![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17616 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000201c44c80 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.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.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 99)
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{
"uptime" : 950000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 34124,
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"build" : "24E263",
"releaseType" : "User"
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"captureTime" : "2025-05-10 23:21:16.8419 +0200",
"codeSigningMonitor" : 1,
"incident" : "11E64316-FDAF-4327-BF79-A23EB4CABC2B",
"pid" : 82598,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-09 16:18:07.0136 +0200",
"procStartAbsTime" : 22501427959013,
"procExitAbsTime" : 22966192062523,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9BC9F223-5472-5769-A7E5-B867E5283938","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1F9E78E0-AECE-060C-BEAF-BA18B4888B96",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["regionIneligible","selectedLanguageDoesNotMatchSelectedSiriLanguage","countryBillingIneligible"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "0BF15505-B337-4B03-8121-B435101D57D0",
"wakeTime" : 15171,
"sleepWakeUUID" : "095467E3-E775-427E-A175-9DD39F60891A",
"sip" : "enabled",
"vmRegionInfo" : "0x7475717af188 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00007475717af188","rawCodes":[1,128047763878280],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00007475717af188"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":82598},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x7475717af188 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS
Current working directory is:
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Changed 0 atom styles
> open cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc
Opened cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc as #1, grid size
548,548,548, pixel 0.5, shown at level 6.93, step 4, values float32
> rename #1 X_DH_map
> open XL_MCM_DH_final_v1_30042025.pdb
Chain information for XL_MCM_DH_final_v1_30042025.pdb #2
---
Chain | Description
2 A | No description available
3 B | No description available
4 C | No description available
5 D | No description available
6 E | No description available
7 F | No description available
X | No description available
Y | No description available
> rename #2 X_DH
> open emdb:19618
Opened emdb 19618 as #3, grid size 400,400,400, pixel 1.08, shown at level
0.33, step 2, values float32, fit PDB 8s09
> rename #3 H_DH_map_Costa
> open 8S09
8s09 title:
H. sapiens MCM2-7 double hexamer bound to double stranded DNA [more info...]
Chain information for 8s09 #4
---
Chain | Description | UniProt
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904
3 B | DNA replication licensing factor MCM3 | MCM3_HUMAN 1-808
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719
X | DNA (45-mer) |
Y | DNA (45-mer) |
Non-standard residues in 8s09 #4
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> rename #4 H_DH_Costa
> open emdb:43708
Opened emdb 43708 as #5, grid size 500,500,500, pixel 0.832, shown at level
0.1, step 2, values float32, fit PDB 8w0f
> rename #5 H_DH_map_Bleichert
> open 8W0F
8w0f title:
Cryo-EM structure of a human MCM2-7 double hexamer on dsDNA [more info...]
Chain information for 8w0f #6
---
Chain | Description | UniProt
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904
3 B | DNA replication licensing factor MCM3 | MCM3_HUMAN 2-808
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719
O | DNA (47-MER) |
S | DNA (47-MER) |
Non-standard residues in 8w0f #6
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> rename #6 H_DH_Bleichert
> open emdb:32258
Opened emdb 32258 as #7, grid size 400,400,400, pixel 1.06, shown at level
0.5, step 2, values float32, fit PDB 7w1y
> rename #7 H_DH_map_Zhai
> open 7W1Y
Summary of feedback from opening 7W1Y fetched from pdb
---
warnings | Ignoring microheterogeneity for label_seq_id 1 in chain S
Ignoring microheterogeneity for label_seq_id 2 in chain S
Ignoring microheterogeneity for label_seq_id 3 in chain S
Ignoring microheterogeneity for label_seq_id 4 in chain S
Ignoring microheterogeneity for label_seq_id 5 in chain S
93 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
7w1y title:
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) [more
info...]
Chain information for 7w1y #8
---
Chain | Description | UniProt
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904
3 B | Isoform 2 of DNA replication licensing factor MCM3 | MCM3_HUMAN -44-808
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719
S | DNA (49-MER) |
Non-standard residues in 7w1y #8
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
DA — 2'-deoxyadenosine-5'-monophosphate
MG — magnesium ion
ZN — zinc ion
2025 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> rename #8 H_DH_Zhai
> open emdb:19186
Opened emdb 19186 as #9, grid size 420,420,420, pixel 1.08, shown at level
0.02, step 2, values float32, fit PDB 8rif
> rename #9 Y_DH_map_Miller
> open 8RIF
8rif title:
Cryo-EM structure of the MCM double hexamer loaded onto dsDNA. [more info...]
Chain information for 8rif #10
---
Chain | Description | UniProt
2 A | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 B | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 C | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 D | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 E | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 F | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
X | DNA (53-MER) |
Y | DNA (53-MER) |
Non-standard residues in 8rif #10
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> rename #10 Y_DH_Miller
> transparency #1,3,5,7,9 60
> matchmaker #4/2 to #2/2 bring #3
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 X_DH, chain 2 (#2) with H_DH_Costa, chain 2 (#4), sequence
alignment score = 3374.7
RMSD between 602 pruned atom pairs is 1.247 angstroms; (across all 692 pairs:
1.498)
> matchmaker #6/2 to #2/2 bring #5
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 X_DH, chain 2 (#2) with H_DH_Bleichert, chain 2 (#6), sequence
alignment score = 3236.1
RMSD between 621 pruned atom pairs is 0.633 angstroms; (across all 646 pairs:
0.877)
> matchmaker #8/2 to #2/2 bring #7
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 X_DH, chain 2 (#2) with H_DH_Zhai, chain 2 (#8), sequence alignment
score = 3342.3
RMSD between 644 pruned atom pairs is 0.653 angstroms; (across all 702 pairs:
1.557)
> matchmaker #10/2 to #2/2 bring #9
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 X_DH, chain 2 (#2) with Y_DH_Miller, chain 2 (#10), sequence
alignment score = 2105.8
RMSD between 515 pruned atom pairs is 1.084 angstroms; (across all 616 pairs:
1.831)
> volume #1,3,5,7,9 step 1
> set bgColor white
> lighting soft
> lighting shadows true intensity 0.5
> volume #1,3,5,7,9 color #b2b2b29a
> color #*/2,A pink
> color #*/3,B dodger blue
> color #*/4,C olive drab
> color #*/5,D gold
> color #*/6,E orange
> color #*/7,F indigo
> color #*/X,S black
> color #*/Y,O light grey
> hide atoms
> show cartoons
> hide #*/X,Y #*/S,O cartoons
> show #*/X,Y #*/S,O atoms
> select #*/X,Y #*/S,O
12687 atoms, 13932 bonds, 390 pseudobonds, 502 residues, 9 models selected
> style sel sphere
Changed 12687 atom styles
> select clear
> show ::name="ADP" atoms
> style ::name="ADP" stick
Changed 876 atom styles
> color ::name="ADP" red
> show ::name="ATP" atoms
> style ::name="ATP" stick
Changed 888 atom styles
> color ::name="ATP" red
> show ::name="AGS" atoms
> style ::name="AGS" stick
Changed 0 atom styles
> color ::name="AGS" red
> show ::name="Zn" atoms
> style ::name="Zn" stick
Changed 50 atom styles
> color ::name="Zn" byhetero
> show ::name="Mg" atoms
> style ::name="Mg" stick
Changed 50 atom styles
> color ::name="Mg" byhetero
> volume #1 level 5
> color zone #1 near #2 distance 6.5
> volume splitbyzone #1
Opened X_DH_map 0 as #11.1, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 1 as #11.2, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 2 as #11.3, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 3 as #11.4, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 4 as #11.5, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 5 as #11.6, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 6 as #11.7, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 7 as #11.8, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 8 as #11.9, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 9 as #11.10, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 10 as #11.11, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
Opened X_DH_map 11 as #11.12, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32
> transparency #11 60
> volume #11 level 6.5
> volume #3 level 0.4
> color zone #3 near #4 distance 6.5
> volume splitbyzone #3
Opened H_DH_map_Costa 0 as #12.1, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 1 as #12.2, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 2 as #12.3, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 3 as #12.4, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 4 as #12.5, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 5 as #12.6, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 6 as #12.7, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 7 as #12.8, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 8 as #12.9, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 9 as #12.10, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32
Opened H_DH_map_Costa 10 as #12.11, grid size 400,400,400, pixel 1.08, shown
at level 0.4, step 1, values float32
Opened H_DH_map_Costa 11 as #12.12, grid size 400,400,400, pixel 1.08, shown
at level 0.4, step 1, values float32
> transparency #12 60
> volume #12 level 0.4
> volume #5 level 0.12
> color zone #5 near #6 distance 6.5
> volume splitbyzone #5
Opened H_DH_map_Bleichert 0 as #13.1, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 1 as #13.2, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 2 as #13.3, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 3 as #13.4, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 4 as #13.5, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 5 as #13.6, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 6 as #13.7, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 7 as #13.8, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 8 as #13.9, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 9 as #13.10, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 10 as #13.11, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
Opened H_DH_map_Bleichert 11 as #13.12, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32
> transparency #13 60
> volume #13 level 0.12
> volume #7 level 0.7
> color zone #7 near #8 distance 6.5
> volume splitbyzone #7
Opened H_DH_map_Zhai 0 as #14.1, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 1 as #14.2, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 2 as #14.3, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 3 as #14.4, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 4 as #14.5, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 5 as #14.6, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 6 as #14.7, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 7 as #14.8, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 8 as #14.9, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 9 as #14.10, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 10 as #14.11, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
Opened H_DH_map_Zhai 11 as #14.12, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32
> transparency #14 60
> volume #14 level 0.7
> volume #9 level 0.022
> color zone #9 near #10 distance 6.5
> volume splitbyzone #9
Opened Y_DH_map_Miller 0 as #15.1, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 1 as #15.2, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 2 as #15.3, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 3 as #15.4, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 4 as #15.5, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 5 as #15.6, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 6 as #15.7, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 7 as #15.8, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 8 as #15.9, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32
Opened Y_DH_map_Miller 9 as #15.10, grid size 420,420,420, pixel 1.08, shown
at level 0.022, step 1, values float32
Opened Y_DH_map_Miller 10 as #15.11, grid size 420,420,420, pixel 1.08, shown
at level 0.022, step 1, values float32
Opened Y_DH_map_Miller 11 as #15.12, grid size 420,420,420, pixel 1.08, shown
at level 0.022, step 1, values float32
> transparency #15 60
> volume #15 level 0.022
> hide #4,6,8,10,12,13,14,15 models
> color ::name="ADP" byhetero
> color ::name="ATP" byhetero
> name xlMCM2_ZNF #2/2:306-356
"#2/2:306-356 ": contains extra trailing text
> name xlMCM3_ZNF #2/3:140-195
"#2/3:140-195 ": contains extra trailing text
> name xlMCM4_ZNF #2/4:293-342
"#2/4:293-342 ": contains extra trailing text
> name xlMCM5_ZNF #2/5:163-224
"#2/5:163-224 ": contains extra trailing text
> name xlMCM6_ZNF #2/6:153-202
"#2/6:153-202 ": contains extra trailing text
> name xlMCM7_ZNF #2/7:177-227
"#2/7:177-227 ": contains extra trailing text
> name xlMCM2_OB #2/2:405-422
"#2/2:405-422 ": contains extra trailing text
> name xlMCM3_OB #2/3:243-258
"#2/3:243-258 ": contains extra trailing text
> name xlMCM4_OB #2/4:392-408
"#2/4:392-408 ": contains extra trailing text
> name xlMCM5_OB #2/5:275-286
"#2/5:275-286 ": contains extra trailing text
> name xlMCM6_OB #2/6:254-264
"#2/6:254-264 ": contains extra trailing text
> name xlMCM7_OB #2/7:280-293
"#2/7:280-293 ": contains extra trailing text
> name xlMCM2_H2I #2/2:543-559
"#2/2:543-559 ": contains extra trailing text
> name xlMCM3_H2I #2/3:380-395
"#2/3:380-395 ": contains extra trailing text
> name xlMCM4_H2I #2/4:540-555
"#2/4:540-555 ": contains extra trailing text
> name xlMCM5_H2I #2/5:417-432
"#2/5:417-432 ": contains extra trailing text
> name xlMCM6_H2I #2/6:433-448
"#2/6:433-448 ": contains extra trailing text
> name xlMCM7_H2I #2/7:405-432
"#2/7:405-432 ": contains extra trailing text
> name xlMCM2_PS1 #2/2:593-605
"#2/2:593-605 ": contains extra trailing text
> name xlMCM3_PS1 #2/3:434-439
"#2/3:434-439 ": contains extra trailing text
> name xlMCM4_PS1 #2/4:594-599
"#2/4:594-599 ": contains extra trailing text
> name xlMCM5_PS1 #2/5:471-476
"#2/5:471-476 ": contains extra trailing text
> name xlMCM6_PS1 #2/6:487-491
"#2/6:487-491 ": contains extra trailing text
> name xlMCM7_PS1 #2/7:468-474
"#2/7:468-474 ": contains extra trailing text
> name xlMCM2_ATP #2/2:ATP
"#2/2:ATP ": contains extra trailing text
> name xlMCM3_ADP #2/3:ADP
"#2/3:ADP ": contains extra trailing text
> name xlMCM4_ATP #2/4:ATP
"#2/4:ATP ": contains extra trailing text
> name xlMCM5_ATP #2/5:ATP
"#2/5:ATP ": contains extra trailing text
> name xlMCM6_ATP #2/6:ATP
"#2/6:ATP ": contains extra trailing text
> name xlMCM7_ATP #2/7:ATP
"#2/7:ATP ": contains extra trailing text
> name xlMCM2_ATP_loop #2/2:508-525
"#2/2:508-525 ": contains extra trailing text
> name xlMCM3_ATP_loop #2/3:346-362
"#2/3:346-362 ": contains extra trailing text
> name xlMCM4_ATP_loop #2/4:506-522
"#2/4:506-522 ": contains extra trailing text
> name xlMCM5_ATP_loop #2/5:383-399
"#2/5:383-399 ": contains extra trailing text
> name xlMCM6_ATP_loop #2/6:399-415
"#2/6:399-415 ": contains extra trailing text
> name xlMCM7_ATP_loop #2/7:382-397
"#2/7:382-397 ": contains extra trailing text
> name DNA_bubble #2/X:22-38 #2/Y:24-38
"#2/X:22-38 #2/Y:24-38 ": contains extra trailing text
> open cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc
Opened X_DH_map as #16, grid size 548,548,548, pixel 0.5, shown at level 6.93,
step 4, values float32
> rename #16 X_DH_map_Mcm3
> open XL_MCM_DH_final_v1_30042025.pdb
Chain information for XL_MCM_DH_final_v1_30042025.pdb #17
---
Chain | Description
2 A | No description available
3 B | No description available
4 C | No description available
5 D | No description available
6 E | No description available
7 F | No description available
X | No description available
Y | No description available
> rename #17 X_DH_Mcm3
> name xlMCM3_ATP_loop #17/3:346-362
"#17/3:346-362 ": contains extra trailing text
> open cryosparc_P49_J1739_map_flipped.mrc
Opened cryosparc_P49_J1739_map_flipped.mrc as #18, grid size 500,500,500,
pixel 0.928, shown at level 0.0257, step 2, values float32
> rename #18 X_DH_map_Mcm4
> open XL_MCM_DH_final_v1_30042025.pdb
Chain information for XL_MCM_DH_final_v1_30042025.pdb #19
---
Chain | Description
2 A | No description available
3 B | No description available
4 C | No description available
5 D | No description available
6 E | No description available
7 F | No description available
X | No description available
Y | No description available
> rename #19 X_DH_Mcm4
> name xlMCM4_ATP_loop #19/4:506-522
"#19/4:506-522 ": contains extra trailing text
> open cryosparc_P49_J1739_map_flipped.mrc
Opened X_DH_map_Mcm4 as #20, grid size 500,500,500, pixel 0.928, shown at
level 0.0257, step 2, values float32
> rename #20 X_DH_map_Mcm5
> open XL_MCM_DH_final_v1_30042025.pdb
Chain information for XL_MCM_DH_final_v1_30042025.pdb #21
---
Chain | Description
2 A | No description available
3 B | No description available
4 C | No description available
5 D | No description available
6 E | No description available
7 F | No description available
X | No description available
Y | No description available
> rename #21 X_DH_Mcm5
> name xlMCM5_ATP_loop #21/5:383-399
"#21/5:383-399 ": contains extra trailing text
> open cryosparc_P49_J1739_map_flipped.mrc
Opened X_DH_map_Mcm5 as #22, grid size 500,500,500, pixel 0.928, shown at
level 0.0257, step 2, values float32
> rename #22 X_DH_map_Mcm6
> open XL_MCM_DH_final_v1_30042025.pdb
Chain information for XL_MCM_DH_final_v1_30042025.pdb #23
---
Chain | Description
2 A | No description available
3 B | No description available
4 C | No description available
5 D | No description available
6 E | No description available
7 F | No description available
X | No description available
Y | No description available
> rename #23 X_DH_Mcm6
> name xlMCM6_ATP_loop #23/6:399-415
"#23/6:399-415 ": contains extra trailing text
> open cryosparc_P49_J1739_map_flipped.mrc
Opened X_DH_map_Mcm6 as #24, grid size 500,500,500, pixel 0.928, shown at
level 0.0257, step 2, values float32
> rename #24 X_DH_map_Mcm7
> open XL_MCM_DH_final_v1_30042025.pdb
Chain information for XL_MCM_DH_final_v1_30042025.pdb #25
---
Chain | Description
2 A | No description available
3 B | No description available
4 C | No description available
5 D | No description available
6 E | No description available
7 F | No description available
X | No description available
Y | No description available
> rename #25 X_DH_Mcm7
> name xlMCM7_ATP_loop #25/7:382-397
"#25/7:382-397 ": contains extra trailing text
> matchmaker xlMCM3_ATP_loop to #2/2 bring #16
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker xlMCM4_ATP_loop to #2/2 bring #18
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker xlMCM5_ATP_loop to #2/2 bring #20
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker xlMCM6_ATP_loop to #2/2 bring #22
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker xlMCM7_ATP_loop to #2/2 bring #24
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> volume #16-24 step 1
> volume #1,3,5,7,9 color #b2b2b29a
> color #*/2,A pink
> color #*/3,B dodger blue
> color #*/4,C olive drab
> color #*/5,D gold
> color #*/6,E orange
> color #*/7,F indigo
> color #*/X,S black
> color #*/Y,O light grey
> hide atoms
> show cartoons
> hide #*/X,Y #*/S,O cartoons
> show #*/X,Y #*/S,O atoms
> select #*/X,Y #*/S,O
30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected
> style sel sphere
Changed 30937 atom styles
> select clear
> show ::name="ADP" atoms
> style ::name="ADP" stick
Changed 1266 atom styles
> color ::name="ADP" red
> show ::name="ATP" atoms
> style ::name="ATP" stick
Changed 3038 atom styles
> color ::name="ATP" red
> show ::name="AGS" atoms
> style ::name="AGS" stick
Changed 0 atom styles
> color ::name="AGS" red
> show ::name="Zn" atoms
> style ::name="Zn" stick
Changed 100 atom styles
> color ::name="Zn" byhetero
> show ::name="Mg" atoms
> style ::name="Mg" stick
Changed 110 atom styles
> color ::name="Mg" byhetero
> volume #16 level 5
> color zone #16 near #17 distance 6.5
> volume splitbyzone #16
Opened X_DH_map_Mcm3 0 as #26.1, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 1 as #26.2, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 2 as #26.3, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 3 as #26.4, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 4 as #26.5, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 5 as #26.6, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 6 as #26.7, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 7 as #26.8, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 8 as #26.9, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 9 as #26.10, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 10 as #26.11, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 11 as #26.12, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
> transparency #26 60
> volume #26 level 6.5
> volume #18 level 5
> color zone #18 near #19 distance 6.5
> volume splitbyzone #18
Opened X_DH_map_Mcm7 0 as #27.1, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 1 as #27.2, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 2 as #27.3, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 3 as #27.4, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 4 as #27.5, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 5 as #27.6, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 6 as #27.7, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 7 as #27.8, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 8 as #27.9, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 9 as #27.10, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 10 as #27.11, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32
Opened X_DH_map_Mcm7 11 as #27.12, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32
> transparency #27 60
> volume #27 level 6.5
> volume #20 level 5
> color zone #20 near #21 distance 6.5
> volume splitbyzone #20
Opened X_DH_map_Mcm7 0 as #28.1, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 1 as #28.2, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 2 as #28.3, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 3 as #28.4, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 4 as #28.5, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 5 as #28.6, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 6 as #28.7, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 7 as #28.8, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 8 as #28.9, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 9 as #28.10, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 10 as #28.11, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32
Opened X_DH_map_Mcm7 11 as #28.12, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32
> transparency #28 60
> volume #28 level 6.5
> volume #22 level 5
> color zone #22 near #23 distance 6.5
> volume splitbyzone #22
Opened X_DH_map_Mcm7 0 as #29.1, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 1 as #29.2, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 2 as #29.3, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 3 as #29.4, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 4 as #29.5, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 5 as #29.6, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 6 as #29.7, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 7 as #29.8, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 8 as #29.9, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 9 as #29.10, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 10 as #29.11, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32
Opened X_DH_map_Mcm7 11 as #29.12, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32
> transparency #29 60
> volume #29 level 6.5
> volume #24 level 5
> color zone #24 near #25 distance 6.5
> volume splitbyzone #24
Opened X_DH_map_Mcm7 0 as #30.1, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 1 as #30.2, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 2 as #30.3, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 3 as #30.4, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 4 as #30.5, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 5 as #30.6, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 6 as #30.7, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 7 as #30.8, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 8 as #30.9, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 9 as #30.10, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm7 10 as #30.11, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32
Opened X_DH_map_Mcm7 11 as #30.12, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32
> transparency #30 60
> volume #30 level 6.5
> color ::name="ADP" byhetero
> color ::name="ATP" byhetero
> view n-term_front
Expected an objects specifier or a view name or a keyword
> view c-term_front
Expected an objects specifier or a view name or a keyword
> view
> view matrix camera
Missing "camera" keyword's argument
> view name c-term_front
> turn y 180
> view name n-term_front
> turn y 180
> view c-term_front
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface.png
> width 2000 height 1352 supersample 3 transparentBackground true
> turn y 180
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_turn_180.png
> width 2000 height 1352 supersample 3 transparentBackground true
> transparency #11 0
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!11 models
> show #!11 models
> hide #!17 models
> hide #!19 models
> hide #!23 models
> hide #!21 models
> hide #!27 models
> hide #!25 models
> hide #!26 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> transparency #11 60
> transparency #11 50
> transparency #11 60
> transparency #11 0
> hide #!2 models
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface.png
> width 2000 height 1352 supersample 3 transparentBackground true
> turn y-180
Expected an axis vector or a keyword
> turn y 180
> view c-term front
Expected an objects specifier or a view name or a keyword
> view c-term_front
> view cN-term_front
Expected an objects specifier or a view name or a keyword
> view N-term_front
Expected an objects specifier or a view name or a keyword
> view n-term_front
> view c-term_front
> view n-term_front
> view c-term_front
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_turn_180.png
> width 2000 height 1352 supersample 3 transparentBackground true
> turn x 180
> turn x 90
> turn x 270
> show #!2 models
> view n-term_front
> transparency #11 60
> clip front -4 back 15
> clip off
> clip front -4 back 20
> clip off
> clip front -4 back 30
> clip off
> clip front -4 back 10
> clip off
> clip front -4 back 15
> clip off
> hide #*/X,Y #*/S,O cartoons
> show #*/X,Y #*/S,O atoms
> select #*/X,Y #*/S,O
30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected
> style sel stick
Changed 30937 atom styles
> show sel atoms
> color sel byhetero
> transparency #11 60
> select clear
> show #*/X,Y #*/S,O cartoons
> show #*/X,Y #*/S,O atoms
> select #*/X,Y #*/S,O
30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected
> style sel stick
Changed 30937 atom styles
> show sel atoms
> color sel byhetero
> transparency #11 60
> select clear
> clip front -4 back 15
> clip off
> clip front -4 back 20
> clip off
> hide #*/X,Y #*/S,O cartoons
> show #*/X,Y #*/S,O atoms
> select #*/X,Y #*/S,O
30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected
> style sel sphere
Changed 30937 atom styles
> select clear
> color #*/X,S black
> color #*/Y,O light grey
> clip front -4 back 15
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_clip.png
> width 2000 height 1352 supersample 3 transparentBackground true
> turn y 180
> clip off
> clip front -4 back 15
> clip off
> view c-term_front
> clip front -4 back 15
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_clip_turn_180.png
> width 2000 height 1352 supersample 3 transparentBackground true
> clip off
> turn x,y 90
Expected an axis vector or a keyword
> turn y 90 x 90
Expected 'forever' or an integer >= 1 or a keyword
> turn y 90
> view c-term_front
> turn y 90
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_top_view_cartoon_surface.png
> width 2000 height 1352 supersample 3 transparentBackground true
> clip front -4 back 15
> clip off
> clip front -2 back 15
> clip off
> clip front 2 back 15
> clip off
> clip front 10
> clip off
> clip front 2
> clip off
> clip back 1
> clip off
> clip front -10
> clip off
> clip front -1
> clip off
> view c-term_front
> hide #!2 models
> view n-term_front
> transparency #11 0
> clip front -4 back 15
> clip off
> clip front -3 back 15
> clip off
> clip front -3 back 10
> clip off
> ui tool show "Side View"
> hide #!11.4 models
> show #!11.4 models
> hide #!11.4 models
> hide #!11.3 models
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_clip_with_side_view.png
> width 2000 height 1352 supersample 3 transparentBackground true
> turn y 180
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_clip_with_side_view_turn_180.png
> width 2000 height 1352 supersample 3 transparentBackground true
> view n-term_front
> save /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM-
> DH_back-map_cut-through.png supersample 5 transparentBackground true
> show #!11.4 models
> show #!11.3 models
> clip off
> hide #!11.1 models
> hide #!11.2 models
> hide #!11.3 models
> hide #!11.4 models
> hide #!11.5 models
> hide #!11.6 models
> hide #!11.7 models
> hide #!11.8 models
> hide #!11.9 models
> hide #!11.10 models
> view n-term
Expected an objects specifier or a view name or a keyword
> view n-term_front
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_surface.png
> width 2000 height 1352 supersample 3 transparentBackground true
> show #!11.10 models
> show #!11.9 models
> show #!11.8 models
> show #!11.7 models
> show #!11.6 models
> hide #!11.6 models
> show #!11.5 models
> show #!11.6 models
> show #!11.4 models
> show #!11.3 models
> show #!11.2 models
> transparency #11 60
> show #!2 models
> view c-term_front
> turn y 90
> transparency #11.4 0
> clip off
> view c-term_front
> turn y 90
> clip front -4 back 15
> clip off
> clip front -4 back 80
> clip off
> clip front 20 back 10
clip back plane is in front of front plane
> clip off
> clip front -1 back 10
> clip off
> clip front 10 back 10
clip back plane is in front of front plane
> clip off
> show ::name="ADP" atoms
> style ::name="ADP" stick
Changed 1266 atom styles
> color ::name="ADP" black
> volume #1 level 5
> color zone #1 near #2 distance 6.5
> volume splitbyzone #1
Opened X_DH_map_Mcm3 0 as #31.1, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 1 as #31.2, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 2 as #31.3, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 3 as #31.4, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 4 as #31.5, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 5 as #31.6, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 6 as #31.7, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 7 as #31.8, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 8 as #31.9, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 9 as #31.10, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 10 as #31.11, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 11 as #31.12, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 12 as #31.13, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 13 as #31.14, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 14 as #31.15, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 15 as #31.16, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
> transparency #31 60
> volume #31 level 6.5
> hide #!11 models
> hide #!11.2 models
> hide #!11.3 models
> hide #!11.4 models
> hide #!11.5 models
> hide #!11.6 models
> hide #!11.7 models
> hide #!11.8 models
> hide #!11.9 models
> hide #!11.10 models
> hide #!11.11 models
> hide #!11.12 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31.11 models
> show #!31.11 models
> hide #!31.11 models
> show #!31.11 models
> hide #!31.11 models
> show #!31.11 models
> hide #!31.11 models
> show #!31.11 models
> close #31
> show #!11 models
> show #!11.1 models
> show #!11.2 models
> hide #!11.2 models
> hide #!11.1 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show ::name="ADP" atoms
> style ::name="ADP" stick
Changed 1266 atom styles
> color ::name="ADP" Dim grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ::name="ADP" dim_grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> show ::name="ADP" atoms
> style ::name="ADP" stick
Changed 1266 atom styles
> color ::name="ADP" Dim Gray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ::name="ADP" Dim_Gray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> show ::name="ADP" atoms
> select ADP
Expected an objects specifier or a keyword
> select ADP atom
Expected an objects specifier or a keyword
> ui tool show "Color Actions"
> show ::name="ADP" atoms
> style ::name="ADP" stick
Changed 1266 atom styles
> color ::name="ADP" Gray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select ::name="ADP"
1266 atoms, 1342 bonds, 38 residues, 10 models selected
> color (#!2 & sel) dim gray
> select clear
> show ::name="ADP" atoms
> style ::name="ADP" stick
Changed 1266 atom styles
> color ::name="ADP" dim gray
> volume #1 level 5
> color zone #1 near #2 distance 6.5
> volume splitbyzone #1
Opened X_DH_map_Mcm3 0 as #31.1, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 1 as #31.2, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 2 as #31.3, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 3 as #31.4, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 4 as #31.5, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 5 as #31.6, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 6 as #31.7, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 7 as #31.8, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 8 as #31.9, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 9 as #31.10, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 10 as #31.11, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 11 as #31.12, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 12 as #31.13, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 13 as #31.14, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 14 as #31.15, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 15 as #31.16, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
Opened X_DH_map_Mcm3 16 as #31.17, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32
> transparency #31 60
> volume #31 level 6.5
> hide #!31.6 models
> show #!31.6 models
> hide #!31.6 models
> show #!31.6 models
> hide #!31.11 models
> show #!31.11 models
> hide #!31.11 models
> show #!31.11 models
> hide #!31.6 models
> show #!31.6 models
> hide #!31.5 models
> show #!31.5 models
> hide #!31.5 models
> show #!31.5 models
> hide #!31.5 models
> show #!31.5 models
> transparency #31.5, 31.6, 31.11 0
> transparency #31.5 0
> transparency #31.4 0
> transparency #31.11 0
> hide #!31.7 models
> hide #!31.6 models
> show #!31.6 models
> hide #!31.6 models
> show #!31.6 models
> hide #!31.5 models
> show #!31.5 models
> hide #!31.5 models
> show #!31.5 models
> transparency #31.11 0
> select add #31.11
4 models selected
> transparency sel 0
> select subtract #31.11
Nothing selected
> select add #31.11
4 models selected
> select subtract #31.11
Nothing selected
> select add #31.11
4 models selected
> select subtract #31.11
Nothing selected
> select add #31.11
4 models selected
> select subtract #31.11
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select ATP
Expected an objects specifier or a keyword
> select add #31.11
4 models selected
> select add #31.6
7 models selected
> select add #31.5
10 models selected
> select transperencey 0
Expected an objects specifier or a keyword
> select transparency 0
Expected an objects specifier or a keyword
> select transparency 0
Expected an objects specifier or a keyword
> transparency #31.5.1#31.6.1#31.11.1 0
> transparency #31.5.1#31.6.1#31.11.1 60
> transparency #31.5.1#31.6.1#31.11.1 0
> select clear
> show ::name="ATP" atoms
> style ::name="ATP" stick
Changed 3038 atom styles
> color ::name="ATP" red
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_top_view_cartoon_surface_ATP_ADP_colored.png
> width 2000 height 1352 supersample 3 transparentBackground true
> clip off
> view c-term_front
> ui tool show "Side View"
> hide #!31 models
> hide #!31.1 models
> hide #!31.2 models
> hide #!31.3 models
> hide #!31.4 models
> hide #!31.5 models
> hide #!31.6 models
> hide #!31.8 models
> hide #!31.9 models
> hide #!31.10 models
> hide #!31.11 models
> hide #!31.12 models
> hide #!31.13 models
> hide #!31.14 models
> hide #!31.15 models
> hide #!31.16 models
> hide #!31.17 models
> show #!11.1 models
> show #!11.2 models
> show #!11.3 models
> show #!11.4 models
> show #!11.5 models
> show #!11.6 models
> show #!11.7 models
> show #!11.8 models
> show #!11.9 models
> show #!11.10 models
> show #!11.11 models
> show #!11.12 models
> hide #!11.4 models
> hide #!11.3 models
> show #!11.3 models
> show #!11.4 models
> hide #!11.4 models
> show #!11.4 models
> hide #!11.4 models
> show #!11.4 models
> hide #!11.4 models
> show #!11.4 models
> hide #!11.4 models
> hide #!11.3 models
> show #!11.3 models
> show #!11.4 models
> hide #!11 models
> view c-term_front
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon.png
> width 2000 height 1352 supersample 3 transparentBackground true
> view n-term_front
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_turn.png
> width 2000 height 1352 supersample 3 transparentBackground true
> show #!11 models
> show #!2 models
> select DNA_bubble
Expected an objects specifier or a keyword
> view sel
No objects specified.
> transparency #11 60
> select #2/X,Y
3650 atoms, 3933 bonds, 114 residues, 1 model selected
> style sel stick
Changed 3650 atom styles
> color sel byhetero
> hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models
> select clear
> view mcm5_dna_melt
Expected an objects specifier or a view name or a keyword
> select mcm5_dna_melt
Expected an objects specifier or a keyword
> show sel atoms
> color sel byhetero
> select clear
> name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 110 atom styles
> color sel byhetero
> select clear
> view mcm5_dna_melt
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 110 atom styles
> color sel byhetero
> select clear
> view mcm5_dna_melt
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select H
456356 atoms, 56737 residues, 7 models selected
> hide (#!2 & sel) target a
> select clear
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_1.png
> width 2000 height 1352 supersample 3 transparentBackground true
> turn y 180
> clip off
> name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 110 atom styles
> color sel byhetero
> select clear
> view mcm5_dna_melt
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select H
456356 atoms, 56737 residues, 7 models selected
> hide (#!2 & sel) target a
> select clear
> show #*/X,Y #*/S,O cartoons
> hide #*/X,Y #*/S,O cartoons
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_2.png
> width 2000 height 1352 supersample 3 transparentBackground true
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> style sel sphere
Changed 110 atom styles
> select clear
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_3.png
> width 2000 height 1352 supersample 3 transparentBackground true
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 110 atom styles
> color sel byhetero
> select clear
> select H
456356 atoms, 56737 residues, 7 models selected
> hide (#!2 & sel) target a
> select clear
> hide #!11
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_4.png
> width 2000 height 1352 supersample 3 transparentBackground true
> nucleotides #!2 tube/slab shape muffler
> nucleotides #!2 tube/slab shape ellipsoid
> nucleotides #!2 slab
> style nucleic & #!2 stick
Changed 3650 atom styles
> nucleotides #!2 fill
> style nucleic & #!2 stick
Changed 3650 atom styles
> nucleotides #!2 atoms
> style nucleic & #!2 stick
Changed 3650 atom styles
> nucleotides #!2 tube/slab shape ellipsoid
> nucleotides #!2 tube/slab shape muffler
> nucleotides #!2 ladder
> nucleotides #!2 stubs
> nucleotides #!2 slab
> style nucleic & #!2 stick
Changed 3650 atom styles
> nucleotides #!2 fill
> style nucleic & #!2 stick
Changed 3650 atom styles
> nucleotides #!2 atoms
> style nucleic & #!2 stick
Changed 3650 atom styles
> show #!11
> show #!2 models
> select DNA_bubble
Expected an objects specifier or a keyword
> view sel
No objects specified.
> transparency #11 60
> select #2/X,Y
3650 atoms, 3933 bonds, 114 residues, 1 model selected
> style sel stick
Changed 3650 atom styles
> color sel byhetero
> hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models
> select clear
> name DNA_bubble #2/X:22-38 #2/Y:24-38
> show #!2 models
> select DNA_bubble
1024 atoms, 1099 bonds, 32 residues, 1 model selected
> view sel
> transparency #11 60
> select #2/X,Y
3650 atoms, 3933 bonds, 114 residues, 1 model selected
> style sel stick
Changed 3650 atom styles
> color sel byhetero
> hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models
> select clear
> hide #!11 models
> hide #!11.1 models
> show #!11 models
> show #!11.1 models
> hide #!11.1 models
> hide #!11.2 models
> hide #!11.3 models
> hide #!11.4 models
> hide #!11.5 models
> hide #!11.6 models
> hide #!11.7 models
> hide #!11.8 models
> hide #!11.9 models
> hide #!11.10 models
> hide #!11.11 models
> show #!11.11 models
> show #!11.10 models
> show #!11.9 models
> show #!11.8 models
> show #!11.7 models
> show #!11.6 models
> show #!11.5 models
> show #!11.4 models
> show #!11.3 models
> show #!11.2 models
> show #!11.1 models
> view mcm5_dna_melt
> select mcm5_dna_melt
110 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> hide #!11.11 models
> show #!11.11 models
> hide #!11.8 models
> hide #!11.9 models
> hide #!11.6 models
> hide #!11.2 models
> select H
456356 atoms, 56737 residues, 7 models selected
> hide (#!2 & sel) target a
> select clear
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_5.png
> width 2000 height 1352 supersample 3 transparentBackground true
> hide #!1-30 target m
> show #!2 models
> view #2/2:ATP
> turn x 270
> clip front -5 back 10 position #2/2:ATP
> show #!11.3 models
> show #!11.4 models
> select #2/2:ATP
43 atoms, 45 bonds, 1 residue, 1 model selected
> surface sel
> transparency (#!2 & sel) 60
> surface style #!2.2 mesh
> select clear
> hide #!1-31 target m
> show #!2 models
> view #2/2:ATP
> turn x 270
> clip front -5 back 10 position #2/2:ATP
> show #!11.3 models
> show #!11.4 models
> select #2/2:ATP
43 atoms, 45 bonds, 1 residue, 1 model selected
> surface sel
> transparency (#!2 & sel) 60
> surface style #!2.2 mesh
> show #!11.9 models
> show #!11.8 models
> show #!11.6 models
> show #!11.2 models
> select clear
> hide #!1-31 target m
> show #!2 models
> view #2/2:ATP
> turn x 270
> clip front -5 back 10 position #2/2:ATP
> show #!11.3 models
> show #!11.4 models
> select #2/2:ATP
43 atoms, 45 bonds, 1 residue, 1 model selected
> surface sel
> transparency (#!2 & sel) 60
> surface style #!2.2 mesh
> select clear
> color ::name="ADP" byhetero
> color ::name="ATP" byhetero
> clip off
> hide #!1-31 target m
> show #!2 models
> view #2/2:ATP
> turn x 270
> clip front -5 back 10 position #2/2:ATP
> show #!11.3 models
> show #!11.4 models
> select #2/2:ATP
43 atoms, 45 bonds, 1 residue, 1 model selected
> surface sel
> transparency (#!2 & sel) 60
> surface style #!2.2 mesh
> select clear
> hide #!1-30 target m
> show #!2 models
> view #2/2:ATP
> turn x 270
> clip front -5 back 10 position #2/2:ATP
> show #!11.3 models
> show #!11.4 models
> select #2/2:ATP
43 atoms, 45 bonds, 1 residue, 1 model selected
> surface sel
> transparency (#!2 & sel) 60
> surface style #!2.2 mesh
> turn y 180
> select clear
> clip off
> hide #!1-30 target m
> show #!2 models
> view #2/2:ATP
> turn x 270
> clip front -5 back 10 position #2/2:ATP
> show #!11.3 models
> show #!11.4 models
> select #2/2:ATP
43 atoms, 45 bonds, 1 residue, 1 model selected
> surface sel
> transparency (#!2 & sel) 60
> surface style #!2.2 mesh
> turn y 180
> select clear
> clip off
> hide #!1-30 target m
> show #!2 models
> view #2/3:ADP
> turn x 270
> clip front -5 back 10 position #2/3:ADP
> show #!11.5 models
> show #!11.6 models
> hide #!11.3 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> hide #!11.4 models
> show #!11.4 models
> hide #!11.4 models
> show #!11.4 models
> clip off
> view #2/2:ATP
> hide #!11 mesh
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!11 surfaces mesh
Expected ',' or a keyword
> surface style #!2.2 surface
Missing or invalid "style" argument: Should be one of 'dot', 'mesh', or
'solid'
> surface style #!2.2 mesh
> hide #!11.1 models
> hide #!11.2 models
> hide #!11.3 models
> hide #!11.5 models
> hide #!11.6 models
> hide #!11.7 models
> hide #!11.8 models
> hide #!11.9 models
> hide #!11.10 models
> hide #!11.11 models
> hide #!11.12 models
> select #11.4
4 models selected
> color #11.4.1 light gray
> color #11.4 light gray
> select #11.4
4 models selected
> surface hidePatches #11.4.1
> select clear
> select #11.4
4 models selected
> surface style #11.4 solid
> select #2/2:ATP
43 atoms, 45 bonds, 1 residue, 1 model selected
> surface hidePatches (#!2 & sel)
> select #11.4
4 models selected
> surface style #11.4 mesh
> select clear
> select #11.4
2 models selected
> select color blue
Expected an objects specifier or a keyword
> color #11.4.1 blue
> select clear
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> select #11.3
2 models selected
> select #11.3
2 models selected
> surface style #11.3 mesh
> color #11.3 blue
> select clear
> hide #!11.3 models
> show #!11.3 models
> undo
> select #11.3
2 models selected
> surface style #11.3 mesh
> color #11.3 blue
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX33DK/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 23 days, 19 hours, 38 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG FHD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 100.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
DiffFit: 0.6.2
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
fsspec: 2024.10.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
Send2Trash: 1.8.3
SEQCROW: 1.8.16
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
sympy: 1.13.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
torch: 2.2.1
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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