J882_class_00_00027_volume.mrc as #16, grid size
128,128,128, pixel 2.38, shown at level 0.148, step 1, values float32
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J882_class_01_00027_volume.mrc
Opened cryosparc_P70_J882_class_01_00027_volume.mrc as #17, grid size
128,128,128, pixel 2.38, shown at level 0.122, step 1, values float32
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J882_class_02_00027_volume.mrc
Opened cryosparc_P70_J882_class_02_00027_volume.mrc as #18, grid size
128,128,128, pixel 2.38, shown at level 0.143, step 1, values float32
> hide #!1 models
> hide #1.1 models
> hide #1.2 models
> select subtract #1.2
Nothing selected
> hide #!14 models
> volume #16 level 0.2141
> volume #16 level 0.2
> volume #17 level 0.2
> volume #18 level 0.2
> volume #18 level 0.247
> volume #16 level 0.1
> volume #16 level 0.4
> volume #16 level 0.3
> volume #17 level 0.3
> volume #18 level 0.3
> close #16-18
> show #!1 models
> show #1.1 models
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J883_volume_map.mrc
Opened cryosparc_P70_J883_volume_map.mrc as #16, grid size 300,300,300, pixel
1.02, shown at level 0.0423, step 2, values float32
> hide #!1 models
> hide #1.1 models
> select subtract #1.2
Nothing selected
> volume #16 level 0.1026
> volume #16 step 1
> volume #16 level 0.1255
> close #16
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J884_volume_map_sharp.mrc
Opened cryosparc_P70_J884_volume_map_sharp.mrc as #16, grid size 300,300,300,
pixel 1.02, shown at level 0.0579, step 2, values float32
> volume #16 level 0.1072
> volume #16 step 1
> volume #16 level 0.1333
> volume #16 level 0.1997
> close #16
> show #!1 models
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> close #1.2
> show #!14 models
> dssp
Computing secondary structure
> dssp
Computing secondary structure
> select #1/B:196
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:196
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide #!14 models
> show #!14 models
> select clear
> distance style symbol false
> distance style symbol true
> ~distance #1/A:194@O #1/B:196@N
> ~distance #1/B:281@OE1 #1/A:443@NH1
> undo
Undo failed, probably because structures have been modified.
> ~distance #1/B:198@OD2 #1/A:193@NZ
> ~distance #1/A:488@O #1/B:356@ND2
> ~distance #1/A:492@OG1 #1/B:356@OD1
> ~distance #1/B:247@ND2 #1/A:412@OD2
> ~distance #1/B:290@NH1 #1/A:447@OD1
> ~distance #1/A:319@NZ #1/B:449@OE2
> ~distance #1/B:194@O #1/A:196@N
> ~distance #1/A:281@OE2 #1/B:443@NH1
> ~distance #1/A:415@NZ #1/B:281@OE2
> ~distance #1/B:412@OD1 #1/A:281@OE2
> ~distance #1/B:447@OD1 #1/A:287@ND1
> ~distance #1/A:290@NH1 #1/B:447@OD2
> ~distance #1/B:287@ND1 #1/B:320@OD1
> ~distance #1/B:319@NZ #1/A:449@OE2
> ~distance #1/B:320@N #1/A:449@OE2
> ~distance #1/B:492@OG1 #1/A:356@ND2
> ~distance #1/B:412@OD2 #1/A:247@ND2
> select #1/A:532
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/a:532,534,603,658,
Expected an objects specifier or a keyword
> select #1/b:658,601,532,535dssp
25 atoms, 22 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/a:532,534,603,658,
Expected an objects specifier or a keyword
> select #1/b:658,601,532,535
34 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/a:532,534,603,658
35 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/b:658,601,532,535
34 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/a:532,534,603,658.
Expected an objects specifier or a keyword
> select #1/b:658,601,532,535
34 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/a:532,534,603,658
35 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/B:655
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:658@NZ
1 atom, 1 residue, 1 model selected
> select add #1/A:532@OD2
2 atoms, 2 residues, 1 model selected
> distance #1/B:658@NZ #1/A:532@OD2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B LYS 658 NZ and /A ASP 532
OD2: 2.54Å
> select #1/A:534@SD
1 atom, 1 residue, 1 model selected
> select add #1/B:601@ND2
2 atoms, 2 residues, 1 model selected
> distance #1/A:534@SD #1/B:601@ND2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A MET 534 SD and /B ASN 601
ND2: 3.05Å
> select clear
> select #1/A:658@NZ
1 atom, 1 residue, 1 model selected
> select add #1/B:532@OD2
2 atoms, 2 residues, 1 model selected
> distance #1/A:658@NZ #1/B:532@OD2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 658 NZ and /B ASP 532
OD2: 3.05Å
> select clear
> select #1/A:603
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/B:532@OD2
1 atom, 1 residue, 1 model selected
> select add #1/A:603@N
2 atoms, 2 residues, 1 model selected
> distance #1/B:532@OD2 #1/A:603@N
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 532 OD2 and /A HIS 603
N: 2.91Å
> select clear
> show #!1 cartoons
> select clear
> hide #14.1 models
> select clear
> select #1/a:532,534,603,658
35 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/b:658,601,532,535
34 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/a:532,534,603,658sel #1/b:658,601,532,535
60 atoms, 54 bonds, 3 pseudobonds, 7 residues, 2 models selected
> view sel
> select #1/A:532
8 atoms, 7 bonds, 1 residue, 1 model selected
> view
> select #1/A:412@OD2
1 atom, 1 residue, 1 model selected
> select add #1/B:247@ND2
2 atoms, 2 residues, 1 model selected
> distance #1/A:412@OD2 #1/B:247@ND2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 412 OD2 and /B ASN 247
ND2: 2.65Å
> select clear
> select #1/B:281@OE2
1 atom, 1 residue, 1 model selected
> select add #1/A:415@NZ
2 atoms, 2 residues, 1 model selected
> distance #1/B:281@OE2 #1/A:415@NZ
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B GLU 281 OE2 and /A LYS 415
NZ: 3.35Å
> select clear
> select #1/A:443@NH1
1 atom, 1 residue, 1 model selected
> select add #1/B:281@OE1
2 atoms, 2 residues, 1 model selected
> distance #1/A:443@NH1 #1/B:281@OE1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 443 NH1 and /B GLU 281
OE1: 6.43Å
> select #1/B:356@ND2
1 atom, 1 residue, 1 model selected
> select add #1/A:492@OG1
2 atoms, 2 residues, 1 model selected
> distance #1/B:356@ND2 #1/A:492@OG1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASN 356 ND2 and /A THR 492
OG1: 5.67Å
> select #1/B:319@NZ
1 atom, 1 residue, 1 model selected
> select add #1/A:449@OE1
2 atoms, 2 residues, 1 model selected
> distance #1/B:319@NZ #1/A:449@OE1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B LYS 319 NZ and /A GLU 449
OE1: 5.58Å
> select clear
> select #1/B:320@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel atoms
> select #1/B:320@N
1 atom, 1 residue, 1 model selected
> select add #1/A:449@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/B:320@N #1/A:449@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 320 N and /A GLU 449
OE2: 3.62Å
> select clear
> show sel cartoons
> select clear
> select add #1/A:447@OD1
1 atom, 1 residue, 1 model selected
> select add #1/B:320@OD2
2 atoms, 2 residues, 1 model selected
> select clear
> select #1/B:290@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:447@OD1
2 atoms, 2 residues, 1 model selected
> distance #1/B:290@NH1 #1/A:447@OD1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ARG 290 NH1 and /A ASP 447
OD1: 3.71Å
> select clear
> select #1/B:287
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:447@OD2
1 atom, 1 residue, 1 model selected
> select add #1/B:287@N
2 atoms, 2 residues, 1 model selected
> distance #1/A:447@OD2 #1/B:287@N
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 447 OD2 and /B HIS 287
N: 4.43Å
> select clear
> show sel cartoons
> select clear
> select #1/B:412@OD2
1 atom, 1 residue, 1 model selected
> select add #1/A:247@ND2
2 atoms, 2 residues, 1 model selected
> distance #1/B:412@OD2 #1/A:247@ND2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 412 OD2 and /A ASN 247
ND2: 3.51Å
> select clear
> select #1/A:281@OE2
1 atom, 1 residue, 1 model selected
> select add #1/B:443@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/A:281@OE2 #1/B:443@NH1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLU 281 OE2 and /B ARG 443
NH1: 3.24Å
> select #1/a:193,194,196
26 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/b:198,194,196
25 atoms, 22 bonds, 3 residues, 1 model selected
> select #1/a:193,194,196sel #1/b:198,194,196
45 atoms, 41 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/A:200
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:193@NZ
1 atom, 1 residue, 1 model selected
> select #1/B:198@OD2
1 atom, 1 residue, 1 model selected
> select add #1/A:193@NZ
2 atoms, 2 residues, 1 model selected
> distance #1/B:198@OD2 #1/A:193@NZ
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 198 OD2 and /A LYS 193
NZ: 3.80Å
> select #1/A:193@CE
1 atom, 1 residue, 1 model selected
> select clear
> select #1/B:196
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/B:196@N
1 atom, 1 residue, 1 model selected
> select add #1/A:194@O
2 atoms, 2 residues, 1 model selected
> distance #1/B:196@N #1/A:194@O
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B SER 196 N and /A ARG 194 O:
2.43Å
> select clear
> select #1/B:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/b:196
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:194@CA
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select clear
> hide sel atoms
> select clear
> select #1/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #1/B:194@CA
1 atom, 1 residue, 1 model selected
> select #1/B:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show sel cartoons
> hide sel atoms
> select clear
> show sel cartoons
> hide sel atoms
> select #1/B:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:278
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:356@ND2
1 atom, 1 residue, 1 model selected
> select add #1/B:492@OG1
2 atoms, 2 residues, 1 model selected
> distance #1/A:356@ND2 #1/B:492@OG1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASN 356 ND2 and /B THR 492
OG1: 4.51Å
> select #1/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:242
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:449@OE2
1 atom, 1 residue, 1 model selected
> select clear
> select #1/B:449@OE2
1 atom, 1 residue, 1 model selected
> select add #1/A:319@NZ
2 atoms, 2 residues, 1 model selected
> distance #1/B:449@OE2 #1/A:319@NZ
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B GLU 449 OE2 and /A LYS 319
NZ: 3.22Å
> select clear
> select #1/B:447@OD1
1 atom, 1 residue, 1 model selected
> select add #1/A:290@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/B:447@OD1 #1/A:290@NH1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 447 OD1 and /A ARG 290
NH1: 3.67Å
> select clear
> select #1/A:287
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:287@N
1 atom, 1 residue, 1 model selected
> select add #1/B:447@OD2
2 atoms, 2 residues, 1 model selected
> distance #1/A:287@N #1/B:447@OD2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A HIS 287 N and /B ASP 447
OD2: 4.19Å
> select clear
> select #1/A:278
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> view
> lighting soft
> lighting simple
> lighting full
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 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
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> lighting soft
> dssp
Computing secondary structure
> show #!2 models
> hide #!1 models
> hide #1.1 models
> show #!1 models
> hide #!2 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 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
> hide #!14 models
> show #!14 models
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 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
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
Exactly two atoms must be selected!
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 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
> hide #!1 models
> hide #!14 models
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J889_008_volume_map_sharp.mrc
Opened cryosparc_P70_J889_008_volume_map_sharp.mrc as #16, grid size
300,300,300, pixel 1.02, shown at level 0.0454, step 2, values float32
> volume #16 level 0.1381
> volume #16 step 1
> volume #16 level 0.2664
> close #16
> show #!1 models
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J879_class_01_00165_volume.mrc
Opened cryosparc_P70_J879_class_01_00165_volume.mrc as #16, grid size
128,128,128, pixel 2.03, shown at level 0.0762, step 1, values float32
> open
> /Users/hrishikeshdas/Downloads/cryosparc_P70_J879_class_02_00165_volume.mrc
Opened cryosparc_P70_J879_class_02_00165_volume.mrc as #17, grid size
128,128,128, pixel 2.03, shown at level 0.196, step 1, values float32
> volume #16 level 0.1605
> hide #!1 models
> volume #17 level 0.2287
> close #17
> volume #16 level 0.2073
> volume #16 level 0.3384
> close #16
> show #!1 models
> select #1/a:281,356,412,447,449,488,416,415,443,247,287,290,283,319,492,290
128 atoms, 116 bonds, 15 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/b:488,449,447,412,356,320,319,283,290,287,247,492,443
107 atoms, 96 bonds, 13 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/A:412@OD2
1 atom, 1 residue, 1 model selected
> select add #1/B:247@ND2
2 atoms, 2 residues, 1 model selected
> ~distance #1/B:532@OD2 #1/A:603@N
> ~distance #1/A:447@OD2 #1/B:287@N
> ~distance #1/B:290@NH1 #1/A:447@OD1
> ~distance #1/B:281@OE2 #1/A:415@NZ
> ~distance #1/A:412@OD2 #1/B:247@ND2
> ~distance #1/B:198@OD2 #1/A:193@NZ
> ~distance #1/B:447@OD1 #1/A:290@NH1
> ~distance #1/A:356@ND2 #1/B:492@OG1
> ~distance #1/B:356@ND2 #1/A:492@OG1
> ~distance #1/B:449@OE2 #1/A:319@NZ
> ~distance #1/A:287@N #1/B:447@OD2
> ~distance #1/A:281@OE2 #1/B:443@NH1
> ~distance #1/B:320@N #1/A:449@OE2
> ~distance #1/B:196@N #1/A:194@O
> ~distance #1/A:443@NH1 #1/B:281@OE1
> ~distance #1/A:658@NZ #1/B:532@OD2
> ~distance #1/B:658@NZ #1/A:532@OD2
> ~distance #1/A:534@SD #1/B:601@ND2
> ~distance #1/B:412@OD2 #1/A:247@ND2
> ~distance #1/B:319@NZ #1/A:449@OE1
> distance #1/A:412@OD2 #1/B:247@ND2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 412 OD2 and /B ASN 247
ND2: 2.65Å
> select #1/A:447@OD1
1 atom, 1 residue, 1 model selected
> select add #1/B:290@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/A:447@OD1 #1/B:290@NH1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 447 OD1 and /B ARG 290
NH1: 3.71Å
> select #1/B:287
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:447@OD2
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #1/B:287@N
1 atom, 1 residue, 1 model selected
> select clear
> hide #14.1 models
> select #1/B:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/A:415@NZ
1 atom, 1 residue, 1 model selected
> select #1/B:281@OE2
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:415@NZ
1 atom, 1 residue, 1 model selected
> select add #1/B:281@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/A:415@NZ #1/B:281@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 415 NZ and /B GLU 281
OE2: 3.35Å
> select clear
> select #1/A:443@NH1
1 atom, 1 residue, 1 model selected
> select add #1/B:281@OE1
2 atoms, 2 residues, 1 model selected
> distance #1/A:443@NH1 #1/B:281@OE1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 443 NH1 and /B GLU 281
OE1: 6.43Å
> select clear
> select #1/B:283
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/B:287@C
1 atom, 1 residue, 1 model selected
> select #1/B:288
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show sel cartoons
> hide sel atoms
> select #1/B:287
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:449
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:252
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:449@O
1 atom, 1 residue, 1 model selected
> select #1/A:449@O
1 atom, 1 residue, 1 model selected
> select #1/A:449@N
1 atom, 1 residue, 1 model selected
> select add #1/B:320@OD2
2 atoms, 2 residues, 1 model selected
> select clear
> select #1/A:449@N
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:492
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/b:492
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:356@ND2
1 atom, 1 residue, 1 model selected
> select add #1/B:492@OG1
2 atoms, 2 residues, 1 model selected
> distance #1/A:356@ND2 #1/B:492@OG1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASN 356 ND2 and /B THR 492
OG1: 4.51Å
> select clear
> select #1/B:449@OE2
1 atom, 1 residue, 1 model selected
> select #1/A:319@NZ
1 atom, 1 residue, 1 model selected
> select add #1/B:449@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/A:319@NZ #1/B:449@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A LYS 319 NZ and /B GLU 449
OE2: 3.22Å
> select #1/B:447@OD1
1 atom, 1 residue, 1 model selected
> select add #1/A:290@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/B:447@OD1 #1/A:290@NH1
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 447 OD1 and /A ARG 290
NH1: 3.67Å
> select clear
> select #1/A:287
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/B:443@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:281@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/B:443@NH1 #1/A:281@OE2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ARG 443 NH1 and /A GLU 281
OE2: 3.24Å
> select #1/A:247@ND2
1 atom, 1 residue, 1 model selected
> select add #1/B:412@OD2
2 atoms, 2 residues, 1 model selected
> distance #1/A:247@ND2 #1/B:412@OD2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASN 247 ND2 and /B ASP 412
OD2: 3.51Å
> select clear
> select #1/B:412@OD1
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:283@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show sel cartoons
Drag select of 2 residues
> select clear
> select #1/B:319@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #1/B:319
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:449@OE2
1 atom, 1 residue, 1 model selected
> select add #1/B:319@N
2 atoms, 2 residues, 1 model selected
> distance #1/A:449@OE2 #1/B:319@N
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLU 449 OE2 and /B LYS 319
N: 3.24Å
> select clear
> select #1/B:319@N
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #1/B:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/B:320@CA
1 atom, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> select add #1/B:320@OD2
1 atom, 3 bonds, 1 residue, 1 model selected
> select add #1/B:320@CB
2 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
Drag select of 2 atoms, 1 residues, 1 bonds
> hide sel atoms
> select clear
> select #1/A:488
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:488@O
1 atom, 1 residue, 1 model selected
> select add #1/B:356@ND2
2 atoms, 2 residues, 1 model selected
> distance #1/A:488@O #1/B:356@ND2
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A GLY 488 O and /B ASN 356
ND2: 3.58Å
> select clear
> show sel cartoons
> select clear
> select #1/B:247@CA
1 atom, 1 residue, 1 model selected
> select add #1/A:412
9 atoms, 7 bonds, 2 residues, 1 model selected
> select add #1/A:443
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add #1/B:281
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #1/A:415
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #1/B:290
49 atoms, 43 bonds, 6 residues, 1 model selected
> select add #1/A:449
58 atoms, 51 bonds, 7 residues, 1 model selected
> select add #1/B:319
67 atoms, 59 bonds, 8 residues, 1 model selected
> select add #1/B:356
75 atoms, 66 bonds, 9 residues, 1 model selected
> select add #1/A:488
79 atoms, 69 bonds, 10 residues, 1 model selected
> select add #1/A:447
87 atoms, 76 bonds, 11 residues, 1 model selected
> view sel
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-2a.jpg
> width 2696 height 1890 supersample 4
> select #1/A:416
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-2a.jpg
> width 2696 height 1890 supersample 4
> style #!1 stick
Changed 8630 atom styles
> hide #!1 models
> show #!1 models
> open /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD1/FASTKD1.pdb
FASTKD1.pdb title:
Alphafold monomer V2.0 prediction for fast kinase domain-containing protein 1,
mitochondrial (Q53R41) [more info...]
Chain information for FASTKD1.pdb #16
---
Chain | Description | UniProt
A | fast kinase domain-containing protein 1, mitochondrial | FAKD1_HUMAN 1-847
Computing secondary structure
> hide #!1 models
> view
> rainbow #16
> select clear
> select #16/A:61
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> close #16
> show #!1 models
> view
> show #1.1 models
> select #1/A:247
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select clear
> select #1/A:283@SG
1 atom, 1 residue, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select #1/A:283
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #1/A:290
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:319
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:412
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:443
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:449
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:492
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #1/a:247,281,290,319,356sel #1/b:412,443,447,449,492
80 atoms, 71 bonds, 4 pseudobonds, 9 residues, 2 models selected
> select #1/A:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/a:247,281,290,319,356 sel #1/b:412,443,447,449,492
Expected a keyword
> select #1/a:247,281,290,319,356, sel #1/b:412,443,447,449,492
88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected
> select clear
> select #1/A:412@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:412@CA
1 atom, 1 residue, 1 model selected
> select #1/A:412
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:443
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:449
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:488
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:488
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:247
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:290
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:354
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:319
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:356@CA
1 atom, 1 residue, 1 model selected
> select #1/B:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/a:412,415,443,447,449,488,sel #1/b:247,281,290,319,356
94 atoms, 83 bonds, 6 pseudobonds, 11 residues, 2 models selected
> view
> view sel
> view orient
> view
> select up
593 atoms, 598 bonds, 6 pseudobonds, 75 residues, 2 models selected
> select down
94 atoms, 83 bonds, 6 pseudobonds, 11 residues, 2 models selected
> turn y 90
> select clear
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> turn y -90
> view
> select #1/a:193,194,196,sel #1/b:198,194,196
51 atoms, 46 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/A:193@NZ
1 atom, 1 residue, 1 model selected
> select #1/B:198@OD2
1 atom, 1 residue, 1 model selected
> select add #1/A:193@NZ
2 atoms, 2 residues, 1 model selected
> distance #1/B:198@OD2 #1/A:193@NZ
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 198 OD2 and /A LYS 193
NZ: 3.80Å
> select clear
> select #1/B:196@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/B:196@OG
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:194@N
1 atom, 1 residue, 1 model selected
> select add #1/B:196@OG
2 atoms, 2 residues, 1 model selected
> distance #1/A:194@N #1/B:196@OG
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ARG 194 N and /B SER 196
OG: 4.37Å
> select clear
> show sel cartoons
> select clear
> select #1/B:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/B:194@O
1 atom, 1 residue, 1 model selected
> select #1/A:196
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:196@N
1 atom, 1 residue, 1 model selected
> select add #1/B:194@O
2 atoms, 2 residues, 1 model selected
> distance #1/A:196@N #1/B:194@O
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A SER 196 N and /B ARG 194 O:
2.45Å
> select clear
> show sel cartoons
> select clear
> select #1/B:196@N
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #1/a:532,534,603,658,sel #1/b:658,601,532,535
69 atoms, 62 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select #1/B:532@OD2
1 atom, 1 residue, 1 model selected
> select add #1/A:658@NZ
2 atoms, 2 residues, 1 model selected
> distance #1/B:532@OD2 #1/A:658@NZ
Distance between F2_coot1-P43_J469-coot-1.pdb #1/B ASP 532 OD2 and /A LYS 658
NZ: 3.05Å
> select clear
> select #1/A:603@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:603
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> select clear
> select #1/A:532@OD2
1 atom, 1 residue, 1 model selected
> select add #1/B:658@NZ
2 atoms, 2 residues, 1 model selected
> distance #1/A:532@OD2 #1/B:658@NZ
Distance between F2_coot1-P43_J469-coot-1.pdb #1/A ASP 532 OD2 and /B LYS 658
NZ: 2.54Å
> select clear
> select add #1/B:601
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:534
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> view
> show #!6 models
> hide #!6 models
> close #5-8
> show #!9 models
> hide #!9 models
> close #9-13
> show #!15 models
> hide #!15 models
> close #15
Cell requested for row 3 is out of bounds for table with 10 rows! Resizing
table model.
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_interactions.cxs
> select #1/B:535
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/B:194@CA
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #1/B:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> turn y 90
> turn y -90
> select ~sel & ##selected
Nothing selected
> turn y 90
> turn y -90
> turn y 90
> turn x 90
> turn x -90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_interactions_atoms-1.jpg
> width 2696 height 1890 supersample 4
> select #1/a:193,194,196,sel #1/b:198,194,196
51 atoms, 46 bonds, 3 pseudobonds, 6 residues, 2 models selected
> turn x 90
> turn x -90
> view sel
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface-1a.jpg
> width 2696 height 1890 supersample 4
> turn x 90
> view
> turn x -90
> select #1/B:198
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> turn x -90
> turn x 90
> select #1/B:532@CA
1 atom, 1 residue, 1 model selected
> select #1/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:532@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #1/B:532@CA
1 atom, 1 residue, 1 model selected
> select #1/B:532@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #1/a:532,534,603,658,sel #1/b:658,601,532,535
69 atoms, 62 bonds, 2 pseudobonds, 8 residues, 2 models selected
> select #1/A:534
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:534
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/a:532,534,603,658,sel #1/b:658,601,532,535
69 atoms, 62 bonds, 2 pseudobonds, 8 residues, 2 models selected
> view sel
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface4-a.jpg
> width 2696 height 1890 supersample 4
> turn x -90
> view
> select #1/a:247,281,290,319,356,sel #1/b:412,443,447,449,492
88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected
> select clear
> view
> select #1/a:247,281,290,319,356,sel #1/b:412,443,447,449,492
88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected
> turn y -90
> view sel
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface3-a.jpg
> width 2696 height 1890 supersample 4
> view
> select #1/A:247
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/a:247,281,290,319,356,sel #1/b:412,443,447,449,492
88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected
> turn y -90
> view sel
> view
> select clear
> select #1/a:247,281,290,319,356,sel #1/b:412,443,447,449,492
88 atoms, 78 bonds, 5 pseudobonds, 10 residues, 2 models selected
> select #1/a:412,415,443,447,449,488,sel #1/b:247,281,290,319,356
94 atoms, 83 bonds, 6 pseudobonds, 11 residues, 2 models selected
> view sel
> view
> turn y 90
> view sel
> select clear
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/interface2-a.jpg
> width 2696 height 1890 supersample 4
> view
> open /Users/hrishikeshdas/Downloads/cryosparc_P70_J927_006_volume_map.mrc
Opened cryosparc_P70_J927_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 1.02, shown at level 0.0167, step 1, values float32
> volume #5 level 0.0624
> volume #5 level 0.08581
> hide #!1 models
> hide #1.1 models
> hide #!5 models
> show #!5 models
> hide #!14 models
> volume #5 level 0.1014
> ui tool show "Hide Dust"
> surface dust #5 size 26.28
> select ~sel & ##selected
Nothing selected
> volume #5 level 0.11
> vop threshold #5 minimum 0.11 set 0
Opened cryosparc_P70_J927_006_volume_map.mrc thresholded as #6, grid size
256,256,256, pixel 1.02, shown at step 1, values float32
> surface dust #6 size 9.98
> surface dust #6 size 11.03
> surface dust #6 size 18.51
> vop threshold #6 maximum 0.1 set 1
Opened cryosparc_P70_J927_006_volume_map.mrc thresholded as #7, grid size
256,256,256, pixel 1.02, shown at step 1, values float32
> volume #7 level 0.08614
> surface dust #6 size 18.51
> surface dust #7 size 6.09
> surface dust #7 size 6.47
> surface dust #7 size 17.03
> surface dust #7 size 16.75
> surface dust #7 size 1.02
> ui tool show "Map Eraser"
> select add #8
1 model selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,91.777,0,1,0,132.21,0,0,1,128.03
> volume erase #7 center 91.777,132.21,128.03 radius 14.343
> view matrix models #8,1,0,0,98.765,0,1,0,154.52,0,0,1,134.97
> volume erase #7 center 98.765,154.52,134.97 radius 14.343
No map chosen to save
> save /Users/hrishikeshdas/Desktop/J972_p70_forMask.mrc models #7
> close #7
> close #6
> show #!5 models
> close #5
> close #8
> show #!1 models
> select clear
> turn y 90
> turn y -90
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> turn y 90
> turn x 90
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs
Opened cryosparc_P43_J469_008_volume_map.mrc as #2, grid size 288,288,288,
pixel 0.902, shown at level 0.0497, step 1, values float32
Opened cryosparc_P43_J469_008_volume_map_sharp.mrc as #3, grid size
288,288,288, pixel 0.902, shown at level 0.171, step 1, values float32
Log from Sun Jan 26 10:09:07 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/FAST42apo_dimer/F2_coot1-P43_J469-coot-1.pdb
Chain information for F2_coot1-P43_J469-coot-1.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/FAST42apo_dimer/cryosparc_P43_J469_008_volume_map.mrc
Opened cryosparc_P43_J469_008_volume_map.mrc as #2, grid size 288,288,288,
pixel 0.902, shown at level 0.00703, step 2, values float32
> lighting soft
[Repeated 1 time(s)]
> color bypolymer
> volume #2 level 0.03766
> volume #2 step 1
> lighting soft
> set bgColor white
> graphics silhouettes true
> select /A
4349 atoms, 4435 bonds, 540 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #fbe7c6ff
> graphics silhouettes false
> graphics silhouettes true
> select clear
> select /B
4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected
> color (#!1 & sel) #a0e7e5ff
> select clear
> dssp
Computing secondary structure
> volume #2 level 0.03946
> volume #2 level 0.04489
> hide #!2 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.04971
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs
> show #!1 models
> show #!2 models
> open
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/Stucture/FAST42apo_dimer/cryosparc_P43_J469_008_volume_map_sharp.mrc
Opened cryosparc_P43_J469_008_volume_map_sharp.mrc as #3, grid size
288,288,288, pixel 0.902, shown at level 0.0405, step 2, values float32
> volume #3 level 0.09217
> volume #3 step 1
> volume #3 level 0.09441
> volume #3 level 0.1191
> volume #3 level 0.1326
> volume #3 level 0.1349
> volume #3 level 0.1506
> volume #3 level 0.1641
> volume #3 level 0.1686
> volume #3 level 0.1708
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> volume #3 color white
> volume #3 color #b2ffff
> volume #3 color #b2b2ff
> volume #3 color #b2b2b2
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs
> color #2 near #1 5
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #2 near #1 distance 5
> lighting soft
> lighting full
> lighting simple
> lighting soft
> view
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/MAP_surface-1.jpg
> width 1163 height 850 supersample 4
> view
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-1.jpg
> width 1163 height 850 supersample 3
> turn y 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-2.jpg
> width 1163 height 850 supersample 3
> turn y 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-3.jpg
> width 1163 height 850 supersample 3
> turn z 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-4.jpg
> width 1163 height 850 supersample 3
> turn z 90
[Repeated 6 time(s)]
> turn y -90
[Repeated 1 time(s)]
> turn x 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-5.jpg
> width 1163 height 850 supersample 3
> select ~sel & ##selected
Nothing selected
> turn x 180
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/paper_FASTKD2/MAP_surface-6.jpg
> width 1163 height 850 supersample 3
> turn x -180
> hide #!2 models
> show #!1 models
> select /A
4349 atoms, 4435 bonds, 540 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #48d6d2ff
> select /A
4349 atoms, 4435 bonds, 540 residues, 1 model selected
> select /B
4281 atoms, 4364 bonds, 1 pseudobond, 531 residues, 2 models selected
> color (#!1 & sel) #fefcbfff
> select clear
> dssp
Computing secondary structure
> select clear
> color zone #2 near #1 distance 4
> show #!2 models
> hide #!1 models
> lighting full
> lighting soft
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> color zone #3 near #1 distance 4
> hide #!3 models
> show #!2 models
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface.jpg
> width 1163 height 850 supersample 4
> select ~sel & ##selected
Nothing selected
> turn y 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface_turnY90.jpg
> width 1163 height 850 supersample 4
> turn y 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface_turnY90Y90.jpg
> width 1163 height 850 supersample 4
> turn y 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface_turnY90Y90Y90.jpg
> width 1163 height 850 supersample 4
> turn y 90
> turn x 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surface-X90.jpg
> width 1163 height 850 supersample 3
> turn x -90
[Repeated 1 time(s)]
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FAST2_paper/F2_surfaceX90.jpg
> width 1163 height 850 supersample 3
> turn x 90
> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD2/FASTKD2_paper.cxs
——— End of log from Sun Jan 26 10:09:07 2025 ———
opened ChimeraX session
OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2,6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
OS Loader Version: 582~3311
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 7 days, 10 hours, 58 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
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