Opened 4 months ago

Closed 4 months ago

#18030 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… 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 pett) 

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x00000001f1e71f00 (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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath (total: 116)


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  "uptime" : 61000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
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    "releaseType" : "User"
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  "captureTime" : "2025-06-18 21:04:17.6869 -0400",
  "codeSigningMonitor" : 1,
  "incident" : "A21F3682-BB0F-4230-8685-A00D05A1B35F",
  "pid" : 6812,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-06-18 10:07:59.6145 -0400",
  "procStartAbsTime" : 721005492901,
  "procExitAbsTime" : 1484509673939,
  "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":"777D8A61-C81E-5246-B2B2-49ABC82B8258","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "E6A071C4-EA66-FC3F-B912-CA5E01E9CDB6",
  "appleIntelligenceStatus" : {"state":"available"},
  "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" : "CBDD442D-87D4-46E2-ABC3-573E2BE06DB8",
  "wakeTime" : 3,
  "sleepWakeUUID" : "30074C8F-D2C2-4798-8990-C2E964F8CBFE",
  "sip" : "enabled",
  "vmRegionInfo" : "0x209daa7beaa8 is not in any region.  Bytes after previous region: 35380505864873  Bytes before following region: 69691574064472\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
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  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":6812},
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ConstantinePetridis/Desktop/BVcap.cxs

Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
0.00641, step 1, values float32  
Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
0.00819, step 1, values float32  
Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
0.00742, step 1, values float32  
Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
0.00667, step 1, values float32  
Opened emd_51808.map zone as #4, grid size 500,500,500, pixel 1.35, shown at
level 0.00684, step 1, values float32  
Opened emd_51808.map zone as #6, grid size 500,500,500, pixel 1.35, shown at
level 0.00742, step 1, values float32  
Log from Wed Jun 18 01:53:42 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ConstantinePetridis/Desktop/BVcap.cxs

Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
0.00641, step 1, values float32  
Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
0.00819, step 1, values float32  
Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
0.00742, step 1, values float32  
Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
0.00667, step 1, values float32  
Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
level 0.00705, step 1, values float32  
Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
level 0.00742, step 1, values float32  
Opened emd_51808.map zone as #9, grid size 500,500,500, pixel 1.35, shown at
level 0.00742, step 1, values float32  
Log from Wed Jun 18 01:06:40 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ConstantinePetridis/Desktop/BVcap.cxs

Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
0.00641, step 1, values float32  
Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
0.00819, step 1, values float32  
Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
0.00742, step 1, values float32  
Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
0.00667, step 1, values float32  
Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
level 0.00705, step 1, values float32  
Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
level 0.00742, step 1, values float32  
Log from Sun Jun 15 21:01:47 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ConstantinePetridis/Desktop/BVcap.cxs

Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
0.00641, step 1, values float32  
Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
0.00819, step 1, values float32  
Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
0.00742, step 1, values float32  
Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
0.00667, step 1, values float32  
Log from Mon Jun 9 23:00:16 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ConstantinePetridis/Desktop/BVcap.cxs format session

Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
0.00641, step 1, values float32  
Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
0.00819, step 1, values float32  
Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
0.00742, step 1, values float32  
Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
0.00667, step 1, values float32  
Log from Mon Jun 9 21:58:32 2025 Startup Messages  
---  
warning | Registration file '/Users/ConstantinePetridis/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ConstantinePetridis/Downloads/emd_51794.map

Opened emd_51794.map as #1, grid size 500,500,500, pixel 1.35, shown at level
0.00783, step 2, values float32  

> ui tool show Registration

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
petridis@mit.edu has been invited to the ChimeraX announcements list  

> volume #1 step 1

> volume #1 level 0.006408

> open /Users/ConstantinePetridis/Downloads/emd_51809.map

Opened emd_51809.map as #2, grid size 300,300,300, pixel 1.35, shown at level
0.00787, step 2, values float32  

> open /Users/ConstantinePetridis/Downloads/emd_51808.map

Opened emd_51808.map as #3, grid size 500,500,500, pixel 1.35, shown at level
0.00734, step 2, values float32  

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,108.6,0,1,0,134.66,0,0,1,242.83

> view matrix models #2,1,0,0,132.26,0,1,0,134.39,0,0,1,239.35

> view matrix models #2,1,0,0,133.6,0,1,0,135.11,0,0,1,235.01

> select clear

> open 9H2J, 9H2K, 9H2H

'9H2J,' has no suffix  

> open 9H2J

Summary of feedback from opening 9H2J fetched from pdb  
---  
notes | Fetching compressed mmCIF 9h2j from http://files.rcsb.org/download/9h2j.cif  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
9h2j title:  
AcMNPV apical cap - C14 anchor complex only [more info...]  
  
Chain information for 9h2j #4  
---  
Chain | Description | UniProt  
A B | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290  
C D | Protein C42 | C42_NPVAC 1-361  
E | Protein AC142 | AC142_NPVAC 1-477  
F G L M | Major capsid protein | MCP_NPVAC 1-347  
H I J | Capsid-associated protein VP80 | VP80_NPVAC 1-691  
K | Protein AC109 | AC109_NPVAC 1-390  
N P | Protein Ac66 | AC66_NPVAC 1-808  
O | Tyrosine-protein phosphatase | PTP_NPVAC 1-168  
  
Non-standard residues in 9h2j #4  
---  
ZN — zinc ion  
  
9h2j mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> open 9H2K

Summary of feedback from opening 9H2K fetched from pdb  
---  
note | Fetching compressed mmCIF 9h2k from http://files.rcsb.org/download/9h2k.cif  
  
9h2k title:  
AcMNPV apical cap - C21 ring [more info...]  
  
Chain information for 9h2k #5  
---  
Chain | Description | UniProt  
A B | Protein Ac66 | AC66_NPVAC 1-808  
C E | Protein Ac102 | AC102_NPVAC 1-122  
D F | Protein C42 | C42_NPVAC 1-361  
  
9h2k mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> open 9H2H

Summary of feedback from opening 9H2H fetched from pdb  
---  
note | Fetching compressed mmCIF 9h2h from http://files.rcsb.org/download/9h2h.cif  
  
9h2h title:  
AcMNPV apical cap - composite map of the C2 plug [more info...]  
  
Chain information for 9h2h #6  
---  
Chain | Description | UniProt  
A B C D | Protein AC54 | AC54_NPVAC 1-365  
E | DNA (58-MER) |   
F | DNA (58-MER) |   
G H K L O P S T | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290  
I J M N Q R U V | Protein C42 | C42_NPVAC 1-361  
  
9h2h mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> show cartoons

> hide atoms

> transparency #1-3, 50

Missing or invalid "percent" argument: Expected a number  

> transparency #1-3 50

> select add #4

28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected  

> view matrix models #4,1,0,0,-46.281,0,1,0,28.188,0,0,1,16.931

> view matrix models #4,1,0,0,-66.8,0,1,0,31.821,0,0,1,22.566

> view matrix models #4,1,0,0,-83.932,0,1,0,-4.1614,0,0,1,3.3295

> view matrix models #4,1,0,0,-86.753,0,1,0,-14.247,0,0,1,2.2438

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.98834,-0.084105,-0.12696,3.7899,0.12496,0.9244,0.36038,-157.79,0.087054,-0.37204,0.92413,172.5

> ui tool show "Fit in Map"

> fitmap #4 inMap #1

Fit molecule 9h2j (#4) to map emd_51794.map (#1) using 28099 atoms  
average map value = 0.00362, steps = 208  
shifted from previous position = 16.5  
rotated from previous position = 26.1 degrees  
atoms outside contour = 20539, contour level = 0.0064084  
  
Position of 9h2j (#4) relative to emd_51794.map (#1) coordinates:  
Matrix rotation and translation  
0.87093476 0.22125067 -0.43877191 8.17307974  
-0.03651218 0.91957262 0.39121997 -98.27311021  
0.49004032 -0.32470655 0.80896610 9.06190185  
Axis -0.59625676 -0.77355784 -0.21467684  
Axis point -4.38407802 0.00000000 113.95591535  
Rotation angle (degrees) 36.89503018  
Shift along axis 69.20130055  
  

> undo

> fitmap #4 inMap #2

Fit molecule 9h2j (#4) to map emd_51809.map (#2) using 28099 atoms  
average map value = 0.0009505, steps = 2000  
shifted from previous position = 32.2  
rotated from previous position = 19.8 degrees  
atoms outside contour = 26476, contour level = 0.0078685  
  
Position of 9h2j (#4) relative to emd_51809.map (#2) coordinates:  
Matrix rotation and translation  
0.97206708 -0.20356372 -0.11682209 -57.64338192  
0.16794355 0.95098530 -0.25965733 -117.85047834  
0.16395290 0.23278483 0.95860872 -372.18017582  
Axis 0.72657867 -0.41427224 0.54814409  
Axis point 0.00000000 965.75111056 -950.58571178  
Rotation angle (degrees) 19.80849290  
Shift along axis -197.06863558  
  

> undo

> fitmap #4 inMap #3

Fit molecule 9h2j (#4) to map emd_51808.map (#3) using 28099 atoms  
average map value = 0.008828, steps = 240  
shifted from previous position = 23.3  
rotated from previous position = 25.7 degrees  
atoms outside contour = 12094, contour level = 0.0073443  
  
Position of 9h2j (#4) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.90107510 -0.43366308 -0.00001525 179.72189974  
0.43366305 0.90107502 0.00041028 -113.14051793  
-0.00016418 -0.00037631 0.99999992 0.26283972  
Axis -0.00090692 0.00017172 0.99999957  
Axis point 337.85156358 337.35875693 0.00000000  
Rotation angle (degrees) 25.70026512  
Shift along axis 0.08041870  
  

> open /Users/ConstantinePetridis/Downloads/emd_51803.map

Opened emd_51803.map as #7, grid size 300,300,300, pixel 1.35, shown at level
0.00751, step 2, values float32  

> select add #1

28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 5 models selected  

> select subtract #4

2 models selected  

> select add #7

4 models selected  

> select subtract #1

2 models selected  

> view matrix models
> #7,0.63982,-0.76148,0.10384,203.6,0.69653,0.63166,0.34036,-143.59,-0.32477,-0.14544,0.93454,110.05

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.63982,-0.76148,0.10384,323.48,0.69653,0.63166,0.34036,12.879,-0.32477,-0.14544,0.93454,319.53

> view matrix models
> #7,0.63982,-0.76148,0.10384,325.29,0.69653,0.63166,0.34036,-6.3507,-0.32477,-0.14544,0.93454,323.74

> view matrix models
> #7,0.63982,-0.76148,0.10384,328.74,0.69653,0.63166,0.34036,-27.175,-0.32477,-0.14544,0.93454,313.1

> view matrix models
> #7,0.63982,-0.76148,0.10384,337.59,0.69653,0.63166,0.34036,-5.7431,-0.32477,-0.14544,0.93454,280.28

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.67081,-0.73895,-0.062905,364.54,0.73898,0.67317,-0.027473,60.615,0.062647,-0.028056,0.99764,163.76

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.67081,-0.73895,-0.062905,368.43,0.73898,0.67317,-0.027473,62.379,0.062647,-0.028056,0.99764,142.56

> fitmap #2 inMap #1

Fit map emd_51809.map in map emd_51794.map using 33729 points  
correlation = 0.9005, correlation about mean = 0.1465, overlap = 2.248  
steps = 96, shift = 1.01, angle = 4 degrees  
  
Position of emd_51809.map (#2) relative to emd_51794.map (#1) coordinates:  
Matrix rotation and translation  
0.99756036 0.06957153 0.00575640 119.32853341  
-0.06957467 0.99757669 0.00034690 148.86563940  
-0.00571832 -0.00074655 0.99998337 236.80790602  
Axis -0.00783142 0.08218369 -0.99658643  
Axis point 2460.92883154 -1603.60164279 0.00000000  
Rotation angle (degrees) 4.00315534  
Shift along axis -224.69973002  
  

> fitmap #3 inMap #1

Fit map emd_51808.map in map emd_51794.map using 156145 points  
correlation = 0.9651, correlation about mean = 0.5761, overlap = 15.43  
steps = 76, shift = 10.1, angle = 1.69 degrees  
  
Position of emd_51808.map (#3) relative to emd_51794.map (#1) coordinates:  
Matrix rotation and translation  
0.99956547 0.02947662 0.00000307 -9.80341163  
-0.02947662 0.99956547 -0.00000496 10.09674613  
-0.00000322 0.00000487 1.00000000 -10.09636804  
Axis 0.00016671 0.00010665 -0.99999998  
Axis point 337.52062125 337.61534124 0.00000000  
Rotation angle (degrees) 1.68913034  
Shift along axis 10.09581033  
  

> fitmap #7 inMap #1

Fit map emd_51803.map in map emd_51794.map using 33716 points  
correlation = 0.8122, correlation about mean = -0.01378, overlap = 1.663  
steps = 160, shift = 25.9, angle = 4.23 degrees  
  
Position of emd_51803.map (#7) relative to emd_51794.map (#1) coordinates:  
Matrix rotation and translation  
0.69259058 -0.72133091 0.00000784 343.32114170  
0.72133091 0.69259058 -0.00003116 51.18973084  
0.00001704 0.00002724 1.00000000 123.95738155  
Axis 0.00004048 -0.00000638 1.00000000  
Axis point 111.59922295 428.38794901 0.00000000  
Rotation angle (degrees) 46.16447282  
Shift along axis 123.97095287  
  

> hide #!1 models

> transparency #1-3,7 50

> select #3

2 models selected  

> select clear

> select add #4

28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 3 models selected  

> select subtract #4

Nothing selected  

> select add #5

3455 atoms, 3509 bonds, 440 residues, 1 model selected  

> view matrix models #5,1,0,0,114.4,0,1,0,365.93,0,0,1,111.77

> view matrix models #5,1,0,0,240.9,0,1,0,294.24,0,0,1,221.01

> view matrix models #5,1,0,0,174.7,0,1,0,215.04,0,0,1,317.11

> view matrix models #5,1,0,0,232.67,0,1,0,162.63,0,0,1,266.73

> view matrix models #5,1,0,0,165.64,0,1,0,140.42,0,0,1,259.08

> view matrix models #5,1,0,0,165.46,0,1,0,122.68,0,0,1,250.56

> view matrix models #5,1,0,0,165.79,0,1,0,135.68,0,0,1,235.75

> fitmap #5 inMap #2

Fit molecule 9h2k (#5) to map emd_51809.map (#2) using 3455 atoms  
average map value = 0.01384, steps = 116  
shifted from previous position = 5.06  
rotated from previous position = 21.1 degrees  
atoms outside contour = 1068, contour level = 0.0078685  
  
Position of 9h2k (#5) relative to emd_51809.map (#2) coordinates:  
Matrix rotation and translation  
0.95550286 0.29498139 -0.00051665 -50.65330010  
-0.29498151 0.95550295 -0.00016089 68.77024810  
0.00044620 0.00030613 0.99999985 -0.15799858  
Axis 0.00079160 -0.00163204 -0.99999835  
Axis point 202.62055632 202.28170834 0.00000000  
Rotation angle (degrees) 17.15645426  
Shift along axis 0.00566547  
  

> select add #6

42553 atoms, 43579 bonds, 214 pseudobonds, 5031 residues, 4 models selected  

> select subtract #5

39098 atoms, 40070 bonds, 214 pseudobonds, 4591 residues, 3 models selected  

> view matrix models #6,1,0,0,10.171,0,1,0,142.23,0,0,1,166.79

> view matrix models #6,1,0,0,126.84,0,1,0,137.47,0,0,1,159.59

> fitmap #6 inMap #7

Fit molecule 9h2h (#6) to map emd_51803.map (#7) using 39098 atoms  
average map value = 0.005833, steps = 248  
shifted from previous position = 37.9  
rotated from previous position = 5.12 degrees  
atoms outside contour = 26889, contour level = 0.0075068  
  
Position of 9h2h (#6) relative to emd_51803.map (#7) coordinates:  
Matrix rotation and translation  
0.71322674 0.69985623 -0.03884423 -74.42080862  
-0.70048731 0.70970069 -0.07511631 214.67231818  
-0.02500284 0.08078485 0.99641792 -14.36437549  
Axis 0.11064171 -0.00982312 -0.99381181  
Axis point 224.12956068 198.79839136 0.00000000  
Rotation angle (degrees) 44.79171059  
Shift along axis 3.93268849  
  

> select clear

> transparency #1-3,7 30

> transparency #1-3,7 70

> select #4/A,B

3475 atoms, 3533 bonds, 7 pseudobonds, 428 residues, 2 models selected  

> select #4/A-D select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> color (#!4 & sel) red

> select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  

> select #6/G-V

25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected  

> color (#!6 & sel) red

> select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  

> select #6/G-V

25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected  

> select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  

> select #6/G-V

25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected  

> select clear

> select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  

> select #6/G-V

25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected  

> select clear

[Repeated 1 time(s)]

> select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  

> select #6/G-V

25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected  

> select add #5

29378 atoms, 29854 bonds, 66 pseudobonds, 3597 residues, 3 models selected  

> select add #4

57477 atoms, 58516 bonds, 114 pseudobonds, 7027 residues, 6 models selected  

> select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  

> select #6/G-V

25923 atoms, 26345 bonds, 66 pseudobonds, 3157 residues, 2 models selected  

> select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  

> color sel red

> select clear

> select #4/A-D,H-J

11510 atoms, 11720 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> select clear

> select add #6

39098 atoms, 40070 bonds, 214 pseudobonds, 4591 residues, 3 models selected  

> select subtract #6

Nothing selected  

> hide #!6 models

> select add #6

39098 atoms, 40070 bonds, 214 pseudobonds, 4591 residues, 3 models selected  

> select subtract #6

Nothing selected  

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select #4/A-B

3475 atoms, 3533 bonds, 7 pseudobonds, 428 residues, 2 models selected  

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select #4/C-D

3349 atoms, 3405 bonds, 6 pseudobonds, 403 residues, 2 models selected  
Alignment identifier is 1  

> select #4/C-D:357

Nothing selected  

> select clear

[Repeated 3 time(s)]

> select #4/C:331

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/C:326-331/D:326-328

73 atoms, 71 bonds, 9 residues, 1 model selected  

> select #4/C-D:317

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #4/C-D:282-317

602 atoms, 620 bonds, 72 residues, 1 model selected  

> select #4/C:134-138,195-196,233-239,262-270,329-331/D:112

173 atoms, 168 bonds, 1 pseudobond, 23 residues, 2 models selected  

> select #4/C:331

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/C:329-331

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select #4/C-D:331

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/C-D:331\0

Nothing selected  

> select #4/C-D:330

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/C-D:325

22 atoms, 22 bonds, 2 residues, 1 model selected  

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  
Alignment identifier is 1  

> select #5/D:76-77

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #5/D:70-77

54 atoms, 54 bonds, 8 residues, 1 model selected  

> select #5/D:68-69

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #5/D:56-69/F:56-64

182 atoms, 180 bonds, 23 residues, 1 model selected  

> select #5/D:71-72

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #5/D:71-78

54 atoms, 54 bonds, 8 residues, 1 model selected  

> select #4/C-D

3349 atoms, 3405 bonds, 6 pseudobonds, 403 residues, 2 models selected  

> select #4-6

70652 atoms, 72241 bonds, 262 pseudobonds, 8461 residues, 7 models selected  

> color (#5#!4 & sel) light gray

> select #4/C,D

3349 atoms, 3405 bonds, 6 pseudobonds, 403 residues, 2 models selected  

> color (#!4 & sel) red

> select #5/D,F

1113 atoms, 1132 bonds, 139 residues, 1 model selected  

> color sel red

> select #5/D,F and #4/C,D

Expected a keyword  

> select #3

2 models selected  

> select clear

> select #5/D:68

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #5/D:63-68/F:63-64

58 atoms, 56 bonds, 8 residues, 1 model selected  

> select #5/D,F:62

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #5/D,F:52-62

176 atoms, 176 bonds, 22 residues, 1 model selected  

> select #5/D,F:63-64

32 atoms, 30 bonds, 4 residues, 1 model selected  

> select #5/D:63-73/F:63-64

98 atoms, 97 bonds, 13 residues, 1 model selected  

> select #4/C,D

3349 atoms, 3405 bonds, 6 pseudobonds, 403 residues, 2 models selected  
Alignment identifier is 2  

> select #6/I,J,M,N,Q,R,U,V

13297 atoms, 13514 bonds, 29 pseudobonds, 1601 residues, 2 models selected  

> show #!6 models

Alignment identifier is 3  

> hide #!6 models

> hide #5 models

> ui tool show "Fit in Map"

> volume #2 step 1

> volume #3 step 1

> volume #7 step 1

> select add #6

39098 atoms, 40070 bonds, 214 pseudobonds, 4591 residues, 3 models selected  

> select subtract #6

Nothing selected  

> fitmap #4 inMap #3

Fit molecule 9h2j (#4) to map emd_51808.map (#3) using 28099 atoms  
average map value = 0.008828, steps = 108  
shifted from previous position = 11.2  
rotated from previous position = 1.68 degrees  
atoms outside contour = 10700, contour level = 0.0073443  
  
Position of 9h2j (#4) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.90100599 -0.43380661 0.00018630 179.75327232  
0.43380654 0.90100598 0.00032773 -113.12278354  
-0.00031003 -0.00021447 0.99999993 0.22425752  
Axis -0.00062493 0.00057206 0.99999964  
Axis point 337.73732720 337.29160338 0.00000000  
Rotation angle (degrees) 25.70938878  
Shift along axis 0.04721037  
  

> fitmap #4 inMap #3

Fit molecule 9h2j (#4) to map emd_51808.map (#3) using 28099 atoms  
average map value = 0.008828, steps = 44  
shifted from previous position = 0.00395  
rotated from previous position = 0.00358 degrees  
atoms outside contour = 10704, contour level = 0.0073443  
  
Position of 9h2j (#4) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.90101456 -0.43378882 0.00013329 179.75565688  
0.43378877 0.90101455 0.00030136 -113.11017006  
-0.00025082 -0.00021371 0.99999995 0.20056965  
Axis -0.00059369 0.00044274 0.99999973  
Axis point 337.72213240 337.32106882 0.00000000  
Rotation angle (degrees) 25.70825572  
Shift along axis 0.04377270  
  

> volume #2 level 0.008402

> volume #2 level 0.008189

> volume #3 level 0.007416

> volume #7 level 0.008601

> volume #7 level 0.00667

> fitmap #2 inMap #1

Fit map emd_51809.map in map emd_51794.map using 256025 points  
correlation = 0.9048, correlation about mean = 0.152, overlap = 17.5  
steps = 40, shift = 0.0494, angle = 0.022 degrees  
  
Position of emd_51809.map (#2) relative to emd_51794.map (#1) coordinates:  
Matrix rotation and translation  
0.99757329 0.06940982 0.00545947 119.41870490  
-0.06941176 0.99758808 0.00016676 148.88130709  
-0.00543473 -0.00054531 0.99998508 236.75638760  
Axis -0.00511360 0.07823468 -0.99692186  
Axis point 2454.71468207 -1618.08965596 0.00000000  
Rotation angle (degrees) 3.99245500  
Shift along axis -224.99059556  
  

> fitmap #3 inMap #1

Fit map emd_51808.map in map emd_51794.map using 1222611 points  
correlation = 0.9653, correlation about mean = 0.5741, overlap = 122  
steps = 28, shift = 0.00253, angle = 0.00246 degrees  
  
Position of emd_51808.map (#3) relative to emd_51794.map (#1) coordinates:  
Matrix rotation and translation  
0.99956421 0.02951925 0.00000072 -9.81624044  
-0.02951925 0.99956421 -0.00000024 10.10990167  
-0.00000073 0.00000022 1.00000000 -10.09814507  
Axis 0.00000768 0.00002460 -1.00000000  
Axis point 337.49379423 337.52186297 0.00000000  
Rotation angle (degrees) 1.69157444  
Shift along axis 10.09831833  
  

> fitmap #3 inMap #1

Fit map emd_51808.map in map emd_51794.map using 1222611 points  
correlation = 0.9653, correlation about mean = 0.5741, overlap = 122  
steps = 40, shift = 0.03, angle = 0.000315 degrees  
  
Position of emd_51808.map (#3) relative to emd_51794.map (#1) coordinates:  
Matrix rotation and translation  
0.99956405 0.02952465 -0.00000031 -9.81701875  
-0.02952465 0.99956405 0.00000009 10.11164600  
0.00000032 -0.00000008 1.00000000 -10.06841949  
Axis -0.00000278 -0.00001066 -1.00000000  
Axis point 337.50199711 337.48493379 0.00000000  
Rotation angle (degrees) 1.69188359  
Shift along axis 10.06833899  
  

> fitmap #7 inMap #1

Fit map emd_51803.map in map emd_51794.map using 343453 points  
correlation = 0.81, correlation about mean = 0.01007, overlap = 15.6  
steps = 40, shift = 0.0562, angle = 0.22 degrees  
  
Position of emd_51803.map (#7) relative to emd_51794.map (#1) coordinates:  
Matrix rotation and translation  
0.68982040 -0.72398053 -0.00001049 344.42004511  
0.72398053 0.68982040 -0.00000583 51.20703324  
0.00001146 -0.00000357 1.00000000 123.90862912  
Axis 0.00000156 -0.00001516 1.00000000  
Axis point 112.44736376 427.55427785 0.00000000  
Rotation angle (degrees) 46.38410619  
Shift along axis 123.90838894  
  

> save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true

> graphics silhouettes true

> lighting depthCue false

> lighting soft

> graphics bgColor white

> graphics silhouettes width 2.3

> cartoon style protein modeHelix tube radius 1.9 sides 24

> graphics silhouettes width 2

> cartoon style protein modeHelix tube radius 1.9 sides 24

> select #2,3,4,7

28099 atoms, 28662 bonds, 48 pseudobonds, 3430 residues, 9 models selected  

> color (#!4 & sel) #8c8dfcff

> select #2,3,7

6 models selected  

> select clear

> color #7 #8c8dfcff models

> color #3 #8c8dfcff models

> color #2 #8c8dfcff models

> transparency #2,3,7 70

> color #4 #c1153cff

> $4 info

Unknown command: $4 info  

> ui tool show "Hide Dust"

> surface dust #2 size 8.1

> surface dust #2 size 7.62

> surface dust #2 size 6.78

> surface dust #3 size 8.1

> surface dust #7 size 8.1

> save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true

——— End of log from Mon Jun 9 21:58:32 2025 ———

opened ChimeraX session  

> open .8I8B

'.8I8B' has no suffix  

> open 8I8B

Summary of feedback from opening 8I8B fetched from pdb  
---  
note | Fetching compressed mmCIF 8i8b from http://files.rcsb.org/download/8i8b.cif  
  
8i8b title:  
Outer shell and inner layer structures of Autographa californica multiple
nucleopolyhedrovirus (AcMNPV) [more info...]  
  
Chain information for 8i8b #8  
---  
Chain | Description | UniProt  
A B C | Viral capsid associated protein | A0A0N7CTI8_9ABAC 1-691  
D | AcOrf-109 peptide | A0A0N7CRZ7_9ABAC 1-390  
E | Early 49 Daa protein | A0A0N7CTL8_9ABAC 1-477  
F G | P40 | A0A0N7CQX9_9ABAC 1-361  
H I | Occlusion-derived virus envelope/capsid protein | A0A0N7CT36_9ABAC 1-290  
J | 38K | A0A0N7CSX4_9ABAC 1-320  
W X Y Z | Major viral capsid protein | A0A0N6WHR0_9ABAC 1-347  
  

> select add #8

30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> view matrix models #8,1,0,0,-194.13,0,1,0,228.1,0,0,1,8.5426

> select #8/A-C

5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected  

> view matrix models #8,1,0,0,-166.55,0,1,0,261.45,0,0,1,-9.8791

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.29376,0.95472,-0.047067,151.85,-0.097249,0.019134,0.99508,200.81,0.95092,0.29689,0.087225,-163.66

> view matrix models
> #8,-0.79614,-0.30724,-0.52131,839.07,0.23184,-0.95065,0.20621,577.91,-0.55894,0.043311,0.82808,271.91

> view matrix models
> #8,-0.67014,0.36916,-0.64392,661.02,-0.21272,-0.92667,-0.30988,936.1,-0.7111,-0.070687,0.69953,408.2

> view matrix models
> #8,-0.74305,0.17658,-0.64551,739.8,-0.10392,-0.98331,-0.14936,849.19,-0.66111,-0.0439,0.749,363.56

> view matrix models
> #8,-0.78629,0.33233,-0.52086,675.94,-0.28602,-0.94304,-0.16992,922.21,-0.54766,0.015373,0.83656,271.21

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.78629,0.33233,-0.52086,772.67,-0.28602,-0.94304,-0.16992,937.74,-0.54766,0.015373,0.83656,315.23

> view matrix models
> #8,-0.78629,0.33233,-0.52086,773.25,-0.28602,-0.94304,-0.16992,901.12,-0.54766,0.015373,0.83656,309.88

> view matrix models
> #8,-0.78629,0.33233,-0.52086,777.17,-0.28602,-0.94304,-0.16992,914.61,-0.54766,0.015373,0.83656,282.01

> view matrix models
> #8,-0.78629,0.33233,-0.52086,784.37,-0.28602,-0.94304,-0.16992,914.8,-0.54766,0.015373,0.83656,278.95

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.87051,-0.081637,-0.48532,909.99,-0.017541,-0.98037,0.19637,685.23,-0.49183,0.17946,0.852,209.56

> view matrix models
> #8,-0.62906,-0.70166,-0.3346,911.14,0.67477,-0.70659,0.21313,322.86,-0.38597,-0.091701,0.91794,209.94

> view matrix models
> #8,-0.60815,-0.79075,-0.069816,832.79,0.75341,-0.54725,-0.36454,450.69,0.25006,-0.2743,0.92857,-13.478

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.60815,-0.79075,-0.069816,812.29,0.75341,-0.54725,-0.36454,456.13,0.25006,-0.2743,0.92857,-31.86

> view matrix models
> #8,-0.60815,-0.79075,-0.069816,809.39,0.75341,-0.54725,-0.36454,463.01,0.25006,-0.2743,0.92857,-30.773

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.63427,-0.77305,0.0094979,788.4,0.72714,-0.60068,-0.33233,476.07,0.26262,-0.20388,0.94311,-58.543

> view matrix models
> #8,-0.81433,-0.56112,-0.14834,865.5,0.57604,-0.7501,-0.32485,573.58,0.07101,-0.34998,0.93406,60.75

> ui tool show "Fit in Map"

> fitmap #8 inMap #3

Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007156, steps = 296  
shifted from previous position = 27.1  
rotated from previous position = 31.1 degrees  
atoms outside contour = 16477, contour level = 0.0074163  
  
Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99159287 -0.12939173 -0.00118038 791.13260992  
0.12900294 -0.98781957 -0.08701022 715.09802323  
0.01009240 -0.08643099 0.99620674 15.43363463  
Axis 0.00223950 -0.04358465 0.99904723  
Axis point 372.32996800 383.59644668 0.00000000  
Rotation angle (degrees) 172.56966900  
Shift along axis -13.97662982  
  

> hide #!4 models

> show #!4 models

> hide #!4 models

Alignment identifier is 1  

> select ~sel & ##selected

24966 atoms, 25528 bonds, 8 pseudobonds, 3055 residues, 2 models selected  

> hide sel cartoons

> show #!4 models

> select #8H-J

Expected an objects specifier or a keyword  

> select #4/H-J

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected  

> select down

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected  

> select ~sel & ##selected

23413 atoms, 23880 bonds, 44 pseudobonds, 2869 residues, 3 models selected  

> hide sel cartoons

> select clear

Alignment identifier is 2  
Alignment identifier is 3  
Alignment identifier is 4  
Alignment identifier is 5  
Alignment identifier is 6  
Alignment identifier is 7  
Alignment identifier is 8  
Alignment identifier is 4/O  
Alignment identifier is 9  
Alignment identifier is 10  
Alignment identifier is 6/E  
Alignment identifier is 6/F  
Alignment identifier is 8/J  

> select #4/H-J

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected  
Alignment identifier is 1  

> select #8/A-C

5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected  
Alignment identifier is 2  

> select clear

> select #4/H-J:536

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select #4/H-J:536-544

237 atoms, 240 bonds, 27 residues, 1 model selected  

> hide #!4 models

> show #!4 models

> select #8/A-C:674

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select #8/A-C:674-680

186 atoms, 186 bonds, 21 residues, 1 model selected  

> select #4/H:674

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/H:674-682

78 atoms, 78 bonds, 9 residues, 1 model selected  

> graphics silhouettes width 2

> cartoon style protein modeHelix tube radius 1.9 sides 24

> graphics silhouettes true

> lighting depthCue false

> lighting soft

> graphics bgColor white

> select clear

> hide #!4 models

> show #!4 models

> select #4/H:674

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/H:674-685

102 atoms, 102 bonds, 12 residues, 1 model selected  

> select #4/H-J:652

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select #4/H:652-663/I:652-662/J:652-666

312 atoms, 316 bonds, 38 residues, 1 model selected  

> select clear

> hide #!4 models

> color #8 #c1153cff

> select clear

> show #!4 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!4 models

> fitmap #8 inMap #3

Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007155, steps = 84  
shifted from previous position = 0.0221  
rotated from previous position = 0.0113 degrees  
atoms outside contour = 16466, contour level = 0.0074163  
  
Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158624 -0.12944071 -0.00136543 791.20111863  
0.12906819 -0.98781514 -0.08696368 715.04336589  
0.00990785 -0.08640823 0.99621057 15.52431854  
Axis 0.00214663 -0.04356736 0.99904819  
Axis point 372.35625880 383.58455770 0.00000000  
Rotation angle (degrees) 172.56637270  
Shift along axis -13.94459507  
  

> fitmap #8 inMap #3

Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007156, steps = 100  
shifted from previous position = 0.0204  
rotated from previous position = 0.00235 degrees  
atoms outside contour = 16464, contour level = 0.0074163  
  
Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158733 -0.12943270 -0.00133408 791.19962794  
0.12905776 -0.98781871 -0.08693861 715.05186086  
0.00993487 -0.08637941 0.99621280 15.49199880  
Axis 0.00216129 -0.04355377 0.99904875  
Axis point 372.35686539 383.58607426 0.00000000  
Rotation angle (degrees) 172.56691018  
Shift along axis -13.95592675  
  

> fitmap #8 inMap #3

Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007155, steps = 64  
shifted from previous position = 0.0187  
rotated from previous position = 0.00323 degrees  
atoms outside contour = 16465, contour level = 0.0074163  
  
Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158276 -0.12946725 -0.00137838 791.21789539  
0.12909601 -0.98781379 -0.08693780 715.02106183  
0.00989402 -0.08638398 0.99621281 15.52329661  
Axis 0.00213990 -0.04355482 0.99904875  
Axis point 372.36051482 383.57925493 0.00000000  
Rotation angle (degrees) 172.56480470  
Shift along axis -13.94095442  
  

> fitmap #8 inMap #3

Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007156, steps = 64  
shifted from previous position = 0.0224  
rotated from previous position = 0.00913 degrees  
atoms outside contour = 16469, contour level = 0.0074163  
  
Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99156918 -0.12957220 -0.00127860 791.20518211  
0.12919260 -0.98780689 -0.08687266 714.97140200  
0.00999328 -0.08630545 0.99621862 15.44343915  
Axis 0.00218993 -0.04351894 0.99905020  
Axis point 372.33728097 383.57216645 0.00000000  
Rotation angle (degrees) 172.55898753  
Shift along axis -13.95334073  
  

> fitmap #8 inMap #3

Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007156, steps = 96  
shifted from previous position = 0.0141  
rotated from previous position = 0.0167 degrees  
atoms outside contour = 16467, contour level = 0.0074163  
  
Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99159042 -0.12940914 -0.00131942 791.18165481  
0.12903132 -0.98780716 -0.08710897 715.12188799  
0.00996936 -0.08654668 0.99619793 15.53024467  
Axis 0.00217365 -0.04363871 0.99904501  
Axis point 372.34988316 383.61718039 0.00000000  
Rotation angle (degrees) 172.56832828  
Shift along axis -13.97182858  
  

> transparency #2,3,7 60

> transparency #2,3,7 68

> color #7 #d2d2d3ff models

> color #7 #d2d2d399 models

> color #7 #d2d2d3f4 models

> color #7 #d2d2d3b3 models

> hide #!3 models

> color #3 #d2d2d3ff models

> color #3 #d2d2d3b2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> color #2 #d2d2d3ff models

> color #2 #d2d2d3b2 models

> ligghting soft\

Unknown command: ligghting soft\  

> ligghting soft

Unknown command: ligghting soft  

> lioghting soft

Unknown command: lioghting soft  

> lighting soft

> lighting gentle

> lighting soft

> lighting gentle

> transparency #2,3,7 75

> transparency #2,3,7 70

> transparency #2,3,7 65

> lighting soft

> lighting gentle

> lighting soft

> lighting gentle

> lighting soft

> transparency #2,3,7 60

> color #7 #c2cafdff models

> color #3 #c2cafdff models

> color #2 #c2cafdff models

> transparency #2,3,7 60

> select #8/A:534

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

74 atoms, 74 bonds, 9 residues, 1 model selected  

> select up

1455 atoms, 1487 bonds, 175 residues, 1 model selected  

> color sel #c1153cff

> color sel #be3c51ff

> color sel #be3b51ff

> color sel #bb3b50ff

> color sel #b7394eff

> color sel #b4384dff

> color sel #b2384cff

> color sel #b1384cff

> color sel #b1374bff

> color sel #b0374bff

> color sel #ae374aff

> color sel #ad364aff

> color sel #a83548ff

> color sel #a63447ff

> color sel #a23345ff

> color sel #9e3143ff

> color sel #9a3042ff

> color sel #962f40ff

> color sel #912d3eff

> color sel #8e2c3cff

> color sel #8d2c3cff

[Repeated 1 time(s)]

> color sel #8c2c3cff

> color sel #8a2b3bff

> color sel #882a3aff

> color sel #832938ff

> color sel #802836ff

> color sel #792633ff

> color sel #782633ff

[Repeated 1 time(s)]

> color sel #762532ff

> color sel #722431ff

> color sel #722430ff

[deleted to fit within ticket limits]


> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!10 models

> show #!10 models

> hide #!11 models

> hide #!7 models

> show #!7 models

> hide #!10 models

> show #!10 models

> close #10

> show #!9 models

> show #!11 models

> transparency #9 70

> transparency #9 50

> hide #8.1 models

> show #8.1 models

> volume zone #9 nearAtoms #8/A-C

> hide #!9 models

> show #!9 models

> hide #!7 models

> show #!7 models

> hide #!9 models

> show #!9 models

> hide #!11 models

> show #!11 models

> close #11

> show #!3 models

> hide #!3 models

> volume zone #9 nearAtoms #8/A-C invert true newMap true

Opened emd_51808.map copy zone as #10, grid size 500,500,500, pixel 1.35,
shown at step 1, values float32  

> color #10 #a8b2ffff models

> transparency #2,7,10 0

> show #!9 models

> transparency #9 70

> view front

> color #10 #b9c2ffff models

> undo

> color #10 #a8b2ffff models

> hide #!10 models

> show #!10 models

> color #10 #dbd3beff models

> color #10 #d2d2d3ff models

> color #10 #dfd9fcff models

> color #10 #75ff79ff models

> color #10 #c2cafdff models

> color #10 #3b8fffff models

> color #10 #f8ccb1ff models

> color #10 #f8c2a6ff models

> color #10 #257bf8ff models

> color #10 #f8e153ff models

> color #10 #f88690ff models

> color #10 #f8cef5ff models

> color #10 #e8f8c3ff models

> color #10 #e8f8c1ff models

> color #10 #f8eb15ff models

> color #10 #f8c97eff models

> color #10 #b2c5f8ff models

> color #10 #d3c0f8ff models

> color #10 #f7f8f4ff models

> color #10 #f7f8f3ff models

> color #10 #f8ae8eff models

> color #10 #edf8f4ff models

> color #10 #d3f8cdff models

> color #10 #b4f8e9ff models

> color #10 #a8b2ffff models

> color #10 #b9c2ffff models

> color #9 #b9c2ffff models

> color #7 #b9c2ffff models

> color #2 #b9c2ffff models

> transparency #9 70

> save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true

> hide #!10 models

> show #!3 models

> measure symmetry #3

Symmetry emd_51808.map: C2, center 250 250 258  

> hide #!9 models

> show #!9 models

> close #9

> close #10

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!8 models

> combine #8

> hide #!9 models

> show #!9 models

> select add #9

30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.98735,-0.15852,-0.003891,712.94,0.15825,-0.98356,-0.087032,715.49,0.009969,-0.086547,0.9962,8.7721

> ui tool show "Fit in Map"

> fitmap #9 inMap #3

Fit molecule copy of 8i8b (#9) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007136, steps = 320  
shifted from previous position = 31.9  
rotated from previous position = 25.7 degrees  
atoms outside contour = 16519, contour level = 0.0074163  
  
Position of copy of 8i8b (#9) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.94925344 0.31237697 0.03658660 582.26413479  
-0.31435289 -0.94603362 -0.07875704 874.59558896  
0.01001027 -0.08626150 0.99622226 15.44026964  
Axis -0.01196239 0.04236365 -0.99903064  
Axis point 361.41668086 390.72405261 0.00000000  
Rotation angle (degrees) 161.71951979  
Shift along axis 14.66049209  
  

> combine #8

> select add #10

60030 atoms, 61358 bonds, 20 pseudobonds, 7320 residues, 4 models selected  

> select subtract #9

30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected  

> view matrix models
> #10,-0.98735,-0.15852,-0.003891,885.33,0.15825,-0.98356,-0.087032,688.64,0.009969,-0.086547,0.9962,7.0211

> fitmap #10 inMap #3

Fit molecule copy of 8i8b (#10) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007154, steps = 280  
shifted from previous position = 14  
rotated from previous position = 25.7 degrees  
atoms outside contour = 16474, contour level = 0.0074163  
  
Position of copy of 8i8b (#10) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.83743424 -0.54513643 -0.03911764 910.14305591  
0.54644743 -0.83384401 -0.07809876 480.97407992  
0.00995647 -0.08677832 0.99617791 15.61062317  
Axis -0.00794307 -0.04491002 0.99895946  
Axis point 383.64334273 376.27006042 0.00000000  
Rotation angle (degrees) 146.88231983  
Shift along axis -13.23550244  
  

> combine #8

> select subtract #10

Nothing selected  

> select add #11

30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected  

> view matrix models
> #11,-0.98735,-0.15852,-0.003891,647.49,0.15825,-0.98356,-0.087032,725.68,0.009969,-0.086547,0.9962,9.1834

> fitmap #11 inMap #3

Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.00327, steps = 452  
shifted from previous position = 75.9  
rotated from previous position = 42.1 degrees  
atoms outside contour = 24361, contour level = 0.0074163  
  
Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.84320714 -0.43778965 -0.31199677 814.71784677  
0.25219295 -0.83466991 0.48961711 413.52774321  
-0.47476360 0.33416525 0.81420706 189.19622244  
Axis -0.21419046 0.22426945 0.95069746  
Axis point 389.99195147 267.01204412 0.00000000  
Rotation angle (degrees) 158.72268536  
Shift along axis 98.10521687  
  

> view matrix models
> #11,-0.83539,-0.46224,-0.29741,734.38,0.27698,-0.82138,0.49862,344.68,-0.47476,0.33417,0.81421,189.82

> fitmap #11 inMap #3

Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.003241, steps = 300  
shifted from previous position = 30.1  
rotated from previous position = 23.8 degrees  
atoms outside contour = 24235, contour level = 0.0074163  
  
Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.91147793 -0.05187608 -0.40806481 731.10046280  
-0.06537740 -0.96113746 0.26821749 597.31034546  
-0.40612044 0.27115253 0.87266404 158.90685757  
Axis 0.21035502 -0.13935337 -0.96764219  
Axis point 383.87827230 285.86350157 0.00000000  
Rotation angle (degrees) 179.60027832  
Shift along axis -83.21153398  
  

> fitmap #11 inMap #3

Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.003241, steps = 44  
shifted from previous position = 0.00647  
rotated from previous position = 0.00353 degrees  
atoms outside contour = 24236, contour level = 0.0074163  
  
Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.91149066 -0.05186828 -0.40803738 731.09314216  
-0.06535521 -0.96115182 0.26817143 597.32073157  
-0.40609546 0.27110311 0.87269102 158.90535884  
Axis 0.21033996 -0.13932770 -0.96764916  
Axis point 383.87197070 285.87246651 0.00000000  
Rotation angle (degrees) 179.60070718  
Shift along axis -83.20985401  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.93785,-0.34691,0.009644,657.66,0.34313,-0.93107,-0.12401,564.89,0.052,-0.11299,0.99223,-5.8209

> view matrix models
> #11,-0.88937,-0.45211,0.067899,638.07,0.45237,-0.89174,-0.01236,472.75,0.066136,0.019723,0.99762,-39.905

> view matrix models
> #11,-0.75515,-0.29587,0.58498,369.72,0.26703,-0.9538,-0.13769,605.6,0.5987,0.05223,0.79927,-196.15

> fitmap #11 inMap #3

Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.00341, steps = 128  
shifted from previous position = 17.9  
rotated from previous position = 5.64 degrees  
atoms outside contour = 23850, contour level = 0.0074163  
  
Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.79425260 -0.30803534 0.52371469 423.32573853  
0.30338390 -0.94787616 -0.09741164 564.42851116  
0.52642289 0.08151715 0.84630605 -179.54895904  
Axis 0.28086269 -0.00425103 0.95973855  
Axis point 189.86976609 319.21672061 0.00000000  
Rotation angle (degrees) 161.42569310  
Shift along axis -55.82305646  
  

> fitmap #11 inMap #3

Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.00341, steps = 76  
shifted from previous position = 0.0195  
rotated from previous position = 0.0111 degrees  
atoms outside contour = 23837, contour level = 0.0074163  
  
Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.79423679 -0.30816124 0.52366458 423.38085284  
0.30341461 -0.94784752 -0.09759458 564.46534613  
0.52642903 0.08137427 0.84631598 -179.50859711  
Axis 0.28085424 -0.00433822 0.95974063  
Axis point 189.87507217 319.24164873 0.00000000  
Rotation angle (degrees) 161.42080325  
Shift along axis -55.82216337  
  

> combine #8

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.78493,-0.33601,0.52055,713.52,0.32673,-0.93834,-0.11301,476.56,0.52643,0.081374,0.84632,-207.08

> view matrix models
> #11,-0.78493,-0.33601,0.52055,693.7,0.32673,-0.93834,-0.11301,533.75,0.52643,0.081374,0.84632,-221.57

> view matrix models
> #11,-0.78493,-0.33601,0.52055,705.44,0.32673,-0.93834,-0.11301,541.84,0.52643,0.081374,0.84632,-231.41

> fitmap #12 inMap #3

Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007156, steps = 60  
shifted from previous position = 0.0162  
rotated from previous position = 0.00835 degrees  
atoms outside contour = 16472, contour level = 0.0074163  
  
Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158996 -0.12941319 -0.00126807 791.16940967  
0.12903227 -0.98781901 -0.08697311 715.07330059  
0.01000285 -0.08640529 0.99620987 15.46353863  
Axis 0.00219496 -0.04356891 0.99904801  
Axis point 372.34489862 383.59084787 0.00000000  
Rotation angle (degrees) 172.56820583  
Shift along axis -13.96956072  
  

> fitmap #12 inMap #3

Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007155, steps = 100  
shifted from previous position = 0.0188  
rotated from previous position = 0.0091 degrees  
atoms outside contour = 16462, contour level = 0.0074163  
  
Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158484 -0.12945084 -0.00141814 791.23356076  
0.12908240 -0.98780932 -0.08700878 715.06127156  
0.00986251 -0.08645965 0.99620655 15.55431667  
Axis 0.00212199 -0.04359169 0.99904718  
Axis point 372.36982684 383.59789292 0.00000000  
Rotation angle (degrees) 172.56566143  
Shift along axis -13.95224264  
  

> view matrix models
> #11,-0.78493,-0.33601,0.52055,699.86,0.32673,-0.93834,-0.11301,542.95,0.52643,0.081374,0.84632,-199.4

> view matrix models
> #11,-0.78493,-0.33601,0.52055,714.99,0.32673,-0.93834,-0.11301,528.78,0.52643,0.081374,0.84632,-201.15

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.80067,-0.59659,-0.054814,975.71,0.52077,-0.73829,0.42863,218.43,-0.29618,0.31464,0.90182,72.16

> fitmap #12 inMap #3

Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007155, steps = 64  
shifted from previous position = 0.013  
rotated from previous position = 0.00603 degrees  
atoms outside contour = 16460, contour level = 0.0074163  
  
Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158487 -0.12945173 -0.00131830 791.19487858  
0.12907498 -0.98781320 -0.08697565 715.04266904  
0.00995692 -0.08641390 0.99620958 15.50296632  
Axis 0.00217081 -0.04357183 0.99904794  
Axis point 372.35138150 383.58538653 0.00000000  
Rotation angle (degrees) 172.56585596  
Shift along axis -13.94998169  
  

> fitmap #12 inMap #3

Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007156, steps = 48  
shifted from previous position = 0.0242  
rotated from previous position = 0.0126 degrees  
atoms outside contour = 16475, contour level = 0.0074163  
  
Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99159194 -0.12939924 -0.00113738 791.11387296  
0.12900820 -0.98783180 -0.08686348 715.04301724  
0.01011653 -0.08627986 0.99621959 15.37902198  
Axis 0.00225636 -0.04350968 0.99905046  
Axis point 372.32125683 383.56768677 0.00000000  
Rotation angle (degrees) 172.56932375  
Shift along axis -13.96183465  
  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.80067,-0.59659,-0.054814,975.98,0.52077,-0.73829,0.42863,245.53,-0.29618,0.31464,0.90182,70.489

> fitmap #12 inMap #3

Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007155, steps = 84  
shifted from previous position = 0.0229  
rotated from previous position = 0.0192 degrees  
atoms outside contour = 16465, contour level = 0.0074163  
  
Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158539 -0.12944658 -0.00142738 791.21930989  
0.12907882 -0.98780857 -0.08702257 715.05883655  
0.00985479 -0.08647456 0.99620534 15.56413078  
Axis 0.00211773 -0.04359891 0.99904687  
Axis point 372.36350064 383.59570975 0.00000000  
Rotation angle (degrees) 172.56588578  
Shift along axis -13.95090046  
  

> fitmap #12 inMap #3

Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007155, steps = 120  
shifted from previous position = 0.00997  
rotated from previous position = 0.00417 degrees  
atoms outside contour = 16461, contour level = 0.0074163  
  
Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158290 -0.12946627 -0.00136553 791.21122951  
0.12909340 -0.98780953 -0.08699002 715.04031812  
0.00991340 -0.08643410 0.99620827 15.52434575  
Axis 0.00214800 -0.04358058 0.99904761  
Axis point 372.35679290 383.58859204 0.00000000  
Rotation angle (degrees) 172.56490025  
Shift along axis -13.95278770  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.59669,-0.80204,-0.026407,922.68,0.80245,-0.59613,-0.026482,261.31,0.005497,-0.036992,0.9993,-18.361

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.59669,-0.80204,-0.026407,918.9,0.80245,-0.59613,-0.026482,245.43,0.005497,-0.036992,0.9993,-16.915

> fitmap #12 inMap #3

Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007156, steps = 64  
shifted from previous position = 0.0242  
rotated from previous position = 0.0168 degrees  
atoms outside contour = 16476, contour level = 0.0074163  
  
Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99159516 -0.12937502 -0.00108988 791.08922604  
0.12897830 -0.98782129 -0.08702722 715.11785477  
0.01018255 -0.08643634 0.99620536 15.39738426  
Axis 0.00228489 -0.04359023 0.99904688  
Axis point 372.31106342 383.60009482 0.00000000  
Rotation angle (degrees) 172.57086216  
Shift along axis -13.98188736  
  

> fitmap #11 inMap #3

Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007129, steps = 144  
shifted from previous position = 13.4  
rotated from previous position = 7.72 degrees  
atoms outside contour = 16510, contour level = 0.0074163  
  
Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.51770630 -0.85277811 -0.06891806 915.69536645  
0.85549986 -0.51504609 -0.05336246 218.45088712  
0.01001036 -0.08658547 0.99619415 15.53328191  
Axis -0.01942386 -0.04614555 0.99874586  
Axis point 396.55805348 367.73548446 0.00000000  
Rotation angle (degrees) 121.21688865  
Shift along axis -12.35307371  
  

> fitmap #8 inMap #3

Fit molecule 8i8b (#8) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007156, steps = 60  
shifted from previous position = 0.0162  
rotated from previous position = 0.00835 degrees  
atoms outside contour = 16472, contour level = 0.0074163  
  
Position of 8i8b (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158996 -0.12941319 -0.00126807 791.16940967  
0.12903227 -0.98781901 -0.08697311 715.07330059  
0.01000285 -0.08640529 0.99620987 15.46353863  
Axis 0.00219496 -0.04356891 0.99904801  
Axis point 372.34489862 383.59084787 0.00000000  
Rotation angle (degrees) 172.56820583  
Shift along axis -13.96956072  
  

> fitmap #9 inMap #3

Fit molecule copy of 8i8b (#9) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007136, steps = 48  
shifted from previous position = 0.0295  
rotated from previous position = 0.0195 degrees  
atoms outside contour = 16528, contour level = 0.0074163  
  
Position of copy of 8i8b (#9) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.94922563 0.31243064 0.03684897 582.13275372  
-0.31443114 -0.94599050 -0.07896236 874.70117765  
0.01018851 -0.08653957 0.99619633 15.42358187  
Axis -0.01207572 0.04248852 -0.99902397  
Axis point 361.37491136 390.77680339 0.00000000  
Rotation angle (degrees) 161.71540948  
Shift along axis 14.72655921  
  

> fitmap #10 inMap #3

Fit molecule copy of 8i8b (#10) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007155, steps = 80  
shifted from previous position = 0.0228  
rotated from previous position = 0.0152 degrees  
atoms outside contour = 16464, contour level = 0.0074163  
  
Position of copy of 8i8b (#10) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.83743571 -0.54515231 -0.03886406 910.07080810  
0.54644204 -0.83385467 -0.07802261 480.95563280  
0.01012723 -0.08657588 0.99619380 15.46315078  
Axis -0.00782746 -0.04483398 0.99896379  
Axis point 383.60821954 376.24666945 0.00000000  
Rotation angle (degrees) 146.88212261  
Shift along axis -13.23957343  
  

> fitmap #11 inMap #3

Fit molecule copy of 8i8b (#11) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.00713, steps = 64  
shifted from previous position = 0.0276  
rotated from previous position = 0.0114 degrees  
atoms outside contour = 16526, contour level = 0.0074163  
  
Position of copy of 8i8b (#11) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.51764871 -0.85279984 -0.06908158 915.74510300  
0.85553660 -0.51499520 -0.05326455 218.38344752  
0.00984732 -0.08667415 0.99618806 15.60319362  
Axis -0.01953224 -0.04614416 0.99874382  
Axis point 396.59938666 367.73547110 0.00000000  
Rotation angle (degrees) 121.21345848  
Shift along axis -12.38007902  
  

> fitmap #12 inMap #3

Fit molecule copy of 8i8b (#12) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007155, steps = 76  
shifted from previous position = 0.0235  
rotated from previous position = 0.0207 degrees  
atoms outside contour = 16463, contour level = 0.0074163  
  
Position of copy of 8i8b (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.99158394 -0.12945761 -0.00143107 791.22700647  
0.12909091 -0.98781408 -0.08694202 715.02758127  
0.00984168 -0.08639506 0.99621236 15.54686751  
Axis 0.00211351 -0.04355865 0.99904864  
Axis point 372.36637181 383.58186833 0.00000000  
Rotation angle (degrees) 172.56523034  
Shift along axis -13.94129314  
  

> view front

> combine #8

> select subtract #11

Nothing selected  

> select add #13

30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected  

> view matrix models
> #13,-0.98735,-0.15852,-0.003891,655.72,0.15825,-0.98356,-0.087032,724.5,0.009969,-0.086547,0.9962,15.553

> view matrix models
> #13,-0.98735,-0.15852,-0.003891,640.23,0.15825,-0.98356,-0.087032,647.89,0.009969,-0.086547,0.9962,47.543

> fitmap #13 inMap #3

Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.003621, steps = 260  
shifted from previous position = 39.3  
rotated from previous position = 15.8 degrees  
atoms outside contour = 23329, contour level = 0.0074163  
  
Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.97326751 -0.18416075 -0.13724144 707.66029233  
0.16366317 -0.97533150 0.14813128 539.23991406  
-0.16113586 0.12170998 0.97939877 65.44032184  
Axis -0.07556641 0.06833941 0.99479618  
Axis point 332.58747192 298.86600265 0.00000000  
Rotation angle (degrees) 169.93171792  
Shift along axis 48.47577371  
  

> view matrix models
> #13,-0.96801,-0.21288,-0.13281,683.19,0.19233,-0.96947,0.15212,518.26,-0.16114,0.12171,0.9794,42.533

> fitmap #13 inMap #3

Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.003621, steps = 260  
shifted from previous position = 34.4  
rotated from previous position = 0.00485 degrees  
atoms outside contour = 23329, contour level = 0.0074163  
  
Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.97328676 -0.18410047 -0.13718574 707.63652673  
0.16361206 -0.97534226 0.14811691 539.26776651  
-0.16107144 0.12171498 0.97940875 65.40965565  
Axis -0.07553541 0.06833652 0.99479873  
Axis point 332.57998105 298.86953806 0.00000000  
Rotation angle (degrees) 169.93500175  
Shift along axis 48.46950495  
  

> view matrix models
> #13,-0.96803,-0.21282,-0.13275,679.51,0.19228,-0.96948,0.1521,547.92,-0.16107,0.12171,0.97941,59.759

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.43132,-0.53774,0.72443,221.1,0.61779,-0.76121,-0.19722,454.04,0.6575,0.36248,0.66053,-213.36

> ui mousemode right "translate selected models"

> view matrix models
> #13,-0.43132,-0.53774,0.72443,248.04,0.61779,-0.76121,-0.19722,442.55,0.6575,0.36248,0.66053,-218.86

> fitmap #13 inMap #3

Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.00325, steps = 204  
shifted from previous position = 33.7  
rotated from previous position = 24.7 degrees  
atoms outside contour = 23928, contour level = 0.0074163  
  
Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.77856351 -0.32137393 0.53903403 417.70671143  
0.39075391 -0.92036183 0.01566958 478.95755449  
0.49107054 0.22282940 0.84213824 -184.48301526  
Axis 0.27874148 0.06453671 0.95819528  
Axis point 187.33514674 288.51786812 0.00000000  
Rotation angle (degrees) 158.18576626  
Shift along axis -29.42822342  
  

> view matrix models
> #13,-0.76669,-0.34841,0.53926,399.38,0.41357,-0.91047,-0.00025197,494.87,0.49107,0.22283,0.84214,-195.41

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.91927,0.16249,0.35854,424.42,-0.16587,-0.98591,0.021529,741.11,0.35698,-0.03968,0.93327,-120.05

> fitmap #13 inMap #3

Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007127, steps = 300  
shifted from previous position = 22.8  
rotated from previous position = 37.6 degrees  
atoms outside contour = 16529, contour level = 0.0074163  
  
Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.71883894 0.69190206 0.06739559 324.88314871  
-0.69510441 -0.71677641 -0.05533054 927.69885470  
0.01002426 -0.08662072 0.99619095 15.53148650  
Axis -0.02253451 0.04131758 -0.99889191  
Axis point 349.60742573 398.44733584 0.00000000  
Rotation angle (degrees) 136.03072354  
Shift along axis 15.49491660  
  

> fitmap #13 inMap #3

Fit molecule copy of 8i8b (#13) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007127, steps = 64  
shifted from previous position = 0.021  
rotated from previous position = 0.0119 degrees  
atoms outside contour = 16536, contour level = 0.0074163  
  
Position of copy of 8i8b (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.71880030 0.69193509 0.06746860 324.83218556  
-0.69514172 -0.71675497 -0.05513918 927.65237469  
0.01020572 -0.08653430 0.99619662 15.41227467  
Axis -0.02260897 0.04123745 -0.99889354  
Axis point 349.58587803 398.42661262 0.00000000  
Rotation angle (degrees) 136.02801080  
Shift along axis 15.51467650  
  

> combine #8

> select subtract #13

Nothing selected  

> select add #14

30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected  

> view matrix models
> #14,-0.15337,-0.97947,0.13083,573.92,0.95957,-0.17924,-0.21702,257.15,0.23602,0.09226,0.96736,-113.11

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.15337,-0.97947,0.13083,788.32,0.95957,-0.17924,-0.21702,181,0.23602,0.09226,0.96736,-72.466

> view matrix models
> #14,-0.15337,-0.97947,0.13083,758.58,0.95957,-0.17924,-0.21702,69.828,0.23602,0.09226,0.96736,-75.68

> fitmap #14 inMap #3

Fit molecule copy of 8i8b (#14) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007107, steps = 276  
shifted from previous position = 48.3  
rotated from previous position = 17.9 degrees  
atoms outside contour = 16591, contour level = 0.0074163  
  
Position of copy of 8i8b (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.09518255 -0.99180092 -0.08527172 806.75837585  
0.99540916 -0.09396336 -0.01820812 -20.63958015  
0.01004642 -0.08661335 0.99619138 15.51851676  
Axis -0.03436291 -0.04788243 0.99826172  
Axis point 413.27522164 356.68473371 0.00000000  
Rotation angle (degrees) 95.53635131  
Shift along axis -11.24275285  
  

> fitmap #14 inMap #3

Fit molecule copy of 8i8b (#14) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007107, steps = 104  
shifted from previous position = 0.00975  
rotated from previous position = 0.0135 degrees  
atoms outside contour = 16591, contour level = 0.0074163  
  
Position of copy of 8i8b (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.09510822 -0.99180556 -0.08530066 806.73582245  
0.99541849 -0.09390815 -0.01798183 -20.73986080  
0.00982406 -0.08662008 0.99619301 15.61922924  
Axis -0.03447975 -0.04778496 0.99826236  
Axis point 413.31210875 356.64958440 0.00000000  
Rotation angle (degrees) 95.53257599  
Shift along axis -11.23290641  
  

> view front

> select clear

> combine #8

> select add #15

30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected  

> view matrix models
> #15,-0.98735,-0.15852,-0.003891,591.43,0.15825,-0.98356,-0.087032,569.81,0.009969,-0.086547,0.9962,-23.671

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.72794,-0.64063,0.24434,492.87,0.62804,-0.76598,-0.13723,350.55,0.27508,0.053559,0.95993,-148.05

> view matrix models
> #15,-0.77289,-0.51176,0.37515,439.78,0.24756,-0.78756,-0.56433,662.02,0.58425,-0.34329,0.73539,-117.68

> view matrix models
> #15,-0.47576,-0.36838,0.79871,139.73,0.052442,-0.91833,-0.39232,707.91,0.87801,-0.14476,0.45623,-179.99

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.47576,-0.36838,0.79871,155.35,0.052442,-0.91833,-0.39232,703.72,0.87801,-0.14476,0.45623,-145.5

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.34277,0.12528,0.93103,-44.102,0.27709,-0.93349,0.22763,395.94,0.89762,0.33601,0.28526,-188.91

> view matrix models
> #15,-0.10038,-0.33683,0.9362,-54.078,0.83305,-0.54294,-0.10602,206.55,0.54401,0.76926,0.33509,-146.71

> fitmap #15 inMap #3

Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.002648, steps = 252  
shifted from previous position = 41.8  
rotated from previous position = 22.9 degrees  
atoms outside contour = 25287, contour level = 0.0074163  
  
Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.45511012 -0.33626603 0.82449983 156.80799843  
0.82909803 -0.49774687 0.25464596 71.53569237  
0.32476342 0.79948312 0.50532712 -141.08499453  
Axis 0.39478286 0.36210337 0.84440964  
Axis point 91.73905266 106.11892433 -0.00000000  
Rotation angle (degrees) 136.36620084  
Shift along axis -31.32510508  
  

> view matrix models
> #15,0.8708,-0.16948,0.46151,-293.25,0.45854,0.61857,-0.63805,320.99,-0.17734,0.76723,0.61636,23.204

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.8708,-0.16948,0.46151,-336.97,0.45854,0.61857,-0.63805,303.66,-0.17734,0.76723,0.61636,49.165

> fitmap #15 inMap #3

Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.003506, steps = 432  
shifted from previous position = 65.9  
rotated from previous position = 30.8 degrees  
atoms outside contour = 24105, contour level = 0.0074163  
  
Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.97535722 -0.18376330 0.12210397 -216.16414053  
0.21792335 0.88884732 -0.40306314 255.84314316  
-0.03446358 0.41973983 0.90698995 -55.63716744  
Axis 0.88577434 0.16855009 0.43242883  
Axis point 0.00000000 105.13499396 677.85095327  
Rotation angle (degrees) 27.67489445  
Shift along axis -172.40937870  
  

> fitmap #15 inMap #3

Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.003506, steps = 40  
shifted from previous position = 0.00515  
rotated from previous position = 0.00876 degrees  
atoms outside contour = 24113, contour level = 0.0074163  
  
Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.97535280 -0.18378837 0.12210159 -216.15304239  
0.21793990 0.88890645 -0.40292376 255.77732346  
-0.03448419 0.41960361 0.90705219 -55.61223151  
Axis 0.88569030 0.16861020 0.43257749  
Axis point 0.00000000 105.01301844 677.98228811  
Rotation angle (degrees) 27.66768014  
Shift along axis -172.37458845  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.72151,0.57752,0.38196,242.16,-0.68073,-0.69252,-0.23879,886.94,0.12661,-0.4323,0.8928,42.128

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.72151,0.57752,0.38196,179.19,-0.68073,-0.69252,-0.23879,892.73,0.12661,-0.4323,0.8928,71.955

> view matrix models
> #15,-0.72151,0.57752,0.38196,195,-0.68073,-0.69252,-0.23879,911.17,0.12661,-0.4323,0.8928,77.246

> fitmap #15 inMap #3

Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007109, steps = 268  
shifted from previous position = 22.7  
rotated from previous position = 34 degrees  
atoms outside contour = 16612, contour level = 0.0074163  
  
Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.34626017 0.93430523 0.08472110 70.16210393  
-0.93808526 -0.34578823 -0.02065362 863.81775833  
0.00999878 -0.08662715 0.99619064 15.52638035  
Axis -0.03518510 0.03985102 -0.99858595  
Axis point 335.40888064 407.58273783 0.00000000  
Rotation angle (degrees) 110.36068810  
Shift along axis 16.45092923  
  

> fitmap #15 inMap #3

Fit molecule copy of 8i8b (#15) to map emd_51808.map (#3) using 30015 atoms  
average map value = 0.007109, steps = 60  
shifted from previous position = 0.0201  
rotated from previous position = 0.0103 degrees  
atoms outside contour = 16596, contour level = 0.0074163  
  
Position of copy of 8i8b (#15) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.34620781 0.93430916 0.08489165 70.08290633  
-0.93810372 -0.34573984 -0.02062536 863.79841473  
0.01007997 -0.08677784 0.99617671 15.55204246  
Axis -0.03527993 0.03989799 -0.99858073  
Axis point 335.37735797 407.59951129 0.00000000  
Rotation angle (degrees) 110.35803510  
Shift along axis 16.46132973  
  

> view front

> select clear

> vop copy #3

Opened emd_51808.map copy as #16, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> close #16

> show #!3 models

> volume zone #3 nearAtoms #8/A-C newMap true

Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> volume zone #3 nearAtoms #8-15/A-C newMap true

Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> close #16

> volume zone #3 nearAtoms #8-15/A-C range 4 newMap true

Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> hide #!16 models

> show #!16 models

> hide #!16 models

> volume #17 level 0.006533

> show #!16 models

> hide #!17 models

> show #!17 models

> hide #!16 models

> close #16

> close #17

> volume zone #3 nearAtoms #8-15/A-C newMap true

Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> volume zone #3 nearAtoms #8-15/A-C invert true newMap true

Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> color #16 #b9c2ffff models

> color #17 #b9c2ffff models

> hide #!16 models

> show #!16 models

> transparency #16 70

> transparency #16 65

> transparency #16 50

> color #16 #dbd3beff models

> color #16 #dbd3be7f models

> color #16 #dfd9fcff models

> color #16 #dfd9fc7c models

> color #16 #d2d2d3ff models

> color #16 #d2d2d380 models

> color #16 #d2d2d391 models

> volume #16 level 0.007053

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> color #16 #ff91aaff models

> color #16 #ff91aa4f models

> color #16 #ff91aa5f models

> hide #!16 models

> show #!16 models

> hide #!17 models

> show #!17 models

> view front

> color #16 #0000005f models

> color #16 #ff92ad5f models

> color #16 #ff92adab models

> color #16 #ff92ad76 models

> color #16 #ffd7e076 models

> color #16 #b9c2ffff models

> color #16 #b9c2ff80 models

> color #16 #b9c2ff72 models

> color #16 #b9c2ffff models

> color #16 #b9c2fff4 models

> color #16 #b9c2ff5c models

> color #16 #fafff15c models

> color #16 #fafff185 models

> color #16 #fafff154 models

> color #16 #ff91aaff models

> color #16 #ff91aa80 models

> view front

> ui tool show "Hide Dust"

> surface dust #2 size 1.35

> surface dust #17 size 8.1

> surface dust #17 size 7.5

> surface dust #17 size 21.62

> surface dust #2 size 1.44

> surface dust #2 size 6.66

> surface dust #7 size 8.43

> surface dust #7 size 10.15

> view front

> lighting gentle

> lighting soft

> lighting gentle

> lighting soft

> save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true

——— End of log from Sun Jun 15 21:01:47 2025 ———

opened ChimeraX session  

> open 8vWi

8vwi title:  
The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised
reconstruction) [more info...]  
  
Chain information for 8vwi #18  
---  
Chain | Description | UniProt  
A B C D E F V W X Y Z a | Major capsid protein | MCP_NPVAC 1-347  
G H I b c d | Capsid-associated protein VP80 | VP80_NPVAC 1-691  
J M Q S e h | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290  
K L R T f g | Protein C42 | C42_NPVAC 1-361  
N i | Protein AC109 | AC109_NPVAC 1-390  
O j | Protein AC142 | AC142_NPVAC 1-477  
P k | 38K (AC98) protein in P143-LEF5 intergenic region | 38K_NPVAC 1-320  
  
Non-standard residues in 8vwi #18  
---  
ZN — zinc ion  
  

> select #13/G,H,I

5001 atoms, 5096 bonds, 2 pseudobonds, 611 residues, 2 models selected  

> select #18/G,H,I

10481 atoms, 10589 bonds, 1 pseudobond, 628 residues, 2 models selected  

> select ~sel & ##selected

145785 atoms, 147346 bonds, 76 pseudobonds, 8986 residues, 3 models selected  

> delete atoms (#!18 & sel)

> delete bonds (#!18 & sel)

> select #18/G,H,I

10481 atoms, 10589 bonds, 1 pseudobond, 628 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> ui mousemode right "translate selected models"

> view matrix models #18,1,0,0,-177.91,0,1,0,67.519,0,0,1,91.008

> view matrix models #18,1,0,0,-204.71,0,1,0,191.65,0,0,1,-10.098

> view matrix models #18,1,0,0,31.513,0,1,0,239.83,0,0,1,100.46

> ui tool show "Fit in Map"

> fitmap #18 inMap #3

Fit molecule 8vwi (#18) to map emd_51808.map (#3) using 10481 atoms  
average map value = 0.006444, steps = 228  
shifted from previous position = 18.1  
rotated from previous position = 42.1 degrees  
atoms outside contour = 6594, contour level = 0.0074163  
  
Position of 8vwi (#18) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.72238697 -0.69121237 -0.01955832 342.84555920  
0.69141014 0.72244279 0.00533183 82.71455050  
0.01044434 -0.01737447 0.99979450 103.81022114  
Axis -0.01641655 -0.02169179 0.99962991  
Axis point 66.63545589 471.53150882 0.00000000  
Rotation angle (degrees) 43.75429421  
Shift along axis 96.34923300  
  

> hide #!8 models

> show #!8 models

> hide #!11 models

> show #!11 models

> hide #!14 models

> show #!14 models

> hide #!13 models

> show #!13 models

> hide #!16 models

> show #!16 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> hide #!9 models

> show #!9 models

> close #12

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> select subtract #18

Nothing selected  

> hide #!18 models

> show #!18 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> graphics silhouettes true

> lighting depthCue false

> lighting soft

> graphics bgColor white

> graphics silhouettes width 2.1

> cartoon style protein modeHelix tube radius 1.9 sides 24

> select clear

> select #18/G

3228 atoms, 3263 bonds, 194 residues, 1 model selected  

> color sel #732433ff

> select clear

> select #18/H

3513 atoms, 3549 bonds, 210 residues, 1 model selected  

> color sel #fb5e85ff

> select #18/I

3740 atoms, 3777 bonds, 1 pseudobond, 224 residues, 2 models selected  

> color (#!18 & sel) #d87a90ff

> select clear

> select #18/H

3513 atoms, 3549 bonds, 210 residues, 1 model selected  

> color sel #fb5d84ff

> select clear

> color #2,7,9-11,13-18 #fb5174ff

> undo

> select #18/H

3513 atoms, 3549 bonds, 210 residues, 1 model selected  

> color sel #fb5377ff

> select clear

> open (H2J

'(H2J' has no suffix  

> open 9H2J

9h2j title:  
AcMNPV apical cap - C14 anchor complex only [more info...]  
  
Chain information for 9h2j #12  
---  
Chain | Description | UniProt  
A B | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290  
C D | Protein C42 | C42_NPVAC 1-361  
E | Protein AC142 | AC142_NPVAC 1-477  
F G L M | Major capsid protein | MCP_NPVAC 1-347  
H I J | Capsid-associated protein VP80 | VP80_NPVAC 1-691  
K | Protein AC109 | AC109_NPVAC 1-390  
N P | Protein Ac66 | AC66_NPVAC 1-808  
O | Tyrosine-protein phosphatase | PTP_NPVAC 1-168  
  
Non-standard residues in 9h2j #12  
---  
ZN — zinc ion  
  
9h2j mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> select #12?H-J

Expected an objects specifier or a keyword  

> select #12/H-J

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected  

> select ~sel & ##selected

23413 atoms, 23880 bonds, 44 pseudobonds, 2869 residues, 3 models selected  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

> show #!9-15,18 cartoons

> hide #!9-15,18 atoms

> fitmap #12 inMap #3

Fit molecule 9h2j (#12) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008124, steps = 88  
shifted from previous position = 11.8  
rotated from previous position = 1.54 degrees  
atoms outside contour = 2070, contour level = 0.0074163  
  
Position of 9h2j (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.99999318 -0.00273077 -0.00248509 2.24305554  
0.00273330 0.99999575 0.00101599 -1.59564477  
0.00248230 -0.00102278 0.99999640 -0.60594412  
Axis -0.26613114 -0.64841793 0.71325199  
Axis point 583.74973499 820.48092021 0.00000000  
Rotation angle (degrees) 0.21946567  
Shift along axis 0.00550691  
  

> hide #!12 models

> show #!12 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> select add #12

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected  

> view matrix models
> #12,0.99964,0.026795,-0.0024543,-102.14,-0.026792,0.99964,0.001089,34.149,0.0024826,-0.0010229,1,-12.381

> fitmap #12 inMap #3

Fit molecule 9h2j (#12) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.00805, steps = 168  
shifted from previous position = 9.61  
rotated from previous position = 25.7 degrees  
atoms outside contour = 2122, contour level = 0.0074163  
  
Position of 9h2j (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.90005241 -0.43577435 -0.00252616 182.09251361  
0.43577488 0.90005562 -0.00036259 -113.29637229  
0.00243169 -0.00077449 0.99999674 -0.70368562  
Axis -0.00047260 -0.00568846 0.99998371  
Axis point 338.04374149 340.32702583 0.00000000  
Rotation angle (degrees) 25.83504600  
Shift along axis -0.14524922  
  

> show #!18 models

> select clear

> hide #!12 models

> show #!12 models

> hide #!18 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> close #9-11

> save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true

> graphics silhouettes true

> lighting depthCue false

> lighting soft

> graphics bgColor white

> graphics silhouettes width 2.1

> cartoon style protein modeHelix tube radius 1.9 sides 24

> select clear

> volume usage

Expected a density maps specifier or a keyword  

> usasge volume

Unknown command: usasge volume  

> volume zone #3 nearAtoms #12/H-J newMap true

Opened emd_51808.map zone as #9, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> show #!18 models

> hide #!18 models

> close #18

> show #!3 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!3 models

> save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true

——— End of log from Wed Jun 18 01:06:40 2025 ———

opened ChimeraX session  

> hide #!15 models

> hide #!14 models

> hide #!13 models

> show #!13 models

> hide #!16 models

> hide #!9 models

> hide #!7 models

> show #!7 models

> hide #!17 models

> show #!17 models

> close #17

> show #!3 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!3 models

> select #12/J:534

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

82 atoms, 82 bonds, 10 residues, 1 model selected  

> select up

340 atoms, 348 bonds, 41 residues, 1 model selected  

> select up

407 atoms, 414 bonds, 49 residues, 1 model selected  

> select up

1430 atoms, 1460 bonds, 171 residues, 1 model selected  

> select up

4686 atoms, 4782 bonds, 561 residues, 1 model selected  

> select down

1430 atoms, 1460 bonds, 171 residues, 1 model selected  

> select #12/J

1430 atoms, 1460 bonds, 2 pseudobonds, 171 residues, 2 models selected  

> color (#!12 & sel) #491620ff

> color (#!12 & sel) #491621ff

[Repeated 1 time(s)]

> color (#!12 & sel) #4a1721ff

> color (#!12 & sel) #4d1823ff

> color (#!12 & sel) #541a26ff

> color (#!12 & sel) #571b27ff

> color (#!12 & sel) #631e2cff

[Repeated 1 time(s)]

> color (#!12 & sel) #68202fff

[Repeated 1 time(s)]

> color (#!12 & sel) #6a2130ff

> color (#!12 & sel) #631f2dff

> color (#!12 & sel) #5e1d2aff

> color (#!12 & sel) #5c1c2aff

> color (#!12 & sel) #591b28ff

> color (#!12 & sel) #571b27ff

> color (#!12 & sel) #551a26ff

> color (#!12 & sel) #521925ff

> color (#!12 & sel) #5c1c29ff

> color (#!12 & sel) #5d1d2aff

> color (#!12 & sel) #5e1d2aff

[Repeated 1 time(s)]

> color (#!12 & sel) #5e1e2bff

[Repeated 1 time(s)]

> color (#!12 & sel) #5e1e2aff

[Repeated 3 time(s)]

> color (#!12 & sel) #5e1d28ff

> color (#!12 & sel) #5e1d26ff

> color (#!12 & sel) #5e1d25ff

[Repeated 1 time(s)]

> color (#!12 & sel) #5e1c24ff

> color (#!12 & sel) #5e1d23ff

> color (#!12 & sel) #5e1d20ff

> color (#!12 & sel) #5e1d1fff

[Repeated 1 time(s)]

> color (#!12 & sel) #5e1c1eff

> color (#!12 & sel) #5e1b1eff

> color (#!12 & sel) #5e1b1fff

> color (#!12 & sel) #5e1a1fff

> color (#!12 & sel) #5e191fff

> color (#!12 & sel) #5e1820ff

[Repeated 2 time(s)]

> color (#!12 & sel) #5e1720ff

[Repeated 1 time(s)]

> color (#!12 & sel) #5e1620ff

> color (#!12 & sel) #5e1520ff

> color (#!12 & sel) #5e1421ff

> color (#!12 & sel) #5e1420ff

> color (#!12 & sel) #5e1421ff

> color (#!12 & sel) #5e1321ff

[Repeated 2 time(s)]

> color (#!12 & sel) #5e1221ff

[Repeated 3 time(s)]

> color (#!12 & sel) #5e1220ff

> color (#!12 & sel) #5e1328ff

> color (#!12 & sel) #5e1429ff

> color (#!12 & sel) #5e142aff

> color (#!12 & sel) #5e142bff

[Repeated 1 time(s)]

> color (#!12 & sel) #5e142cff

[Repeated 1 time(s)]

> color (#!12 & sel) #5e142eff

> color (#!12 & sel) #5e142fff

> color (#!12 & sel) #5e1530ff

[Repeated 1 time(s)]

> select clear

> select #12/i

1462 atoms, 1493 bonds, 176 residues, 1 model selected  

> color sel #fb5377ff

> color sel #fb547aff

> color sel #fa5379ff

> color sel #f85379ff

> color sel #f75378ff

> color sel #f45176ff

> color sel #f25176ff

> color sel #ef5074ff

> color sel #e94e71ff

> color sel #e34c6eff

> color sel #e14b6dff

> color sel #df4b6cff

> color sel #da496aff

> color sel #d64768ff

> color sel #d34666ff

> color sel #d24666ff

> color sel #d84869ff

> color sel #da496aff

[Repeated 1 time(s)]

> select #12/H

1794 atoms, 1829 bonds, 2 pseudobonds, 214 residues, 2 models selected  

> color (#!12 & sel) #fca5c2ff

> color (#!12 & sel) #fca5c4ff

> color (#!12 & sel) #fba4c3ff

> color (#!12 & sel) #f9a2c1ff

> color (#!12 & sel) #f7a1c0ff

> color (#!12 & sel) #f39ebdff

> color (#!12 & sel) #f29ebcff

> color (#!12 & sel) #ef9cb9ff

> color (#!12 & sel) #ed9bb8ff

> select clear

> close #13-15

> show #!16 models

> close #16

> show #!9 models

> hide #!9 models

> close #9

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #!3 models

> close #8

> check symmetry #3

Unknown command: check symmetry #3  

> measure symmetry #3

Symmetry emd_51808.map: C2, center 250 250 258  

> show #!7 models

> hide #!7 models

> hide #!2 models

> show #!2 models

> show #!7 models

> combine #12/H-J

> select add #12

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.91253,-0.40901,-0.0025361,79.681,0.40901,0.91253,-0.00028776,-103.75,0.0024319,-0.0007747,1,-7.6978

> combine #12/H-J

> select add #8

9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 5 models selected  

> select subtract #12

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> select add #12

9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 5 models selected  

> select add #9

14058 atoms, 14346 bonds, 12 pseudobonds, 1683 residues, 8 models selected  

> view matrix models
> #12,0.91253,-0.40901,-0.0025361,58.802,0.40901,0.91253,-0.00028776,-111.99,0.0024319,-0.0007747,1,-7.8898,#8,0.91253,-0.40901,-0.0025361,147.97,0.40901,0.91253,-0.00028776,-116.76,0.0024319,-0.0007747,1,-10.964,#9,0.91253,-0.40901,-0.0025361,58.802,0.40901,0.91253,-0.00028776,-111.99,0.0024319,-0.0007747,1,-7.8898

> select subtract #12

9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 6 models selected  

> select subtract #9

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> select subtract #8

Nothing selected  

> view front

> select add #8

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> view matrix models
> #8,0.91253,-0.40901,-0.0025361,263.05,0.40901,0.91253,-0.00028776,-134.6,0.0024319,-0.0007747,1,-7.0615

> select add #12

9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 5 models selected  

> select subtract #8

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 2 models selected  

> view matrix models
> #12,0.91253,-0.40901,-0.0025361,169.62,0.40901,0.91253,-0.00028776,-129.28,0.0024319,-0.0007747,1,-10.558

> ui tool show "Fit in Map"

> fitmap #12 inMap #3

Fit molecule 9h2j (#12) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.00805, steps = 220  
shifted from previous position = 20.8  
rotated from previous position = 0.0134 degrees  
atoms outside contour = 2118, contour level = 0.0074163  
  
Position of 9h2j (#12) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.89997855 -0.43592761 -0.00239316 182.16175413  
0.43592784 0.89998151 -0.00045246 -113.28031022  
0.00235104 -0.00063604 0.99999703 -0.75164500  
Axis -0.00021057 -0.00544141 0.99998517  
Axis point 337.94735710 340.33112542 0.00000000  
Rotation angle (degrees) 25.84475250  
Shift along axis -0.17358585  
  

> fitmap #9 inMap #3

Fit molecule copy of 9h2j (#9) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008067, steps = 192  
shifted from previous position = 18.8  
rotated from previous position = 25.7 degrees  
atoms outside contour = 2099, contour level = 0.0074163  
  
Position of copy of 9h2j (#9) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.62158229 -0.78334695 -0.00173858 393.14200315  
0.78334624 0.62158442 -0.00121467 -136.11104005  
0.00203218 -0.00060689 0.99999775 -0.63815363  
Axis 0.00038793 -0.00240681 0.99999703  
Axis point 337.45120495 338.85949584 0.00000000  
Rotation angle (degrees) 51.56823043  
Shift along axis -0.15804494  
  

> fitmap #8 inMap #3

Fit molecule copy of 9h2j (#8) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008124, steps = 172  
shifted from previous position = 9.7  
rotated from previous position = 25.7 degrees  
atoms outside contour = 2069, contour level = 0.0074163  
  
Position of copy of 9h2j (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.99999359 -0.00272428 -0.00232336 2.18361006  
0.00272673 0.99999573 0.00104894 -1.60363375  
0.00232049 -0.00105526 0.99999675 -0.51987891  
Axis -0.28192500 -0.62219354 0.73033793  
Axis point 588.80595766 800.40533547 0.00000000  
Rotation angle (degrees) 0.21381932  
Shift along axis 0.00246900  
  

> select clear

> combine #12/H-J

> select add #8

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> select add #9

9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 6 models selected  

> select add #10

14058 atoms, 14346 bonds, 12 pseudobonds, 1683 residues, 9 models selected  

> select subtract #9

9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 6 models selected  

> select subtract #8

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> select add #12

9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 5 models selected  

> select subtract #12

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> view matrix models
> #10,0.91246,-0.40917,-0.0024058,-5.2451,0.40917,0.91246,-0.00038152,-117.68,0.0023513,-0.00063625,1,-1.7477

> view matrix models
> #10,0.91246,-0.40917,-0.0024058,6.0685,0.40917,0.91246,-0.00038152,-167.41,0.0023513,-0.00063625,1,17.238

> fitmap #10 inMap #3

Fit molecule copy of 9h2j (#10) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.005529, steps = 148  
shifted from previous position = 22.2  
rotated from previous position = 6.12 degrees  
atoms outside contour = 3059, contour level = 0.0074163  
  
Position of copy of 9h2j (#10) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.90204797 -0.42538232 0.07320748 -2.12972818  
0.42047121 0.90431073 0.07366184 -216.34367525  
-0.09753675 -0.03566488 0.99459268 84.18985729  
Axis -0.12568996 0.19630000 0.97245480  
Axis point 507.95649835 -110.25127704 0.00000000  
Rotation angle (degrees) 25.77933457  
Shift along axis 39.67025376  
  

> fitmap #10 inMap #3

Fit molecule copy of 9h2j (#10) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.005529, steps = 60  
shifted from previous position = 0.019  
rotated from previous position = 0.00947 degrees  
atoms outside contour = 3062, contour level = 0.0074163  
  
Position of copy of 9h2j (#10) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.90205379 -0.42539478 0.07306326 -2.06098965  
0.42049649 0.90430530 0.07358412 -216.31682850  
-0.09737379 -0.03565399 0.99460904 84.10348636  
Axis -0.12559310 0.19595466 0.97253696  
Axis point 507.86667095 -110.06962014 0.00000000  
Rotation angle (degrees) 25.77823154  
Shift along axis 39.66430515  
  

> view matrix models
> #10,0.91408,-0.39851,0.075204,-36.692,0.39368,0.91647,0.071395,-201.29,-0.097374,-0.035654,0.99461,51.872

> fitmap #10 inMap #3

Fit molecule copy of 9h2j (#10) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008103, steps = 488  
shifted from previous position = 15.9  
rotated from previous position = 52.5 degrees  
atoms outside contour = 2069, contour level = 0.0074163  
  
Position of copy of 9h2j (#10) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.22005060 -0.97548761 -0.00128377 593.25703314  
0.97548641 0.22005264 -0.00175945 -65.05565033  
0.00199882 -0.00086514 0.99999763 -0.48706362  
Axis 0.00045839 -0.00168254 0.99999848  
Axis point 337.31158469 338.46776553 0.00000000  
Rotation angle (degrees) 77.28800469  
Shift along axis -0.10565891  
  

> fitmap #10 inMap #3

Fit molecule copy of 9h2j (#10) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008103, steps = 76  
shifted from previous position = 0.00242  
rotated from previous position = 0.00552 degrees  
atoms outside contour = 2069, contour level = 0.0074163  
  
Position of copy of 9h2j (#10) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.21999869 -0.97549939 -0.00123397 593.26836800  
0.97549826 0.22000059 -0.00169656 -65.05737940  
0.00192647 -0.00083049 0.99999780 -0.47258372  
Axis 0.00044391 -0.00161991 0.99999859  
Axis point 337.31609761 338.45374235 0.00000000  
Rotation angle (degrees) 77.29105268  
Shift along axis -0.10383708  
  

> select subtract #10

Nothing selected  

> combine #12/H-J

> select add #11

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> view matrix models
> #11,0.91246,-0.40917,-0.0024058,325.71,0.40917,0.91246,-0.00038152,-194.43,0.0023513,-0.00063625,1,-1.127

> fitmap #11 inMap #3

Fit molecule copy of 9h2j (#11) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008113, steps = 328  
shifted from previous position = 16.3  
rotated from previous position = 51.4 degrees  
atoms outside contour = 2068, contour level = 0.0074163  
  
Position of copy of 9h2j (#11) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.90217111 0.43137547 -0.00158165 -111.75969148  
-0.43137241 0.90217185 0.00194823 177.46726907  
0.00226734 -0.00107535 0.99999685 -0.48439830  
Axis -0.00350454 -0.00446125 -0.99998391  
Axis point 335.39824842 335.13967814 0.00000000  
Rotation angle (degrees) 25.55522633  
Shift along axis 0.08433080  
  

> view front

> combine #12/H-J

> select add #13

9372 atoms, 9564 bonds, 8 pseudobonds, 1122 residues, 6 models selected  

> select subtract #11

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> view matrix models
> #13,0.91246,-0.40917,-0.0024058,342.27,0.40917,0.91246,-0.00038152,-286.57,0.0023513,-0.00063625,1,5.0769

> fitmap #13 inMap #3

Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.00562, steps = 312  
shifted from previous position = 21.6  
rotated from previous position = 49.8 degrees  
atoms outside contour = 3231, contour level = 0.0074163  
  
Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.91945451 0.38746306 0.06690132 -99.31052235  
-0.39318178 0.90748090 0.14794085 20.81499994  
-0.00339006 -0.16232926 0.98673082 86.01920655  
Axis -0.36806356 0.08338443 -0.92605413  
Axis point -7.47986169 294.05363565 0.00000000  
Rotation angle (degrees) 24.92868391  
Shift along axis -41.37020973  
  

> fitmap #13 inMap #3

Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.00562, steps = 44  
shifted from previous position = 0.00607  
rotated from previous position = 0.00809 degrees  
atoms outside contour = 3232, contour level = 0.0074163  
  
Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.91949117 0.38736217 0.06698166 -99.30442707  
-0.39309512 0.90752455 0.14790342 20.76658332  
-0.00349531 -0.16232605 0.98673098 86.06984775  
Axis -0.36809096 0.08362176 -0.92602184  
Axis point -7.55882537 294.14233104 0.00000000  
Rotation angle (degrees) 24.92321429  
Shift along axis -41.41295932  
  

> view matrix models
> #13,0.90748,0.41399,0.071319,-92.991,-0.42007,0.89569,0.14586,25.823,-0.003495,-0.16233,0.98673,84.261

> fitmap #13 inMap #3

Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008043, steps = 188  
shifted from previous position = 10.3  
rotated from previous position = 29.6 degrees  
atoms outside contour = 2110, contour level = 0.0074163  
  
Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.62540387 0.78030080 -0.00080651 -136.64337522  
-0.78029751 0.62540375 0.00243810 388.44994392  
0.00240685 -0.00089548 0.99999670 -0.64198151  
Axis -0.00213608 -0.00205905 -0.99999560  
Axis point 336.25961586 336.54282700 0.00000000  
Rotation angle (degrees) 51.28828857  
Shift along axis 0.13402367  
  

> fitmap #13 inMap #3

Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008043, steps = 44  
shifted from previous position = 0.0249  
rotated from previous position = 0.00832 degrees  
atoms outside contour = 2103, contour level = 0.0074163  
  
Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.62548870 0.78023290 -0.00071051 -136.65886359  
-0.78022971 0.62548836 0.00243151 388.38578651  
0.00234156 -0.00096653 0.99999679 -0.58976226  
Axis -0.00217757 -0.00195586 -0.99999572  
Axis point 336.24125162 336.54660427 0.00000000  
Rotation angle (degrees) 51.28206464  
Shift along axis 0.12771450  
  

> fitmap #13 inMap #3

Fit molecule copy of 9h2j (#13) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008043, steps = 48  
shifted from previous position = 0.0296  
rotated from previous position = 0.0116 degrees  
atoms outside contour = 2112, contour level = 0.0074163  
  
Position of copy of 9h2j (#13) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.62550544 0.78021964 -0.00051153 -136.74508465  
-0.78021671 0.62550467 0.00240450 388.36971399  
0.00219600 -0.00110492 0.99999698 -0.43341938  
Axis -0.00224899 -0.00173511 -0.99999597  
Axis point 336.19205086 336.63216766 0.00000000  
Rotation angle (degrees) 51.28084399  
Shift along axis 0.06709267  
  

> combine #12/H-J

> select subtract #13

Nothing selected  

> select add #14

4686 atoms, 4782 bonds, 4 pseudobonds, 561 residues, 3 models selected  

> view matrix models
> #14,0.91246,-0.40917,-0.0024058,-63.704,0.40917,0.91246,-0.00038152,-199.82,0.0023513,-0.00063625,1,6.8614

> view matrix models
> #14,0.91246,-0.40917,-0.0024058,-47.684,0.40917,0.91246,-0.00038152,-236.16,0.0023513,-0.00063625,1,19.227

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.005454, steps = 156  
shifted from previous position = 22.7  
rotated from previous position = 20.5 degrees  
atoms outside contour = 3124, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.96735530 -0.25166263 0.02982690 -150.11807775  
0.23252009 0.92820125 0.29047693 -282.33790136  
-0.10078756 -0.27405905 0.95641702 222.35437906  
Axis -0.74761901 0.17297366 0.64120662  
Axis point 0.00000000 149.48567957 1131.58050632  
Rotation angle (degrees) 22.18237314  
Shift along axis 205.96920963  
  

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.005454, steps = 64  
shifted from previous position = 0.0238  
rotated from previous position = 0.00196 degrees  
atoms outside contour = 3125, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.96734788 -0.25169019 0.02983494 -150.09959510  
0.23254254 0.92819033 0.29049386 -282.33058598  
-0.10080695 -0.27407073 0.95641162 222.38668885  
Axis -0.74759928 0.17299665 0.64122343  
Axis point 0.00000000 149.56426002 1131.53218767  
Rotation angle (degrees) 22.18417383  
Shift along axis 205.97165777  
  

> view matrix models
> #14,0.97379,-0.22418,0.038398,-189.36,0.20388,0.93522,0.28949,-268.17,-0.10081,-0.27407,0.95641,209.17

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.005454, steps = 156  
shifted from previous position = 21.4  
rotated from previous position = 0.00948 degrees  
atoms outside contour = 3131, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.96736636 -0.25160849 0.02992493 -150.16985353  
0.23245091 0.92824741 0.29038477 -282.28830679  
-0.10084101 -0.27395238 0.95644194 222.32675316  
Axis -0.74755518 0.17322049 0.64121441  
Axis point 0.00000000 149.59849898 1131.91943807  
Rotation angle (degrees) 22.17613946  
Shift along axis 205.92125140  
  

> view matrix models
> #14,0.97381,-0.22409,0.038485,-187.42,0.20379,0.93527,0.28937,-281.11,-0.10084,-0.27395,0.95644,193.55

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.005057, steps = 148  
shifted from previous position = 16.7  
rotated from previous position = 21.6 degrees  
atoms outside contour = 3453, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.84743544 -0.43092698 0.31008889 -111.61706948  
0.28405814 0.86148443 0.42089850 -314.68029233  
-0.44851327 -0.26860103 0.85246075 383.67953894  
Axis -0.55167191 0.60696126 0.57206305  
Axis point 580.86386831 0.00000000 485.50385093  
Rotation angle (degrees) 38.67617687  
Shift along axis 90.06614474  
  

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.005057, steps = 48  
shifted from previous position = 0.00732  
rotated from previous position = 0.0298 degrees  
atoms outside contour = 3451, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.84745061 -0.43063705 0.31044999 -111.90017932  
0.28360755 0.86159562 0.42097476 -314.56494215  
-0.44876968 -0.26870935 0.85229165 383.91108390  
Axis -0.55179602 0.60742938 0.57144615  
Axis point 580.89812132 -0.00000000 485.82403723  
Rotation angle (degrees) 38.67813643  
Shift along axis 90.05459612  
  

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.005057, steps = 48  
shifted from previous position = 0.00826  
rotated from previous position = 0.0316 degrees  
atoms outside contour = 3454, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
0.84749889 -0.43088450 0.30997448 -111.63021772  
0.28399936 0.86145527 0.42099783 -314.67270743  
-0.44843059 -0.26876264 0.85245331 383.72612953  
Axis -0.55189550 0.60681985 0.57199739  
Axis point 580.99005721 0.00000000 485.45630776  
Rotation angle (degrees) 38.67494585  
Shift along axis 90.14891535  
  

> view matrix models
> #14,0.85551,-0.40526,0.32227,-141.21,0.25885,0.8738,0.41166,-302.29,-0.44843,-0.26876,0.85245,371.94

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.89716,-0.37034,0.24072,-148.69,0.22136,0.84859,0.48052,-297.16,-0.38223,-0.37782,0.8433,402.24

> view matrix models
> #14,0.50401,-0.85752,-0.10311,397.1,0.69275,0.33006,0.64122,-294.28,-0.51582,-0.39461,0.7604,499.03

> view matrix models
> #14,0.26685,-0.87396,0.40618,329.76,0.89852,0.37803,0.22307,-261.63,-0.34851,0.30544,0.88614,20.118

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008053, steps = 184  
shifted from previous position = 9.18  
rotated from previous position = 41.6 degrees  
atoms outside contour = 2100, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.22508318 -0.97433950 -0.00031500 742.60891926  
0.97433710 -0.22508188 -0.00231503 85.91975961  
0.00218472 -0.00082799 0.99999727 -0.58981658  
Axis 0.00076310 -0.00128278 0.99999889  
Axis point 337.13766431 338.26745131 0.00000000  
Rotation angle (degrees) 103.00781132  
Shift along axis -0.13334495  
  

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008053, steps = 48  
shifted from previous position = 0.00934  
rotated from previous position = 0.00919 degrees  
atoms outside contour = 2104, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.22501832 -0.97435449 -0.00029112 742.57206285  
0.97435175 -0.22501695 -0.00245903 85.92560319  
0.00233046 -0.00083698 0.99999693 -0.65461631  
Axis 0.00083237 -0.00134529 0.99999875  
Axis point 337.11463885 338.27583713 0.00000000  
Rotation angle (degrees) 103.00400544  
Shift along axis -0.15211300  
  

> fitmap #14 inMap #3

Fit molecule copy of 9h2j (#14) to map emd_51808.map (#3) using 4686 atoms  
average map value = 0.008053, steps = 76  
shifted from previous position = 0.00603  
rotated from previous position = 0.00676 degrees  
atoms outside contour = 2100, contour level = 0.0074163  
  
Position of copy of 9h2j (#14) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.22503991 -0.97434947 -0.00038064 742.61410000  
0.97434698 -0.22503840 -0.00238541 85.91234090  
0.00223856 -0.00090769 0.99999708 -0.57415084  
Axis 0.00075831 -0.00134408 0.99999881  
Axis point 337.14163687 338.27927836 0.00000000  
Rotation angle (degrees) 103.00526624  
Shift along axis -0.12649191  
  

> select clear

> view front

> name veiew front

"front": invalid atom specifier  

> view name front

> save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true

> volume zone #3 nearAtoms #8-14/H-J newMap true

Opened emd_51808.map zone as #15, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> hide #15.1 models

> show #15.1 models

> hide #15.1 models

> show #15.1 models

> hide #15.1 models

> hide #!8-14 atoms

[Repeated 1 time(s)]

> hide #!8-14 cartoons

> show #!8-14 cartoons

[Repeated 1 time(s)]

> hide pbonds

> show #15.1 models

> volume zone #3 nearAtoms #8-14/H-J invertMap truenewMap true

Expected a keyword  

> volume zone #3 nearAtoms #8-14/H-J invertMap true newMap true

Expected a keyword  

> volume zone #3 nearAtoms #8-14/H-J invert true newMap true

Opened emd_51808.map zone as #16, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> volume #16 level 0.006624

> volume #15 level 0.00726

> volume #15 level 0.007312

> color #16 #d2d2d3ff models

> color #16 #f1f2f4ff models

> hide #15.1 models

> show #15.1 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!7 models

> show #!7 models

> color #15 #ff91aaff models

> color #15 #ff91aa41 models

> color #15 #ff91aa54 models

> color #15 #ff91aa68 models

> color #15 #ff91aa66 models

> color #2 #f1f2f4ff models

> color #3 #f1f2f4ff models

> select clear

> color #7 #f1f2f4ff models

> volume zone #3 nearAtoms #8-14/H-J range 4 newMap true

Opened emd_51808.map zone as #17, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> hide #!16 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> show #!16 models

> color #16 #f1f2f48e models

> volume zone #3 nearAtoms #8-14/H-J range 4 invert true newMap true

Opened emd_51808.map zone as #18, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> close #15-16

> volume #17 level 0.006994

> volume #18 level 0.006192

> ui tool show "Hide Dust"

> surface dust #2 size 1.35

> surface dust #18 size 15.44

[Repeated 1 time(s)]

> surface dust #18 size 14.68

> surface dust #18 size 19.21

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> color #17 #b2ffff3b models

> hide #!17 models

> show #!17 models

> volume zone #3 nearAtoms #8-14/H-J range 5 invert true newMap true

Opened emd_51808.map zone as #15, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> hide #!18 models

> show #!18 models

> hide #!18 models

> volume #15 level 0.006264

> surface dust #15 size 8.1

> surface dust #15 size 7.75

> surface dust #15 size 24.31

> close #18

> hide #!15 models

> show #!15 models

> color #15 #f1f2f4ff models

> color #17 #ff91aaff models

> color #17 #ff91aa49 models

> color #17 #ff91aa2b models

> color #17 #ff91aa3d models

> color #17 #ff91aa4d models

> color #17 #ff91aa60 models

> color #17 #ff91aa65 models

> view front

> combine #8-11,13,14

Remapping chain ID 'H' in copy of 9h2j #9 to 'K'  
Remapping chain ID 'I' in copy of 9h2j #9 to 'L'  
Remapping chain ID 'J' in copy of 9h2j #9 to 'M'  
Remapping chain ID 'H' in copy of 9h2j #10 to 'N'  
Remapping chain ID 'I' in copy of 9h2j #10 to 'O'  
Remapping chain ID 'J' in copy of 9h2j #10 to 'P'  
Remapping chain ID 'H' in copy of 9h2j #11 to 'Q'  
Remapping chain ID 'I' in copy of 9h2j #11 to 'R'  
Remapping chain ID 'J' in copy of 9h2j #11 to 'S'  
Remapping chain ID 'H' in copy of 9h2j #13 to 'T'  
Remapping chain ID 'I' in copy of 9h2j #13 to 'U'  
Remapping chain ID 'J' in copy of 9h2j #13 to 'V'  
Remapping chain ID 'H' in copy of 9h2j #14 to 'W'  
Remapping chain ID 'I' in copy of 9h2j #14 to 'X'  
Remapping chain ID 'J' in copy of 9h2j #14 to 'Y'  

> select add #16

28116 atoms, 28692 bonds, 24 pseudobonds, 3366 residues, 3 models selected  

> select subtract #16

Nothing selected  

> hide #!16 models

> show #!16 models

> close #8-11

> close #13-14

> hide #!17 models

> show #!17 models

> hide #!16 models

> show #!16 models

> combine #12,16

Remapping chain ID 'H' in combination #16 to 'Z'  
Remapping chain ID 'I' in combination #16 to 'a'  
Remapping chain ID 'J' in combination #16 to 'b'  

> select add #8

32802 atoms, 33474 bonds, 28 pseudobonds, 3927 residues, 3 models selected  

> view matrix models
> #8,-0.92259,0.3699,0.10958,477.16,-0.3563,-0.92589,0.12561,877.74,0.14792,0.076847,0.98601,-90.493

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.92259,0.3699,0.10958,500.67,-0.3563,-0.92589,0.12561,718.05,0.14792,0.076847,0.98601,-81.445

> ui tool show "Fit in Map"

> fitmap #8 inMap #3

Fit molecule combination (#8) to map emd_51808.map (#3) using 32802 atoms  
average map value = 0.008079, steps = 188  
shifted from previous position = 22.3  
rotated from previous position = 9.87 degrees  
atoms outside contour = 14643, contour level = 0.0074163  
  
Position of combination (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.89994101 0.43600528 0.00236655 492.78893619  
-0.43600543 -0.89994393 0.00047849 788.29312292  
0.00233839 -0.00060122 0.99999711 -0.75151604  
Axis -0.00123818 0.00003230 -0.99999923  
Axis point 336.84511483 337.60302966 0.00000000  
Rotation angle (degrees) 154.15069564  
Shift along axis 0.16681444  
  

> fitmap #8 inMap #3

Fit molecule combination (#8) to map emd_51808.map (#3) using 32802 atoms  
average map value = 0.008079, steps = 40  
shifted from previous position = 0.0226  
rotated from previous position = 0.00386 degrees  
atoms outside contour = 14631, contour level = 0.0074163  
  
Position of combination (#8) relative to emd_51808.map (#3) coordinates:  
Matrix rotation and translation  
-0.89995651 0.43597358 0.00231330 492.83129699  
-0.43597365 -0.89995931 0.00049986 788.26495943  
0.00229980 -0.00055868 0.99999722 -0.77156368  
Axis -0.00121400 0.00001548 -0.99999926  
Axis point 336.85574521 337.58866909 0.00000000  
Rotation angle (degrees) 154.15271718  
Shift along axis 0.18546542  
  

> select clear

> hide #!16 models

> show #!16 models

> combine #8,16

Remapping chain ID 'H' in combination #16 to 'c'  
Remapping chain ID 'I' in combination #16 to 'd'  
Remapping chain ID 'J' in combination #16 to 'e'  
Remapping chain ID 'K' in combination #16 to 'f'  
Remapping chain ID 'L' in combination #16 to 'g'  
Remapping chain ID 'M' in combination #16 to 'h'  
Remapping chain ID 'N' in combination #16 to 'i'  
Remapping chain ID 'O' in combination #16 to 'j'  
Remapping chain ID 'P' in combination #16 to 'k'  
Remapping chain ID 'Q' in combination #16 to 'l'  
Remapping chain ID 'R' in combination #16 to 'm'  
Remapping chain ID 'S' in combination #16 to 'n'  
Remapping chain ID 'T' in combination #16 to 'o'  
Remapping chain ID 'U' in combination #16 to 'p'  
Remapping chain ID 'V' in combination #16 to 'q'  
Remapping chain ID 'W' in combination #16 to 'r'  
Remapping chain ID 'X' in combination #16 to 's'  
Remapping chain ID 'Y' in combination #16 to 't'  

> select add #9

60918 atoms, 62166 bonds, 52 pseudobonds, 7293 residues, 2 models selected  

> select subtract #9

Nothing selected  

> hide #!8 models

> close #8

> close #16

> hide #!17 models

> show #!17 models

> color #17 #ff91aaff models

> hide #!9 models

> show #!9 models

> hide #!17 models

> show #!17 models

> color #17 #ff91aa53 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> show #!4 models

> hide #!9 models

> show #!9 models

> hide #!12 models

> close #4

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> close #5

> show #!6 models

> hide #!6 models

> close #6

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!12 models

> hide #!12 models

> hide #!15 models

> hide #!9 models

> show #!12 models

> show #!9 models

> hide #!12 models

> show #!12 models

> volume zone #3 nearAtoms #9,12/H-J range 5 invert true newMap true

Opened emd_51808.map zone as #4, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> volume zone #3 nearAtoms #9,12/H-J range 4 newMap true

Opened emd_51808.map zone as #5, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> hide #!17 models

> hide #!4 models

> hide #!5 models

> show #!17 models

> hide #!17 models

> close #17

> show #!15 models

> hide #!15 models

> close #15

> hide #!7 models

> show #!7 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!4 models

> volume zone #3 nearAtoms #9-12/H-J range 4 newMap true

Opened emd_51808.map zone as #6, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> hide #!7 models

> show #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!4 models

> hide #!5 models

> hide #!7 models

> show #!7 models

> show #!4 models

> hide #!4 models

> show #!4 models

> color #4 #fbc7c5ff models

> color #4 #fbc7c579 models

> hide #!4 models

> show #!4 models

> close #4

> show #!5 models

> close #5

> show #!6 models

> close #6

> hide #!12 models

> show #!12 models

> hide #!7 models

> show #!7 models

> combine #9,12

Remapping chain ID 'H' in 9h2j #12 to 'u'  
Remapping chain ID 'I' in 9h2j #12 to 'v'  
Remapping chain ID 'J' in 9h2j #12 to 'w'  

> combine #4 name AC104x14

> select add #5

65604 atoms, 66948 bonds, 56 pseudobonds, 7854 residues, 2 models selected  

> select subtract #5

Nothing selected  

> select add #4

65604 atoms, 66948 bonds, 56 pseudobonds, 7854 residues, 2 models selected  

> select subtract #4

Nothing selected  

> close #4

> select add #5

65604 atoms, 66948 bonds, 56 pseudobonds, 7854 residues, 2 models selected  

> hide #!9 models

> hide #!12 models

> hide #!7 models

> show #!7 models

> view front

> select clear

> volume zone #3 nearAtoms #5 range 5 invert true newMap true

Opened emd_51808.map zone as #4, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> volume zone #3 nearAtoms #5 range 4 newMap true

Opened emd_51808.map zone as #6, grid size 500,500,500, pixel 1.35, shown at
step 1, values float32  

> color #6 #cccc994d models

> select clear

> color #6 #cccc99ff models

> color #6 #cccc99a1 models

> color #6 #ff91aaff models

> color #6 #ff91aa5e models

> color #6 #ff91aa54 models

> color #6 #ff91aa50 models

> color #6 #ff91aa4e models

> color #6 #ff91aa4c models

> color #4 #f1f2f4ff models

No surface chosen for hiding dust  

> hide #!4 models

> show #!4 models

> surface dust #4 size 8.1

> hide #!7 models

> show #!7 models

> surface dust #4 size 7.89

> surface dust #4 size 21.25

> volume #4 level 0.00684

> surface dust #4 size 24.31

> surface dust #4 size 26

> surface dust #2 size 4.03

> surface dust #2 size 3.96

> surface dust #2 size 50.91

> surface dust #2 size 43.77

> surface dust #2 size 3.29

> surface dust #2 size 7.13

> surface dust #7 size 18.27

> save /Users/ConstantinePetridis/Desktop/BVcap.cxs includeMaps true

——— End of log from Wed Jun 18 01:53:42 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 21 hours, 19 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        XV272U V3:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 180.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by pett, 4 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by pett, 4 months ago

Resolution: → duplicate
Status: assigned → closed
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