Opened 21 months ago

Closed 21 months ago

#14502 closed defect (can't reproduce)

Crash in garbage collection

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-12.7.2-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000290217000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000104cb4580 (most recent call first):
  Garbage-collecting
  File "", line 1219 in _handle_fromlist
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 68 in residue_or_none
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 71 in 
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 71 in residues_or_nones
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 177 in get_prop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 123 in save
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 184 in _run_commands
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 171 in open_command_script
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 48 in open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 496 in collated_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1977 in _open_dropped_file
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 612 in dropEvent
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 124 in handle_drag_and_drop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 54 in event
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.mmcif.mmcif_write (total: 53)


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{
  "uptime" : 1100000,
  "procLaunch" : "2024-01-29 14:55:50.5309 -0500",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 503,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,4",
  "procStartAbsTime" : 28069136428889,
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  "captureTime" : "2024-01-29 15:00:03.8887 -0500",
  "incident" : "365D563E-9671-41B8-95D8-3E3DEA737EC6",
  "bug_type" : "309",
  "pid" : 16319,
  "procExitAbsTime" : 28075216681602,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "FB1C5F2D-E5C5-FBFC-F30C-CCCE6C3DF276",
  "wakeTime" : 17268,
  "sleepWakeUUID" : "93F2EECA-A275-451F-9404-D86AF5D446CF",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 68719476567\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
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    "path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
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    "path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
    "name" : "QtGui"
  },
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    "base" : 5096783872,
    "size" : 622592,
    "uuid" : "a07d6b8c-b467-339b-8483-3ba6dc00495e",
    "path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
  {
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    "uuid" : "2f9d63e8-f87c-3348-b5c5-39de32463324",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.60.148"
  },
  {
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    "size" : 393216,
    "uuid" : "1202938d-75b0-36e9-bfc6-9f4cec003d15",
    "path" : "\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices",
    "name" : "HIServices"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
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    "CFBundleShortVersionString" : "6.9",
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    "size" : 5533696,
    "uuid" : "07e05b49-8c3c-354e-89a7-cc7994572dfe",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
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    "size" : 3358720,
    "uuid" : "07987381-b579-3f72-8ba8-97fa5b5a3352",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
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    "name" : "ChimeraX",
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    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
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    "uuid" : "21c8f378-4426-330a-89d1-26ab67c6fa56",
    "path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
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],
  "sharedCache" : {
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=4.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG backing stores                 6400K        8 \nCG image                           224K       10 \nColorSync                          624K       27 \nCoreAnimation                      208K        9 \nCoreGraphics                        48K        3 \nCoreUI image data                 3632K       25 \nDispatch continuations            80.0M        1 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                             2.3G      945 \nMALLOC guard page                  192K       10 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        576K       36 \nStack                            177.3M       37 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                        1.5G     2963 \nVM_ALLOCATE (reserved)           192.0M        1         reserved VM address space (unallocated)\n__AUTH                            2611K      308 \n__AUTH_CONST                      20.6M      506 \n__CTF                               756        1 \n__DATA                            24.9M      654 \n__DATA_CONST                      27.8M      660 \n__DATA_DIRTY                      1804K      216 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       609.7M      153 \n__OBJC_CONST                      3646K      279 \n__OBJC_RO                         83.0M        1 \n__OBJC_RW                         3168K        1 \n__TEXT                           728.7M      678 \n__UNICODE                          592K        1 \ndyld private memory               1216K        3 \nmapped file                      187.2M       45 \nshared memory                     3632K       24 \n===========                     =======  ======= \nTOTAL                              6.0G     7622 \nTOTAL, minus reserved VM space     5.8G     7622 \n",
  "legacyInfo" : {
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===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/kbui2/Downloads/cu428_g0_J273_f7.mrc

Opened cu428_g0_J273_f7.mrc as #1, grid size 512,512,512, pixel 1.37, shown at
level 0.996, step 2, values float32  

> volume #1 level 0.4088

> volume #1 level 0.4459

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NA.cif

Chain information for Tubulin_B1_NA.cif #2  
---  
Chain | Description  
NA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_NB.cif #3  
---  
Chain | Description  
NB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NC.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NC.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_NC.cif #4  
---  
Chain | Description  
NC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_ND.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_ND.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_ND.cif #5  
---  
Chain | Description  
ND | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NE.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NE.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_NE.cif #6  
---  
Chain | Description  
NE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_NF.cif #7  
---  
Chain | Description  
NF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NG.cif

Chain information for Tubulin_B1_NG.cif #8  
---  
Chain | Description  
NG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_NH.cif #9  
---  
Chain | Description  
NH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NI.cif

Chain information for Tubulin_B1_NI.cif #10  
---  
Chain | Description  
NI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_NJ.cif #11  
---  
Chain | Description  
NJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NK.cif

Chain information for Tubulin_B1_NK.cif #12  
---  
Chain | Description  
NK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_NL.cif #13  
---  
Chain | Description  
NL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NM.cif

Chain information for Tubulin_B1_NM.cif #14  
---  
Chain | Description  
NM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B1_NN.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B1_NN.cif #15  
---  
Chain | Description  
NN | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OA.cif

Chain information for Tubulin_B2_OA.cif #16  
---  
Chain | Description  
OA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_OB.cif #17  
---  
Chain | Description  
OB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OC.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OC.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_OC.cif #18  
---  
Chain | Description  
OC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_OD.cif #19  
---  
Chain | Description  
OD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OE.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OE.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_OE.cif #20  
---  
Chain | Description  
OE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_OF.cif #21  
---  
Chain | Description  
OF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OG.cif

Chain information for Tubulin_B2_OG.cif #22  
---  
Chain | Description  
OG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_OH.cif #23  
---  
Chain | Description  
OH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OI.cif

Chain information for Tubulin_B2_OI.cif #24  
---  
Chain | Description  
OI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_OJ.cif #25  
---  
Chain | Description  
OJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OK.cif

Chain information for Tubulin_B2_OK.cif #26  
---  
Chain | Description  
OK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_OL.cif #27  
---  
Chain | Description  
OL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_OM.cif

Chain information for Tubulin_B2_OM.cif #28  
---  
Chain | Description  
OM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_ON.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B2_ON.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B2_ON.cif #29  
---  
Chain | Description  
ON | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PA.cif

Chain information for Tubulin_B3_PA.cif #30  
---  
Chain | Description  
PA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B3_PB.cif #31  
---  
Chain | Description  
PB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PC.cif

Chain information for Tubulin_B3_PC.cif #32  
---  
Chain | Description  
PC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B3_PD.cif #33  
---  
Chain | Description  
PD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PE.cif

Chain information for Tubulin_B3_PE.cif #34  
---  
Chain | Description  
PE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B3_PF.cif #35  
---  
Chain | Description  
PF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PG.cif

Chain information for Tubulin_B3_PG.cif #36  
---  
Chain | Description  
PG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B3_PH.cif #37  
---  
Chain | Description  
PH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PI.cif

Chain information for Tubulin_B3_PI.cif #38  
---  
Chain | Description  
PI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B3_PJ.cif #39  
---  
Chain | Description  
PJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PK.cif

Chain information for Tubulin_B3_PK.cif #40  
---  
Chain | Description  
PK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B3_PL.cif #41  
---  
Chain | Description  
PL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PM.cif

Chain information for Tubulin_B3_PM.cif #42  
---  
Chain | Description  
PM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B3_PN.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B3_PN.cif #43  
---  
Chain | Description  
PN | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QA.cif

Chain information for Tubulin_B4_QA.cif #44  
---  
Chain | Description  
QA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B4_QB.cif #45  
---  
Chain | Description  
QB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QC.cif

Chain information for Tubulin_B4_QC.cif #46  
---  
Chain | Description  
QC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B4_QD.cif #47  
---  
Chain | Description  
QD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QE.cif

Chain information for Tubulin_B4_QE.cif #48  
---  
Chain | Description  
QE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B4_QF.cif #49  
---  
Chain | Description  
QF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QG.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QG.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B4_QG.cif #50  
---  
Chain | Description  
QG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B4_QH.cif #51  
---  
Chain | Description  
QH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QI.cif

Chain information for Tubulin_B4_QI.cif #52  
---  
Chain | Description  
QI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B4_QJ.cif #53  
---  
Chain | Description  
QJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QK.cif

Chain information for Tubulin_B4_QK.cif #54  
---  
Chain | Description  
QK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B4_QL.cif #55  
---  
Chain | Description  
QL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QM.cif

Chain information for Tubulin_B4_QM.cif #56  
---  
Chain | Description  
QM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B4_QN.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B4_QN.cif #57  
---  
Chain | Description  
QN | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RA.cif

Chain information for Tubulin_B5_RA.cif #58  
---  
Chain | Description  
RA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B5_RB.cif #59  
---  
Chain | Description  
RB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RC.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RC.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B5_RC.cif #60  
---  
Chain | Description  
RC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B5_RD.cif #61  
---  
Chain | Description  
RD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RE.cif

Chain information for Tubulin_B5_RE.cif #62  
---  
Chain | Description  
RE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B5_RF.cif #63  
---  
Chain | Description  
RF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RG.cif

Chain information for Tubulin_B5_RG.cif #64  
---  
Chain | Description  
RG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B5_RH.cif #65  
---  
Chain | Description  
RH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RI.cif

Chain information for Tubulin_B5_RI.cif #66  
---  
Chain | Description  
RI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B5_RJ.cif #67  
---  
Chain | Description  
RJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RK.cif

Chain information for Tubulin_B5_RK.cif #68  
---  
Chain | Description  
RK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B5_RL.cif #69  
---  
Chain | Description  
RL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RM.cif

Chain information for Tubulin_B5_RM.cif #70  
---  
Chain | Description  
RM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B5_RN.cif  
---  
warnings | Unknown polymer entity '1' near line 125  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B5_RN.cif #71  
---  
Chain | Description  
RN | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SA.cif

Chain information for Tubulin_B6_SA.cif #72  
---  
Chain | Description  
SA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B6_SB.cif #73  
---  
Chain | Description  
SB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SC.cif

Chain information for Tubulin_B6_SC.cif #74  
---  
Chain | Description  
SC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B6_SD.cif #75  
---  
Chain | Description  
SD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SE.cif

Chain information for Tubulin_B6_SE.cif #76  
---  
Chain | Description  
SE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B6_SF.cif #77  
---  
Chain | Description  
SF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SG.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SG.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B6_SG.cif #78  
---  
Chain | Description  
SG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B6_SH.cif #79  
---  
Chain | Description  
SH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SI.cif

Chain information for Tubulin_B6_SI.cif #80  
---  
Chain | Description  
SI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B6_SJ.cif #81  
---  
Chain | Description  
SJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SK.cif

Chain information for Tubulin_B6_SK.cif #82  
---  
Chain | Description  
SK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B6_SL.cif #83  
---  
Chain | Description  
SL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SM.cif

Chain information for Tubulin_B6_SM.cif #84  
---  
Chain | Description  
SM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B6_SN.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B6_SN.cif #85  
---  
Chain | Description  
SN | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TA.cif

Chain information for Tubulin_B7_TA.cif #86  
---  
Chain | Description  
TA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B7_TB.cif #87  
---  
Chain | Description  
TB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TC.cif

Chain information for Tubulin_B7_TC.cif #88  
---  
Chain | Description  
TC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B7_TD.cif #89  
---  
Chain | Description  
TD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TE.cif

Chain information for Tubulin_B7_TE.cif #90  
---  
Chain | Description  
TE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B7_TF.cif #91  
---  
Chain | Description  
TF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TG.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TG.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B7_TG.cif #92  
---  
Chain | Description  
TG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B7_TH.cif #93  
---  
Chain | Description  
TH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TI.cif

Chain information for Tubulin_B7_TI.cif #94  
---  
Chain | Description  
TI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B7_TJ.cif #95  
---  
Chain | Description  
TJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TK.cif

Chain information for Tubulin_B7_TK.cif #96  
---  
Chain | Description  
TK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B7_TL.cif #97  
---  
Chain | Description  
TL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TM.cif

Chain information for Tubulin_B7_TM.cif #98  
---  
Chain | Description  
TM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B7_TN.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B7_TN.cif #99  
---  
Chain | Description  
TN | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UA.cif

Chain information for Tubulin_B8_UA.cif #100  
---  
Chain | Description  
UA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B8_UB.cif #101  
---  
Chain | Description  
UB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UC.cif

Chain information for Tubulin_B8_UC.cif #102  
---  
Chain | Description  
UC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B8_UD.cif #103  
---  
Chain | Description  
UD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UE.cif

Chain information for Tubulin_B8_UE.cif #104  
---  
Chain | Description  
UE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B8_UF.cif #105  
---  
Chain | Description  
UF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UG.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UG.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B8_UG.cif #106  
---  
Chain | Description  
UG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B8_UH.cif #107  
---  
Chain | Description  
UH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UI.cif

Chain information for Tubulin_B8_UI.cif #108  
---  
Chain | Description  
UI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B8_UJ.cif #109  
---  
Chain | Description  
UJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UK.cif

Chain information for Tubulin_B8_UK.cif #110  
---  
Chain | Description  
UK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B8_UL.cif #111  
---  
Chain | Description  
UL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UM.cif

Chain information for Tubulin_B8_UM.cif #112  
---  
Chain | Description  
UM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B8_UN.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B8_UN.cif #113  
---  
Chain | Description  
UN | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VA.cif

Chain information for Tubulin_B9_VA.cif #114  
---  
Chain | Description  
VA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VB.cif #115  
---  
Chain | Description  
VB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VC.cif

Chain information for Tubulin_B9_VC.cif #116  
---  
Chain | Description  
VC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VD.cif #117  
---  
Chain | Description  
VD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VE.cif

Chain information for Tubulin_B9_VE.cif #118  
---  
Chain | Description  
VE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VF.cif #119  
---  
Chain | Description  
VF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VG.cif

Chain information for Tubulin_B9_VG.cif #120  
---  
Chain | Description  
VG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VH.cif #121  
---  
Chain | Description  
VH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VI.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VI.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VI.cif #122  
---  
Chain | Description  
VI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VJ.cif #123  
---  
Chain | Description  
VJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VK.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VK.cif  
---  
warnings | Unknown polymer entity '1' near line 128  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VK.cif #124  
---  
Chain | Description  
VK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VL.cif #125  
---  
Chain | Description  
VL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VM.cif

Chain information for Tubulin_B9_VM.cif #126  
---  
Chain | Description  
VM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B9_VN.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B9_VN.cif #127  
---  
Chain | Description  
VN | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WA.cif

Chain information for Tubulin_B10_WA.cif #128  
---  
Chain | Description  
WA | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WB.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WB.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B10_WB.cif #129  
---  
Chain | Description  
WB | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WC.cif

Chain information for Tubulin_B10_WC.cif #130  
---  
Chain | Description  
WC | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WD.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WD.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B10_WD.cif #131  
---  
Chain | Description  
WD | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WE.cif

Chain information for Tubulin_B10_WE.cif #132  
---  
Chain | Description  
WE | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WF.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WF.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B10_WF.cif #133  
---  
Chain | Description  
WF | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WG.cif

Chain information for Tubulin_B10_WG.cif #134  
---  
Chain | Description  
WG | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WH.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WH.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B10_WH.cif #135  
---  
Chain | Description  
WH | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WI.cif

Chain information for Tubulin_B10_WI.cif #136  
---  
Chain | Description  
WI | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WJ.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WJ.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B10_WJ.cif #137  
---  
Chain | Description  
WJ | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WK.cif

Chain information for Tubulin_B10_WK.cif #138  
---  
Chain | Description  
WK | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WL.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WL.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B10_WL.cif #139  
---  
Chain | Description  
WL | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WM.cif

Chain information for Tubulin_B10_WM.cif #140  
---  
Chain | Description  
WM | No description available  
  

> open /Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WN.cif

Summary of feedback from opening
/Users/kbui2/Downloads/Combine/K40R_Tubulin_New/Tubulin_B10_WN.cif  
---  
warnings | Unknown polymer entity '1' near line 124  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for Tubulin_B10_WN.cif #141  
---  
Chain | Description  
WN | No description available  
  

> volume #1 transparency .5

> open /Users/kbui2/Desktop/saveBtubule.cxc

> fitmap #2 inMap #1

Fit molecule Tubulin_B1_NA.cif (#2) to map cu428_g0_J273_f7.mrc (#1) using
3443 atoms  
average map value = 0.643, steps = 60  
shifted from previous position = 1.59  
rotated from previous position = 0.359 degrees  
atoms outside contour = 956, contour level = 0.44593  
  
Position of Tubulin_B1_NA.cif (#2) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99998897 0.00469502 -0.00012926 -2.37547296  
-0.00469444 0.99998041 0.00414016 0.52423045  
0.00014870 -0.00413950 0.99999142 0.94219254  
Axis -0.66122712 -0.02219796 -0.74985728  
Axis point 114.09057883 386.15033340 0.00000000  
Rotation angle (degrees) 0.35872145  
Shift along axis 0.85258036  
  

> fitmap #3 inMap #1

Fit molecule Tubulin_B1_NB.cif (#3) to map cu428_g0_J273_f7.mrc (#1) using
3332 atoms  
average map value = 0.5618, steps = 48  
shifted from previous position = 1.61  
rotated from previous position = 0.292 degrees  
atoms outside contour = 1160, contour level = 0.44593  
  
Position of Tubulin_B1_NB.cif (#3) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99998701 0.00509614 -0.00002180 -2.53853842  
-0.00509614 0.99998699 -0.00024131 3.08432447  
0.00002057 0.00024142 0.99999997 -1.23926800  
Axis 0.04730876 -0.00415183 -0.99887169  
Axis point 604.82536250 509.92889131 0.00000000  
Rotation angle (degrees) 0.29231835  
Shift along axis 1.10496902  
  

> fitmap #4 inMap #1

Fit molecule Tubulin_B1_NC.cif (#4) to map cu428_g0_J273_f7.mrc (#1) using
3397 atoms  
average map value = 0.6995, steps = 48  
shifted from previous position = 1.05  
rotated from previous position = 0.474 degrees  
atoms outside contour = 860, contour level = 0.44593  
  
Position of Tubulin_B1_NC.cif (#4) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99996912 0.00392582 0.00680833 -5.51206089  
-0.00394345 0.99998890 0.00257873 1.08141647  
-0.00679813 -0.00260550 0.99997350 3.37113164  
Axis -0.31322658 0.82209014 -0.47545442  
Axis point 563.73585302 0.00000000 765.57117143  
Rotation angle (degrees) 0.47415798  
Shift along axis 1.01272634  
  

> fitmap #5 inMap #1

Fit molecule Tubulin_B1_ND.cif (#5) to map cu428_g0_J273_f7.mrc (#1) using
3394 atoms  
average map value = 0.6934, steps = 52  
shifted from previous position = 1.34  
rotated from previous position = 0.564 degrees  
atoms outside contour = 797, contour level = 0.44593  
  
Position of Tubulin_B1_ND.cif (#5) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99998434 0.00460716 0.00317647 -4.07192768  
-0.00463273 0.99995657 0.00808722 -1.35531608  
-0.00313907 -0.00810181 0.99996225 4.69783044  
Axis -0.82256672 0.32089325 -0.46948004  
Axis point 0.00000000 620.00596737 199.04898044  
Rotation angle (degrees) 0.56383149  
Shift along axis 0.70898281  
  

> fitmap #6 inMap #1

Fit molecule Tubulin_B1_NE.cif (#6) to map cu428_g0_J273_f7.mrc (#1) using
3443 atoms  
average map value = 0.7267, steps = 48  
shifted from previous position = 0.893  
rotated from previous position = 0.301 degrees  
atoms outside contour = 835, contour level = 0.44593  
  
Position of Tubulin_B1_NE.cif (#6) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99999983 0.00018635 0.00055481 -0.63130750  
-0.00018924 0.99998633 0.00522513 -1.22101437  
-0.00055383 -0.00522524 0.99998619 2.53521724  
Axis -0.99378547 0.10542641 -0.03571699  
Axis point 0.00000000 487.33407347 243.19014200  
Rotation angle (degrees) 0.30125462  
Shift along axis 0.40810673  
  

> fitmap #7 inMap #1

Fit molecule Tubulin_B1_NF.cif (#7) to map cu428_g0_J273_f7.mrc (#1) using
3332 atoms  
average map value = 0.7298, steps = 44  
shifted from previous position = 1.27  
rotated from previous position = 0.289 degrees  
atoms outside contour = 792, contour level = 0.44593  
  
Position of Tubulin_B1_NF.cif (#7) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99999075 0.00365928 0.00225918 -3.07312235  
-0.00366525 0.99998979 0.00264381 1.32151866  
-0.00224948 -0.00265207 0.99999395 2.15321527  
Axis -0.52431147 0.44637295 -0.72515423  
Axis point 280.55521796 748.86049180 0.00000000  
Rotation angle (degrees) 0.28936334  
Shift along axis 0.63975032  
  

> fitmap #8 inMap #1

Fit molecule Tubulin_B1_NG.cif (#8) to map cu428_g0_J273_f7.mrc (#1) using
3397 atoms  
average map value = 0.7283, steps = 48  
shifted from previous position = 1.11  
rotated from previous position = 0.466 degrees  
atoms outside contour = 779, contour level = 0.44593  
  
Position of Tubulin_B1_NG.cif (#8) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99997221 0.00443145 0.00599429 -4.07629613  
-0.00441184 0.99998488 -0.00328200 3.66547738  
-0.00600874 0.00325546 0.99997665 0.91414674  
Axis 0.40158141 0.73731971 -0.54322373  
Axis point 200.78933396 0.00000000 719.08547490  
Rotation angle (degrees) 0.46637206  
Shift along axis 0.56907778  
  

> fitmap #9 inMap #1

Fit molecule Tubulin_B1_NH.cif (#9) to map cu428_g0_J273_f7.mrc (#1) using
3394 atoms  
average map value = 0.7368, steps = 48  
shifted from previous position = 1.1  
rotated from previous position = 0.283 degrees  
atoms outside contour = 776, contour level = 0.44593  
  
Position of Tubulin_B1_NH.cif (#9) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99998811 0.00165667 0.00458690 -2.70056694  
-0.00165328 0.99999836 -0.00074352 1.83464538  
-0.00458813 0.00073593 0.99998920 1.68360565  
Axis 0.14996337 0.93002293 -0.33551206  
Axis point 419.35427733 0.00000000 613.91924191  
Rotation angle (degrees) 0.28262348  
Shift along axis 0.73640614  
  

> fitmap #10 inMap #1

Fit molecule Tubulin_B1_NI.cif (#10) to map cu428_g0_J273_f7.mrc (#1) using
3443 atoms  
average map value = 0.7209, steps = 44  
shifted from previous position = 1.52  
rotated from previous position = 0.318 degrees  
atoms outside contour = 839, contour level = 0.44593  
  
Position of Tubulin_B1_NI.cif (#10) relative to cu428_g0_J273_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99998481 0.00296326 0.00464703 -2.51667990  
-0.00296654 0.99999536 0.00069886 2.18214364  
-0.00464494 -0.00071264 0.99998896 2.74455515  
Axis -0.12701476 0.83614556 -0.53359897  
Axis point 667.71050743 0.00000000 525.17060533  
Rotation angle (degrees) 0.31836144  
Shift along axis 0.67975340  
  


[deleted to fit within ticket limits]

> fitmap #141 inMap #1

Fit molecule Tubulin_B10_WN.cif (#141) to map k40r_g1234_J280_f7.mrc (#1)
using 3394 atoms  
average map value = 0.9082, steps = 64  
shifted from previous position = 3.15  
rotated from previous position = 0.992 degrees  
atoms outside contour = 1238, contour level = 0.77052  
  
Position of Tubulin_B10_WN.cif (#141) relative to k40r_g1234_J280_f7.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99996662 -0.00318288 0.00752577 -0.42958901  
0.00316253 0.99999132 0.00271405 -1.18858761  
-0.00753435 -0.00269016 0.99996800 3.57816285  
Axis -0.31396607 0.87494271 0.36864693  
Axis point 454.47882372 0.00000000 41.82649967  
Rotation angle (degrees) 0.49311344  
Shift along axis 0.41400907  
  

> combine #2-141

> save /Users/kbui2/Desktop/k40r_g1234_Btubule.cif models #142

Not saving entity_poly_seq for non-authoritative sequences  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,4
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 7459.141.1.701.1

Software:

    System Software Overview:

      System Version: macOS 12.7.2 (21G1974)
      Kernel Version: Darwin 21.6.0
      Time since boot: 42 days 13:50

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.3
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by pett, 21 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Description: modified (diff)
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by pett, 21 months ago

Resolution: → can't reproduce
Status: accepted → closed
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