Opened 4 weeks ago

Closed 4 weeks ago

#19299 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: oswanson@… 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 Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 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

Thread 0x000000030704f000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000306043000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000305037000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030402b000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030301f000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000302013000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000301007000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017f2e3000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017e2d7000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017d2cb000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017c2bf000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000209ac8800 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.atom_search.ast, PIL._imagingmath, chimerax.chem_group._chem_group (total: 119)


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{
  "uptime" : 760000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac15,13",
  "coalitionID" : 49319,
  "osVersion" : {
    "train" : "macOS 26.0.1",
    "build" : "25A362",
    "releaseType" : "User"
  },
  "captureTime" : "2025-11-05 15:02:38.5848 -0800",
  "codeSigningMonitor" : 2,
  "incident" : "C83632B4-604D-4989-BBF9-6EA8AF8D5DAA",
  "pid" : 42815,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-10-31 13:49:32.0207 -0700",
  "procStartAbsTime" : 15109589833818,
  "procExitAbsTime" : 18326989253161,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"7BA6C159-904F-576D-925A-564D55528586","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "C7CE9648-6482-023B-B664-5752AC9E2116",
  "developerMode" : 1,
  "bootProgressRegister" : "0x2f000000",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "2EB669B7-CCF8-491B-A979-02E1847B52E6",
  "wakeTime" : 14184,
  "sleepWakeUUID" : "444002E8-475F-4001-B9EB-2EB2C314DBA4",
  "sip" : "enabled",
  "vmRegionInfo" : "0xffff80d4aa81c4e0 is not in any region.  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      UNUSED SPACE AT END",
  "exception" : {"codes":"0x0000000000000001, 0xa18200d4aa81c4e0","rawCodes":[1,-6808878773237070624],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0xa18200d4aa81c4e0 -> 0xffff80d4aa81c4e0 (possible pointer authentication failure)"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":42815},
  "vmregioninfo" : "0xffff80d4aa81c4e0 is not in any region.  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      UNUSED SPACE AT END",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs

Log from Fri Oct 31 13:49:15 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/oswanson/Desktop/Primocalins/231023_poly310-DH270UCA3_refine_001.pdb

Chain information for 231023_poly310-DH270UCA3_refine_001.pdb #1  
---  
Chain | Description  
E | No description available  
H | No description available  
L | No description available  
  
Computing secondary structure  

> open /Users/oswanson/Desktop/Primocalins/Y513apo_refine_31.pdb

Summary of feedback from opening
/Users/oswanson/Desktop/Primocalins/Y513apo_refine_31.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2022-07-08 Time 12:55:39 CDT -0500 (1657302939.20 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/Users/danielwrapp/Desktop/PEDVnumber/Y513apo/Refine_4/Y513apo_refine_4.mtz  
  
40 messages similar to the above omitted  
  
Chain information for Y513apo_refine_31.pdb #2  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> hide #!1 models

> set bgColor white

> hide #2 models

> show #!1 models

> select #1/E:108

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

> select up

61 atoms, 60 bonds, 8 residues, 1 model selected  

> select up

604 atoms, 618 bonds, 74 residues, 1 model selected  

> select up

616 atoms, 629 bonds, 76 residues, 1 model selected  

> select up

1313 atoms, 1346 bonds, 164 residues, 1 model selected  

> select up

4851 atoms, 4757 bonds, 812 residues, 1 model selected  

> select down

1313 atoms, 1346 bonds, 164 residues, 1 model selected  

> color sel byhetero

> color sel bychain

> ui tool show H-Bonds

> hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
> intraMol false intraRes false select true reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.8 angstroms and 20 degrees
    Models used:
    	1 231023_poly310-DH270UCA3_refine_001.pdb
    
    25 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O   no hydrogen  2.874  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 71 N    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 86 O     no hydrogen  2.780  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O     no hydrogen  2.993  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1   no hydrogen  3.440  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 N    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O    no hydrogen  2.550  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASN 164 N   231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 242 O    no hydrogen  2.990  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH   231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1   no hydrogen  2.679  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2  231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1   no hydrogen  3.050  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2  231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O     no hydrogen  3.339  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 44 O    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O     no hydrogen  3.746  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 49 O    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 O    no hydrogen  2.651  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 49 O    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 OD2  no hydrogen  2.434  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1   no hydrogen  3.428  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD2   no hydrogen  2.642  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O    231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 75 O     no hydrogen  3.183  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O    231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O     no hydrogen  3.912  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 86 O    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 51 O     no hydrogen  2.817  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 242 O   231023_poly310-DH270UCA3_refine_001.pdb #1/E GLU 163 OE1  no hydrogen  2.752  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 409 O   231023_poly310-DH270UCA3_refine_001.pdb #1/E VAL 34 O     no hydrogen  2.557  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 409 O   231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 169 O    no hydrogen  3.211  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O   231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O     no hydrogen  4.003  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O   231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O     no hydrogen  3.243  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O   231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 38 O     no hydrogen  2.357  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O   231023_poly310-DH270UCA3_refine_001.pdb #1/E VAL 41 O     no hydrogen  2.400  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O   231023_poly310-DH270UCA3_refine_001.pdb #1/E HIS 165 O    no hydrogen  3.686  N/A
    

  
25 hydrogen bonds found  

> select ::name="HOH"::name="SO4"

234 atoms, 24 bonds, 210 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select #1/E:109

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

61 atoms, 60 bonds, 8 residues, 1 model selected  

> select up

604 atoms, 618 bonds, 74 residues, 1 model selected  

> select up

616 atoms, 629 bonds, 76 residues, 1 model selected  

> select up

1313 atoms, 1346 bonds, 164 residues, 1 model selected  

> select up

4647 atoms, 4757 bonds, 608 residues, 1 model selected  

> select down

1313 atoms, 1346 bonds, 164 residues, 1 model selected  

> hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
> intraMol false intraRes false select true reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.8 angstroms and 20 degrees
    Models used:
    	1 231023_poly310-DH270UCA3_refine_001.pdb
    
    6 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O  no hydrogen  2.874  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O    no hydrogen  2.993  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1  no hydrogen  3.440  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH   231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  no hydrogen  2.679  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2  231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  no hydrogen  3.050  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2  231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O    no hydrogen  3.339  N/A
    

  
6 hydrogen bonds found  

> select up

93 atoms, 88 bonds, 10 residues, 1 model selected  

> color sel byhetero

> select clear

> select #1/E:128

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

> hide sel atoms

> open /Users/oswanson/Downloads/9NPI-sf.cif

Summary of feedback from opening /Users/oswanson/Downloads/9NPI-sf.cif  
---  
warning | No mmCIF models found.  
  

> open /Users/oswanson/Downloads/9NPI-sf.cif

Summary of feedback from opening /Users/oswanson/Downloads/9NPI-sf.cif  
---  
warning | No mmCIF models found.  
  

> open /Users/oswanson/coot_sessions/3FW4.mtz
> /Users/oswanson/coot_sessions/3FW4.pdb

Install the Clipper bundle to open "MTZ" format files.  
Opener for format 'MTZ' is not installed; see log for more info  

> open /Users/oswanson/coot_sessions/3FW4.pdb

3FW4.pdb title:  
Crystal structure of siderocalin (ngal, lipocalin 2) complexed with ferric
catechol [more info...]  
  
Chain information for 3FW4.pdb #3  
---  
Chain | Description | UniProt  
A B C | neutrophil gelatinase-associated lipocalin | NGAL_HUMAN 1-178  
  
Non-standard residues in 3FW4.pdb #3  
---  
CAQ — catechol (1,2-dihydroxybenzene)  
CL — chloride ion  
FE — Fe (III) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NA — sodium ion  
  
31 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open /Users/oswanson/coot_sessions/3FW4-sf.cif

Summary of feedback from opening /Users/oswanson/coot_sessions/3FW4-sf.cif  
---  
warning | No mmCIF models found.  
  

> open /Users/oswanson/Desktop/Primocalins/Structures/Cluster2c_lib1.pdb
> /Users/oswanson/Desktop/Primocalins/Structures/design_start.pdb
> /Users/oswanson/Desktop/Primocalins/Structures/RMSD4_NNK1.pdb
> /Users/oswanson/Desktop/Primocalins/Structures/RMSD6_NNK1.pdb

Chain information for Cluster2c_lib1.pdb #4  
---  
Chain | Description  
A | No description available  
G | No description available  
H | No description available  
  
Chain information for design_start.pdb #5  
---  
Chain | Description  
A | No description available  
G | No description available  
H | No description available  
  
Chain information for RMSD4_NNK1.pdb #6  
---  
Chain | Description  
A | No description available  
G | No description available  
H | No description available  
  
Chain information for RMSD6_NNK1.pdb #7  
---  
Chain | Description  
A | No description available  
G | No description available  
H | No description available  
  
Computing secondary structure  
[Repeated 3 time(s)]

> select #1/E:68

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

> select up

53 atoms, 53 bonds, 7 residues, 1 model selected  

> select up

709 atoms, 728 bonds, 90 residues, 1 model selected  

> select up

727 atoms, 746 bonds, 92 residues, 1 model selected  

> select up

1313 atoms, 1346 bonds, 164 residues, 1 model selected  

> select up

4647 atoms, 4757 bonds, 608 residues, 1 model selected  

> select down

1313 atoms, 1346 bonds, 164 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #2,4-7#!3 to #1 & sel

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
Y513apo_refine_31.pdb, chain B (#2), sequence alignment score = 692  
RMSD between 154 pruned atom pairs is 0.689 angstroms; (across all 164 pairs:
1.591)  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
Cluster2c_lib1.pdb, chain A (#4), sequence alignment score = 692  
RMSD between 151 pruned atom pairs is 0.676 angstroms; (across all 164 pairs:
1.416)  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
design_start.pdb, chain A (#5), sequence alignment score = 709.7  
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
1.402)  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
RMSD4_NNK1.pdb, chain A (#6), sequence alignment score = 692.2  
RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs:
1.442)  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
RMSD6_NNK1.pdb, chain A (#7), sequence alignment score = 683.1  
RMSD between 152 pruned atom pairs is 0.697 angstroms; (across all 164 pairs:
1.421)  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
3FW4.pdb, chain A (#3), sequence alignment score = 709.7  
RMSD between 150 pruned atom pairs is 0.624 angstroms; (across all 164 pairs:
1.389)  
  

> matchmaker #4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
Cluster2c_lib1.pdb, chain A (#4), sequence alignment score = 692  
RMSD between 151 pruned atom pairs is 0.676 angstroms; (across all 164 pairs:
1.416)  
  

> matchmaker #5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
design_start.pdb, chain A (#5), sequence alignment score = 709.7  
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
1.402)  
  

> matchmaker #6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
RMSD4_NNK1.pdb, chain A (#6), sequence alignment score = 692.2  
RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs:
1.442)  
  

> matchmaker #7 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
RMSD6_NNK1.pdb, chain A (#7), sequence alignment score = 683.1  
RMSD between 152 pruned atom pairs is 0.697 angstroms; (across all 164 pairs:
1.421)  
  

> show #2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #4 models

> hide #!1 models

> hide #5 models

> hide #6 models

> hide #7 models

> show #!1 models

> show #!3 models

> hide #!3 models

> select #2/A:126

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

> select up

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

> select up

1459 atoms, 1497 bonds, 181 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #2 & sel to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
Y513apo_refine_31.pdb, chain A (#2), sequence alignment score = 689  
RMSD between 154 pruned atom pairs is 0.695 angstroms; (across all 164 pairs:
1.580)  
  

> hide #!1 models

> show #5 models

> show #6 models

> hide #5 models

> select add #6

7768 atoms, 7887 bonds, 591 residues, 2 models selected  

> color sel bychain

> color sel byhetero

> hide #6 models

> show #7 models

> color sel & #2 bychain

> select add #7

14068 atoms, 14269 bonds, 1001 residues, 3 models selected  

> select subtract #6

7759 atoms, 7879 bonds, 591 residues, 2 models selected  

> color sel bychain

> color sel byhetero

> show #6 models

> hide #6 models

> show #6 models

> select add #6

14068 atoms, 14269 bonds, 1001 residues, 3 models selected  

> color sel bychain

> select subtract #6

7759 atoms, 7879 bonds, 591 residues, 2 models selected  

> select add #2

9248 atoms, 9400 bonds, 778 residues, 2 models selected  

> select subtract #2

6300 atoms, 6382 bonds, 410 residues, 1 model selected  

> hide #6 models

> hide #2 models

> show #2 models

> hide #7 models

> select #2/A:80

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

> select up

79 atoms, 81 bonds, 9 residues, 1 model selected  

[deleted to fit within ticket limits]

> select up

1590 atoms, 1630 bonds, 197 residues, 1 model selected  

> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    97 contacts
                        atom1                                           atom2                       overlap  distance
    fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CB    0.972    2.788
    fold_poly28_uca3_model_0.cif #11/A ASN 131 CB   fold_poly28_uca3_model_0.cif #11/C TYR 51 OH     0.818    2.522
    fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1   fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2   0.767    2.633
    fold_poly28_uca3_model_0.cif #11/A SER 70 CB    fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   0.592    3.168
    fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1  fold_poly28_uca3_model_0.cif #11/B ARG 72 NH2    0.548    2.972
    fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2  fold_poly28_uca3_model_0.cif #11/B ARG 72 NH1    0.481    3.039
    fold_poly28_uca3_model_0.cif #11/A MET 79 CE    fold_poly28_uca3_model_0.cif #11/B LEU 104 CD2   0.440    3.320
    fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CG    0.367    3.123
    fold_poly28_uca3_model_0.cif #11/A GLU 81 CB    fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   0.341    3.419
    fold_poly28_uca3_model_0.cif #11/A GLU 134 OE1  fold_poly28_uca3_model_0.cif #11/B TYR 106 CE1   0.329    2.851
    fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1  fold_poly28_uca3_model_0.cif #11/B TYR 111 CE2   0.304    3.096
    fold_poly28_uca3_model_0.cif #11/A LEU 9 CB     fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ     0.273    3.247
    fold_poly28_uca3_model_0.cif #11/A ASN 131 O    fold_poly28_uca3_model_0.cif #11/C TYR 51 OH     0.230    2.250
    fold_poly28_uca3_model_0.cif #11/A LEU 44 CD1   fold_poly28_uca3_model_0.cif #11/C TYR 32 CD1    0.219    3.421
    fold_poly28_uca3_model_0.cif #11/A MET 79 SD    fold_poly28_uca3_model_0.cif #11/B ILE 102 CG2   0.197    3.453
    fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2   fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2   0.197    3.203
    fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1   fold_poly28_uca3_model_0.cif #11/C TYR 93 CE1    0.186    2.994
    fold_poly28_uca3_model_0.cif #11/A ASN 131 CA   fold_poly28_uca3_model_0.cif #11/C TYR 51 OH     0.181    3.159
    fold_poly28_uca3_model_0.cif #11/A ARG 132 CZ   fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1    0.177    2.853
    fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CD1   0.170    3.470
    fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2   fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ    0.124    3.126
    fold_poly28_uca3_model_0.cif #11/A GLU 134 OE1  fold_poly28_uca3_model_0.cif #11/B TYR 106 CD1   0.120    3.060
    fold_poly28_uca3_model_0.cif #11/A ASN 131 C    fold_poly28_uca3_model_0.cif #11/C TYR 51 OH     0.117    2.953
    fold_poly28_uca3_model_0.cif #11/A ASN 131 CB   fold_poly28_uca3_model_0.cif #11/C TYR 51 CZ     0.113    3.377
    fold_poly28_uca3_model_0.cif #11/A ARG 132 CD   fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1    0.108    3.192
    fold_poly28_uca3_model_0.cif #11/A LEU 44 CD1   fold_poly28_uca3_model_0.cif #11/C LEU 34 CD1    0.106    3.654
    fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1   fold_poly28_uca3_model_0.cif #11/C TYR 32 CE1    0.102    3.078
    fold_poly28_uca3_model_0.cif #11/A ASP 75 CG    fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2    0.098    3.542
    fold_poly28_uca3_model_0.cif #11/A ARG 83 CZ    fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2   0.062    3.308
    fold_poly28_uca3_model_0.cif #11/A MET 79 CE    fold_poly28_uca3_model_0.cif #11/B LEU 104 CG    0.045    3.715
    fold_poly28_uca3_model_0.cif #11/A GLU 46 CD    fold_poly28_uca3_model_0.cif #11/C TYR 93 OH     0.032    3.308
    fold_poly28_uca3_model_0.cif #11/A GLU 134 CD   fold_poly28_uca3_model_0.cif #11/B TYR 106 CE1   -0.011    3.651
    fold_poly28_uca3_model_0.cif #11/A PHE 54 CZ    fold_poly28_uca3_model_0.cif #11/B LEU 104 O     -0.023    3.203
    fold_poly28_uca3_model_0.cif #11/A SER 70 C     fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   -0.039    3.529
    fold_poly28_uca3_model_0.cif #11/A SER 70 O     fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   -0.043    3.343
    fold_poly28_uca3_model_0.cif #11/A ASP 75 OD2   fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2    -0.062    3.242
    fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1   fold_poly28_uca3_model_0.cif #11/B TYR 105 CD2   -0.064    3.464
    fold_poly28_uca3_model_0.cif #11/A GLU 46 CD    fold_poly28_uca3_model_0.cif #11/C TYR 32 OH     -0.077    3.417
    fold_poly28_uca3_model_0.cif #11/A LEU 9 CD2    fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ     -0.080    3.600
    fold_poly28_uca3_model_0.cif #11/A LEU 9 CD1    fold_poly28_uca3_model_0.cif #11/C GLU 52 OE2    -0.089    3.389
    fold_poly28_uca3_model_0.cif #11/A MET 79 CG    fold_poly28_uca3_model_0.cif #11/B ASN 54 ND2    -0.098    3.618
    fold_poly28_uca3_model_0.cif #11/A TYR 108 OH   fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2   -0.101    3.321
    fold_poly28_uca3_model_0.cif #11/A SER 7 CB     fold_poly28_uca3_model_0.cif #11/C ASN 33 OD1    -0.104    3.404
    fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2   fold_poly28_uca3_model_0.cif #11/B TYR 105 OH    -0.121    2.821
    fold_poly28_uca3_model_0.cif #11/A LEU 9 CB     fold_poly28_uca3_model_0.cif #11/C LYS 55 CE     -0.127    3.887
    fold_poly28_uca3_model_0.cif #11/A PHE 125 CE1  fold_poly28_uca3_model_0.cif #11/B TYR 105 OH    -0.143    3.363
    fold_poly28_uca3_model_0.cif #11/A PHE 54 CE1   fold_poly28_uca3_model_0.cif #11/B LEU 104 O     -0.144    3.324
    fold_poly28_uca3_model_0.cif #11/A ALA 42 CB    fold_poly28_uca3_model_0.cif #11/B TYR 111 OH    -0.148    3.488
    fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1    fold_poly28_uca3_model_0.cif #11/C SER 54 OG     -0.156    2.636
    fold_poly28_uca3_model_0.cif #11/A SER 70 CA    fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   -0.170    3.930
    fold_poly28_uca3_model_0.cif #11/A ARG 132 NE   fold_poly28_uca3_model_0.cif #11/C GLU 52 CD     -0.177    3.697
    fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1   fold_poly28_uca3_model_0.cif #11/C TYR 32 CZ     -0.182    3.212
    fold_poly28_uca3_model_0.cif #11/A MET 79 SD    fold_poly28_uca3_model_0.cif #11/B ASN 52 ND2    -0.184    3.194
    fold_poly28_uca3_model_0.cif #11/A ARG 132 CZ   fold_poly28_uca3_model_0.cif #11/C GLU 52 CD     -0.186    3.676
    fold_poly28_uca3_model_0.cif #11/A ALA 42 O     fold_poly28_uca3_model_0.cif #11/B TYR 111 OH    -0.188    2.668
    fold_poly28_uca3_model_0.cif #11/A LEU 9 CD1    fold_poly28_uca3_model_0.cif #11/C GLU 52 CD     -0.198    3.958
    fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CA    -0.200    3.960
    fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2  fold_poly28_uca3_model_0.cif #11/B ARG 72 NH2    -0.206    3.726
    fold_poly28_uca3_model_0.cif #11/A GLU 46 OE2   fold_poly28_uca3_model_0.cif #11/C GLY 95 CA     -0.224    3.524
    fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1   fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ    -0.226    3.476
    fold_poly28_uca3_model_0.cif #11/A PHE 125 CZ   fold_poly28_uca3_model_0.cif #11/B TYR 105 OH    -0.235    3.455
    fold_poly28_uca3_model_0.cif #11/A SER 7 OG     fold_poly28_uca3_model_0.cif #11/C VAL 53 CG1    -0.238    3.578
    fold_poly28_uca3_model_0.cif #11/A LEU 38 CD2   fold_poly28_uca3_model_0.cif #11/B TYR 105 O     -0.243    3.543
    fold_poly28_uca3_model_0.cif #11/A PRO 103 O    fold_poly28_uca3_model_0.cif #11/B TYR 32 OH     -0.244    2.724
    fold_poly28_uca3_model_0.cif #11/A SER 7 CB     fold_poly28_uca3_model_0.cif #11/C ASN 33 ND2    -0.246    3.766
    fold_poly28_uca3_model_0.cif #11/A GLU 46 CD    fold_poly28_uca3_model_0.cif #11/C TYR 93 CE1    -0.250    3.890
    fold_poly28_uca3_model_0.cif #11/A ASP 75 CB    fold_poly28_uca3_model_0.cif #11/B GLY 57 CA     -0.259    4.019
    fold_poly28_uca3_model_0.cif #11/A SER 7 CB     fold_poly28_uca3_model_0.cif #11/C ASN 33 CG     -0.259    3.749
    fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2  fold_poly28_uca3_model_0.cif #11/B ARG 72 CZ     -0.259    3.749
    fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CD2   -0.263    3.903
    fold_poly28_uca3_model_0.cif #11/A ARG 132 CD   fold_poly28_uca3_model_0.cif #11/C GLU 52 CD     -0.269    4.029
    fold_poly28_uca3_model_0.cif #11/A GLU 81 N     fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   -0.276    3.796
    fold_poly28_uca3_model_0.cif #11/A ALA 77 CB    fold_poly28_uca3_model_0.cif #11/B SER 55 O      -0.282    3.582
    fold_poly28_uca3_model_0.cif #11/A ASP 75 OD1   fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2    -0.283    3.463
    fold_poly28_uca3_model_0.cif #11/A THR 138 CG2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CD1   -0.286    3.926
    fold_poly28_uca3_model_0.cif #11/A GLU 46 CD    fold_poly28_uca3_model_0.cif #11/C GLY 95 CA     -0.289    4.049
    fold_poly28_uca3_model_0.cif #11/A PHE 54 CZ    fold_poly28_uca3_model_0.cif #11/B TYR 105 CA    -0.291    3.931
    fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1  fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1    -0.302    2.962
    fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1  fold_poly28_uca3_model_0.cif #11/B ARG 72 CZ     -0.303    3.793
    fold_poly28_uca3_model_0.cif #11/A SER 7 OG     fold_poly28_uca3_model_0.cif #11/C VAL 53 CG2    -0.304    3.644
    fold_poly28_uca3_model_0.cif #11/A LEU 9 CG     fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ     -0.320    3.840
    fold_poly28_uca3_model_0.cif #11/A ARG 132 NE   fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1    -0.324    2.984
    fold_poly28_uca3_model_0.cif #11/A ASN 131 CB   fold_poly28_uca3_model_0.cif #11/C TYR 51 CE1    -0.333    3.973
    fold_poly28_uca3_model_0.cif #11/A PRO 103 CB   fold_poly28_uca3_model_0.cif #11/B TYR 32 OH     -0.338    3.678
    fold_poly28_uca3_model_0.cif #11/A ARG 132 CG   fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ     -0.338    3.858
    fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1  fold_poly28_uca3_model_0.cif #11/B TYR 111 CD2   -0.350    3.750
    fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1    fold_poly28_uca3_model_0.cif #11/C SER 54 CB     -0.363    3.663
    fold_poly28_uca3_model_0.cif #11/A MET 79 CE    fold_poly28_uca3_model_0.cif #11/B ILE 102 CG2   -0.367    4.127
    fold_poly28_uca3_model_0.cif #11/A ARG 130 CZ   fold_poly28_uca3_model_0.cif #11/C SER 58 OG     -0.368    3.438
    fold_poly28_uca3_model_0.cif #11/A ARG 83 CZ    fold_poly28_uca3_model_0.cif #11/B TYR 105 OH    -0.369    3.439
    fold_poly28_uca3_model_0.cif #11/A ASN 131 ND2  fold_poly28_uca3_model_0.cif #11/C PRO 57 CA     -0.373    3.893
    fold_poly28_uca3_model_0.cif #11/A ASP 49 CB    fold_poly28_uca3_model_0.cif #11/C SER 96 CA     -0.379    4.139
    fold_poly28_uca3_model_0.cif #11/A GLU 134 CD   fold_poly28_uca3_model_0.cif #11/B TYR 106 CZ    -0.382    3.872
    fold_poly28_uca3_model_0.cif #11/A GLU 46 CG    fold_poly28_uca3_model_0.cif #11/C TYR 93 OH     -0.382    3.722
    fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1  fold_poly28_uca3_model_0.cif #11/B ARG 72 NH1    -0.386    3.906
    fold_poly28_uca3_model_0.cif #11/A PHE 125 CE1  fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ    -0.387    3.757
    fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1   fold_poly28_uca3_model_0.cif #11/C TYR 32 OH     -0.392    2.872
    

  
97 contacts  

> select clear

> select #11/A:194

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

133 atoms, 136 bonds, 15 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select #11/A:197

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #11/A:4

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

> select up

104 atoms, 107 bonds, 14 residues, 1 model selected  

> show #!1 models

> hide #10.1 models

> hide #!11 models

> show #1.2 models

> show #1.3 models

> select #1/E:126

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

> select up

63 atoms, 63 bonds, 8 residues, 1 model selected  

> select up

604 atoms, 618 bonds, 74 residues, 1 model selected  

> select up

616 atoms, 629 bonds, 76 residues, 1 model selected  

> select up

1313 atoms, 1346 bonds, 164 residues, 1 model selected  

> hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
> intraMol false intraRes false select true reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.8 angstroms and 20 degrees
    Models used:
    	1 231023_poly310-DH270UCA3_refine_001.pdb
    
    6 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O  no hydrogen  2.874  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O    no hydrogen  2.993  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1  no hydrogen  3.440  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH   231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  no hydrogen  2.679  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2  231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  no hydrogen  3.050  N/A
    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2  231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O    no hydrogen  3.339  N/A
    

  
6 hydrogen bonds found  

> hide #1.3 models

> select #1/E:79

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

> select up

78 atoms, 80 bonds, 9 residues, 1 model selected  

> select up

709 atoms, 728 bonds, 90 residues, 1 model selected  

> select up

727 atoms, 746 bonds, 92 residues, 1 model selected  

> select up

1313 atoms, 1346 bonds, 164 residues, 1 model selected  

> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    64 contacts
                             atom1                                                     atom2                            overlap  distance
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 68 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD1   0.171    3.589
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CD1    0.157    3.483
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 111 O      0.142    3.158
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CA   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O     0.137    3.163
    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE   231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2    0.135    3.625
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CZ2    0.103    3.537
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CE2   0.101    3.539
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CB    0.095    3.205
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD2   0.080    3.560
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 CE   231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O       0.077    3.223
    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2     0.069    3.451
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CA    0.058    3.242
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CH2     0.052    3.588
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 CE1     0.052    3.128
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 NE1    0.046    3.474
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 CB  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 37 OH      0.028    3.312
    231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 70 CA   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   0.025    3.735
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CH2     0.022    3.618
    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 SD   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 CB      -0.019    3.669
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 37 OH      -0.052    3.392
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CG    -0.060    3.360
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CD   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.118    3.878
    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.120    3.880
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB    -0.127    3.887
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2    -0.129    3.619
    231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 62 CB      -0.147    3.447
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD1   -0.154    3.794
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O     -0.159    3.459
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CH2    -0.166    3.806
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CA    -0.172    3.472
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH      -0.172    3.512
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CB    -0.184    3.484
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH      -0.199    2.679
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2    -0.212    3.972
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O     -0.214    2.874
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CB  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2    -0.251    3.741
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB    -0.252    3.742
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB    -0.254    3.894
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CA   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CG    -0.259    4.019
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CE1  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CB    -0.259    3.899
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CB  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CD2    -0.263    3.753
    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 CG      -0.267    3.757
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH      -0.268    3.608
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CZ    -0.280    3.770
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 CZ      -0.289    3.319
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD1   -0.291    3.931
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2    -0.307    3.797
    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE   231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CB     -0.315    4.075
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CA   231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 111 O      -0.318    3.618
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111C CA    -0.322    3.842
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O       -0.333    2.993
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CG     -0.334    3.824
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111C C     -0.335    3.585
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CG    -0.339    3.829
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D N     -0.340    3.620
    231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 70 N    231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.342    3.862
    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.361    4.121
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CE1   -0.370    4.010
    231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 SD   231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2    -0.372    4.022
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CZ2     -0.386    4.026
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.388    4.148
    231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD1   -0.388    4.028
    231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2     -0.390    3.050
    231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.396    4.156
    

  
64 contacts  

> select clear

> hide #1.4 models

> show #1.4 models

> hide #1.4 models

> show #1.3 models

> hide #1.3 models

> show #1.4 models

> show #1.3 models

> hide #1.3 models

> open
> /Users/oswanson/Downloads/fold_lee_rdrp_trimer_dimer/fold_lee_rdrp_trimer_dimer_model_0.cif

Chain information for fold_lee_rdrp_trimer_dimer_model_0.cif #12  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
  

> hide #!1 models

> hide #12 atoms

> show #12 cartoons

Computing secondary structure  

> color #12 bychain

> open pdb:6QWL

Summary of feedback from opening 6QWL fetched from pdb  
---  
note | Fetching compressed mmCIF 6qwl from http://files.rcsb.org/download/6qwl.cif  
  
6qwl title:  
Influenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5'
cRNA promoter [more info...]  
  
Chain information for 6qwl #13  
---  
Chain | Description | UniProt  
E | Polymerase acidic protein | PA_INBP9 1-726  
K | RNA-directed RNA polymerase catalytic subunit | RDRP_INBP9 1-752  
Q | Polymerase basic protein 2 | PB2_INBP9 1-770  
T | 3' cRNA |   
W | 5' cRNA |   
  

> ui tool show Matchmaker

> matchmaker #!13 to #12

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#12) with 6qwl,
chain K (#13), sequence alignment score = 3220.4  
RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs:
3.053)  
  

> select add #13

10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide #12 models

> nucleotides #!13 atoms

> style nucleic & #!13 stick

Changed 553 atom styles  

> nucleotides #!13 fill

> style nucleic & #!13 stick

Changed 553 atom styles  

> nucleotides #!13 fill

> style nucleic & #!13 stick

Changed 553 atom styles  

> nucleotides #!13 tube/slab shape box

> nucleotides #!13 ladder

> select #13/T:6

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

249 atoms, 275 bonds, 12 residues, 1 model selected  

> nucleotides sel ladder

> nucleotides sel tube/slab shape box

> nucleotides sel fill

> style nucleic & sel stick

Changed 249 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 249 atom styles  

> select add #13

10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected  

> color sel bychain

> select clear

> show #12 models

> hide #12 models

> show #12 models

> hide #12 models

> show #12 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #12 models

> close #12#13

> show #!1 models

> save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs

> hide #1.4 models

> show #1.3 models

> show #1.4 models

> hide #1.4 models

> show #1.4 models

> hide #1.3 models

> show #1.3 models

> hide #1.4 models

> close #1.4

> color #1.3 #0433ffff models

> color #1.3 #7a81ffff models

> color #1.3 #0433ffff models

> color #1.3 #f3f3f3ff models

> color #1.3 #0433ffff models

> color #1.3 #0b1e97ff models

> color #1.2 #ea99faff models

> hide #1.3 models

> select add #1

4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected  

> size stickRadius 0.25

Changed 41190 bond radii  

> size stickRadius 0.

Bond radius must be greater than 0.  

> size stickRadius 0.3

Changed 41190 bond radii  

> size stickRadius 0.275

Changed 41190 bond radii  

> size stickRadius 0.25

Changed 41190 bond radii  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/H

Alignment identifier is 1/H  

> select #1/H:190

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

> select #1/H:190

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

> select #1/H:111A

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

> select #1/H:111A

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

> select #1/H:112D

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

> select #1/H:112D

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

> select #1/H:111A,112D

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

> select #1/H:111A,112B,112D

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> select #1/H:112B

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

> hide sel atoms

> select #1/H:111B

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #1/H:111B-111C,112A,112B,112C,112D

48 atoms, 49 bonds, 6 residues, 1 model selected  

> open pdb:8sax

Summary of feedback from opening 8sax fetched from pdb  
---  
notes | Fetching compressed mmCIF 8sax from http://files.rcsb.org/download/8sax.cif  
Fetching CCD BMA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif  
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif  
  
8sax title:  
CryoEM structure of DH270.UCA-CH848.10.17DT [more info...]  
  
Chain information for 8sax #12  
---  
Chain | Description | UniProt  
A E I | CH848.10.17.SOSIP gp120 | A0A1W6IPB2_9HIV1 34-511  
B F J | CH848.10.17.SOSIP gp41 |   
C G K | DH270.UCA heavy chain |   
D H L | DH270.UCA light chain |   
  
Non-standard residues in 8sax #12  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select clear

> select #1/H:66

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

> select add #1/L:109

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select up

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

> select up

3334 atoms, 3411 bonds, 444 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #12 to #1 & sel

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1) with 8sax,
chain C (#12), sequence alignment score = 647.8  
RMSD between 126 pruned atom pairs is 0.769 angstroms; (across all 127 pairs:
0.792)  
  

> select add #12

23194 atoms, 23760 bonds, 2991 residues, 2 models selected  

> select #12/G:23@CE

1 atom, 1 residue, 1 model selected  

> select #12/G:23@CE

1 atom, 1 residue, 1 model selected  

> select add #12

19860 atoms, 20349 bonds, 2547 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide #!1 models

> ui mousemode right select

Drag select of 29 residues  

> select up

508 atoms, 510 bonds, 67 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
> intraMol false intraRes false select true reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.8 angstroms and 20 degrees
    Models used:
    	12 8sax
    
    6 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8sax #12/A LYS 327 NZ   8sax #12/C TYR 33 OH    no hydrogen  3.095  N/A
    8sax #12/A THR 415 OG1  8sax #12/N NAG 1 O5     no hydrogen  3.662  N/A
    8sax #12/A THR 415 OG1  8sax #12/N NAG 1 O6     no hydrogen  3.431  N/A
    8sax #12/C TYR 33 OH    8sax #12/A ASP 325 OD2  no hydrogen  2.827  N/A
    8sax #12/N NAG 1 N2     8sax #12/A HIS 330 NE2  no hydrogen  3.281  N/A
    8sax #12/N NAG 1 O6     8sax #12/A THR 415 OG1  no hydrogen  3.431  N/A
    

  
6 hydrogen bonds found  

> select up

60 atoms, 57 bonds, 6 residues, 1 model selected  

> style sel stick

Changed 60 atom styles  

> color sel byhetero

> select clear

> select #12/A:414

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

> select up

73 atoms, 72 bonds, 9 residues, 1 model selected  

> select up

3582 atoms, 3664 bonds, 462 residues, 1 model selected  

> select down

73 atoms, 72 bonds, 9 residues, 1 model selected  

> select clear

Drag select of 9 atoms, 43 residues, 7 bonds  

> select up

636 atoms, 638 bonds, 84 residues, 1 model selected  

> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true color #ff2600 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    31 contacts
             atom1                   atom2           overlap  distance
    8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 C1      1.117    2.403
    8sax #12/A ASN 332 CG    8sax #12/N NAG 1 C1      0.545    2.945
    8sax #12/A ASN 332 OD1   8sax #12/N NAG 1 C1      0.528    2.772
    8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 C2      0.307    3.213
    8sax #12/A HIS 330 NE2   8sax #12/N NAG 1 C8      0.296    3.224
    8sax #12/A HIS 330 CE1   8sax #12/C TYR 105 O     0.162    3.018
    8sax #12/A THR 415 CG2   8sax #12/C TYR 105 CE1   0.118    3.522
    8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 C7      0.059    3.191
    8sax #12/A HIS 330 CB    8sax #12/C TYR 105 CD1   0.051    3.589
    8sax #12/A HIS 330 NE2   8sax #12/N NAG 1 N2      -0.001    3.281
    8sax #12/A PRO 299 CG    8sax #12/C TYR 105 O     -0.063    3.363
    8sax #12/A HIS 330 ND1   8sax #12/C TYR 105 CD1   -0.063    3.463
    8sax #12/A HIS 330 CE1   8sax #12/C TYR 105 CB    -0.079    3.719
    8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 N2      -0.087    3.367
    8sax #12/A THR 138 O     8sax #12/C GLY 57 CA     -0.102    3.402
    8sax #12/A ILE 323c CG2  8sax #12/D SER 96 CB     -0.107    3.867
    8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 O7      -0.136    2.796
    8sax #12/A HIS 330 CG    8sax #12/C TYR 105 CD1   -0.144    3.514
    8sax #12/A THR 138 CG2   8sax #12/C ASN 59 ND2    -0.165    3.685
    8sax #12/A HIS 330 CB    8sax #12/C TYR 105 CE1   -0.182    3.822
    8sax #12/A HIS 330 ND1   8sax #12/C TYR 105 CB    -0.258    3.778
    8sax #12/A THR 297 CG2   8sax #12/N NAG 1 C8      -0.283    4.043
    8sax #12/A LYS 327 CD    8sax #12/C LEU 104 CA    -0.296    4.056
    8sax #12/A THR 413 CG2   8sax #12/N NAG 1 O5      -0.304    3.644
    8sax #12/A LYS 327 CE    8sax #12/C TYR 33 OH     -0.323    3.663
    8sax #12/A ASP 325 OD2   8sax #12/C TYR 33 OH     -0.347    2.827
    8sax #12/A HIS 330 CE1   8sax #12/C TYR 105 C     -0.350    3.720
    8sax #12/A THR 415 CG2   8sax #12/C TYR 105 CZ    -0.354    3.844
    8sax #12/A HIS 330 CE1   8sax #12/C TYR 105 CA    -0.358    3.998
    8sax #12/A ILE 323c CG2  8sax #12/D SER 96 CA     -0.368    4.128
    8sax #12/A LYS 327 NZ    8sax #12/C TYR 33 OH     -0.395    3.095
    

  
31 contacts  

> select add #12

19860 atoms, 20349 bonds, 37 pseudobonds, 2547 residues, 3 models selected  

> style sel stick

Changed 19860 atom styles  

> select clear

> show #!1 models

> hide #!1 models

> select add #12

19860 atoms, 20349 bonds, 37 pseudobonds, 2547 residues, 3 models selected  

> color sel byhetero

> select subtract #12

Nothing selected  

> hide #12.2 models

> show #!1 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #12.2 models

> hide #!12 models

> show #1.3 models

> hide #1.2 models

> show #!12 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> open pdb:9aug

Summary of feedback from opening 9aug fetched from pdb  
---  
note | Fetching compressed mmCIF 9aug from http://files.rcsb.org/download/9aug.cif  
  
9aug title:  
Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R [more info...]  
  
Chain information for 9aug #13  
---  
Chain | Description | UniProt  
A B C | HIV-1 BG505 DS-SOSIP glycoprotein gp120 | Q2N0S6_9HIV1 31-498  
D E F | HIV-1 BG505 DS-SOSIP glycoprotein gp41 | Q2N0S6_9HIV1 512-664  
G H I | UCA3.G57R heavy chain |   
J K L | UCA3.G57R light chain |   
  
Non-standard residues in 9aug #13  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> matchmaker #!13 to #1 & sel

No 'to' model specified  

> show #!1 models

> select #1/H:112D

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

> select up

181 atoms, 190 bonds, 22 residues, 1 model selected  

> select up

1725 atoms, 1772 bonds, 228 residues, 1 model selected  

> select up

4647 atoms, 4757 bonds, 608 residues, 1 model selected  

> select down

1725 atoms, 1772 bonds, 228 residues, 1 model selected  

> select subtract #1/H:74

1721 atoms, 1767 bonds, 227 residues, 1 model selected  

> select up

1725 atoms, 1772 bonds, 228 residues, 1 model selected  

> select add #1/L:56

1734 atoms, 1780 bonds, 229 residues, 1 model selected  

> select up

1828 atoms, 1876 bonds, 241 residues, 1 model selected  

> select up

3334 atoms, 3411 bonds, 444 residues, 1 model selected  

> select up

4647 atoms, 4757 bonds, 608 residues, 1 model selected  

> select down

3334 atoms, 3411 bonds, 444 residues, 1 model selected  

> matchmaker #!13 to #1 & sel

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1) with 9aug,
chain G (#13), sequence alignment score = 999.8  
RMSD between 125 pruned atom pairs is 0.728 angstroms; (across all 126 pairs:
0.755)  
  

> hide #!1 models

> select add #1

4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected  

> select subtract #1

Nothing selected  

> select add #13

20211 atoms, 20745 bonds, 3 pseudobonds, 2544 residues, 2 models selected  

> show sel cartoons

> style sel stick

Changed 20211 atom styles  

> hide sel atoms

> select clear

> hide #!12 models

Drag select of 32 residues  

> select up

392 atoms, 391 bonds, 53 residues, 1 model selected  

> hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
> intraMol false intraRes false select true reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.8 angstroms and 20 degrees
    Models used:
    	13 9aug
    
    12 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9aug #13/A SER 136 OG   9aug #13/G THR 58 O     no hydrogen  3.683  N/A
    9aug #13/A SER 136 OG   9aug #13/G THR 58 OG1   no hydrogen  3.145  N/A
    9aug #13/A GLY 138 N    9aug #13/G SER 55 OG    no hydrogen  3.662  N/A
    9aug #13/A ASP 325 N    9aug #13/G ASP 107 OD2  no hydrogen  3.149  N/A
    9aug #13/A LYS 327 NZ   9aug #13/G TYR 33 OH    no hydrogen  3.222  N/A
    9aug #13/A THR 415 OG1  9aug #13/G TYR 105 OH   no hydrogen  3.764  N/A
    9aug #13/G TYR 33 OH    9aug #13/A ASP 325 OD2  no hydrogen  2.362  N/A
    9aug #13/G ASN 52 ND2   9aug #13/A ASP 325 OD1  no hydrogen  3.191  N/A
    9aug #13/G SER 55 OG    9aug #13/A GLY 138 O    no hydrogen  3.500  N/A
    9aug #13/G ARG 57 NH2   9aug #13/A ILE 322 O    no hydrogen  3.168  N/A
    9aug #13/G THR 58 OG1   9aug #13/A SER 136 OG   no hydrogen  3.145  N/A
    9aug #13/G TYR 105 OH   9aug #13/A GLN 417 OE1  no hydrogen  3.170  N/A
    

  
12 hydrogen bonds found  

> select add #13

20211 atoms, 20745 bonds, 15 pseudobonds, 2544 residues, 3 models selected  

> color sel byhetero

> select clear

Drag select of 5 atoms, 15 residues, 3 bonds  

> select up

113 atoms, 105 bonds, 17 residues, 1 model selected  

> select up

128 atoms, 121 bonds, 17 residues, 1 model selected  

> select down

113 atoms, 105 bonds, 17 residues, 1 model selected  

> select #13/G:57

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #13/G:57

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 8 atoms, 33 residues, 7 bonds, 2 pseudobonds  

> select subtract #13/G:57

240 atoms, 5 bonds, 1 pseudobond, 33 residues, 2 models selected  

> select up

530 atoms, 533 bonds, 1 pseudobond, 72 residues, 2 models selected  

> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true color #ff2600 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    25 contacts
            atom1                   atom2           overlap  distance
    9aug #13/A ASP 325 CG   9aug #13/G ASN 52 ND2    0.265    3.255
    9aug #13/A ASP 325 CG   9aug #13/G TYR 33 OH     0.200    3.140
    9aug #13/A HIS 330 ND1  9aug #13/G TYR 105 CD1   0.133    3.267
    9aug #13/A ILE 326 CG1  9aug #13/G ARG 57 NH1    0.123    3.397
    9aug #13/A ASP 325 OD2  9aug #13/G TYR 33 OH     0.118    2.362
    9aug #13/A ASP 325 OD2  9aug #13/G ASN 52 ND2    0.066    2.594
    9aug #13/A HIS 330 CE1  9aug #13/G TYR 105 CB    0.064    3.576
    9aug #13/A GLN 417 OE1  9aug #13/G TYR 105 CE1   0.062    3.118
    9aug #13/A GLY 324 CA   9aug #13/J SER 97 OG     0.047    3.293
    9aug #13/A ILE 323 CG2  9aug #13/J SER 96 CA     0.041    3.719
    9aug #13/A GLY 137 CA   9aug #13/G ARG 57 CD     0.022    3.738
    9aug #13/A LYS 327 CD   9aug #13/G LEU 104 CA    0.006    3.754
    9aug #13/A HIS 330 CE1  9aug #13/G TYR 105 O     -0.009    3.189
    9aug #13/A ILE 323 CG2  9aug #13/J SER 96 CB     -0.042    3.802
    9aug #13/A HIS 330 CE1  9aug #13/G TYR 105 CD1   -0.045    3.565
    9aug #13/A LYS 327 CE   9aug #13/G TYR 106 O     -0.048    3.348
    9aug #13/A ASP 325 CB   9aug #13/G TYR 33 OH     -0.116    3.456
    9aug #13/A SER 136 CB   9aug #13/G THR 58 OG1    -0.136    3.476
    9aug #13/A ILE 326 CD1  9aug #13/G ARG 57 NH1    -0.178    3.698
    9aug #13/A ILE 323 CG2  9aug #13/J SER 96 O      -0.194    3.494
    9aug #13/A HIS 330 CE1  9aug #13/G TYR 105 CA    -0.208    3.848
    9aug #13/A ILE 323 CG2  9aug #13/J SER 96 C      -0.226    3.716
    9aug #13/A HIS 330 CG   9aug #13/G TYR 105 CD1   -0.287    3.657
    9aug #13/A LYS 327 CE   9aug #13/G LEU 104 CA    -0.364    4.124
    9aug #13/A GLY 324 C    9aug #13/G TRP 50 CH2    -0.385    3.755
    

  
25 contacts  

> select clear

> hide #13.3 models

> hide #13.2 models

> show #13.3 models

> show #13.2 models

> hide #13.3 models

Desktop color scheme is dark  
Desktop color scheme is light  

> open pdb:6QWL

6qwl title:  
Influenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5'
cRNA promoter [more info...]  
  
Chain information for 6qwl #14  
---  
Chain | Description | UniProt  
E | Polymerase acidic protein | PA_INBP9 1-726  
K | RNA-directed RNA polymerase catalytic subunit | RDRP_INBP9 1-752  
Q | Polymerase basic protein 2 | PB2_INBP9 1-770  
T | 3' cRNA |   
W | 5' cRNA |   
  

> hide #!13 models

> select add #14

10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected  

> view orient

> select clear

> select #14/E:549@NH1

1 atom, 1 residue, 1 model selected  

> select add #14/K:331@CD1

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance #14/E:549@NH1 #14/K:331@CD1

Distance between 6qwl #14/E ARG 549 NH1 and /K ILE 331 CD1: 104.224Å  

> open
> /Users/oswanson/Downloads/fold_lee_rdrp_trimer_dimer/fold_lee_rdrp_trimer_dimer_model_0.cif

Chain information for fold_lee_rdrp_trimer_dimer_model_0.cif #16  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
  

> select clear

> select add #16

35830 atoms, 36512 bonds, 4496 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #16

35830 atoms, 36512 bonds, 4496 residues, 1 model selected  

> view orient

> hide #!14 models

> view orient

> select clear

> select #16/D:196@NH1

1 atom, 1 residue, 1 model selected  

> select add #16/C:196@NH2

2 atoms, 2 residues, 1 model selected  

> distance #16/D:196@NH1 #16/C:196@NH2

Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/D ARG 196 NH1 and
/C ARG 196 NH2: 197.716Å  

> select #16/A:621@OE1

1 atom, 1 residue, 1 model selected  

> select add #16/E:631@ND2

2 atoms, 2 residues, 1 model selected  

> distance #16/A:621@OE1 #16/E:631@ND2

Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/A GLU 621 OE1 and
/E ASN 631 ND2: 126.822Å  

> select clear

> select #16/A:621@OE1

1 atom, 1 residue, 1 model selected  

> select add #16/E:631@CB

2 atoms, 2 residues, 1 model selected  

> distance #16/A:621@OE1 #16/E:631@CB

Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/A GLU 621 OE1 and
/E ASN 631 CB: 128.258Å  

> select #16/B:321@CG

1 atom, 1 residue, 1 model selected  

> select add #16/B:100@O

2 atoms, 2 residues, 1 model selected  

> distance #16/B:321@CG #16/B:100@O

Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/B ASP 321 CG and
GLY 100 O: 131.686Å  

> select #16/D:194@CE

1 atom, 1 residue, 1 model selected  

> select add #16/B:206@OE1

2 atoms, 2 residues, 1 model selected  

> distance #16/D:194@CE #16/B:206@OE1

Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/D LYS 194 CE and
/B GLN 206 OE1: 62.308Å  

> select add #16

35830 atoms, 36512 bonds, 5 pseudobonds, 4496 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

Computing secondary structure  

> select clear

Desktop color scheme is dark  

> molmap #16 4

Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 4 as #17, grid size
142,148,110, pixel 1.33, shown at level 0.102, step 1, values float32  

> hide #!17 models

> select add #16

35830 atoms, 36512 bonds, 5 pseudobonds, 4496 residues, 2 models selected  

> color sel bychain

> select clear

Desktop color scheme is light  

> show #!17 models

> molmap #16 8

Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 8 as #17, grid size
80,83,64, pixel 2.67, shown at level 0.0919, step 1, values float32  

> save
> /Users/oswanson/Desktop/Primocalins/Structures/initial_models_plusRdRp.cxs

Cell requested for row 0 is out of bounds for table with 28 rows! Resizing
table model.  

> show #!14 models

> hide #!15 models

> show #!13 models

> hide #!14 models

> hide #16 models

> hide #!17 models

> close #1-2,4-5,8,10,16#3,6-7,9,11-15,17

> open
> /Users/oswanson/Desktop/Primocalins/Structures/initial_models_plusRdRp.cxs
> format session

Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 8 as #17, grid size
80,83,64, pixel 2.67, shown at level 0.0919, step 1, values float32  

> view name session-start

opened ChimeraX session  

> close #1

> close #2,4-5,8#3,6-7,9-12

> show #!13 models

> close #13

> show #!14 models

> ui tool show Matchmaker

> matchmaker #!14 to #16

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#16) with 6qwl,
chain K (#14), sequence alignment score = 3220.4  
RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs:
3.053)  
  

> hide #!17 models

> select add #14

10408 atoms, 10668 bonds, 25 pseudobonds, 1270 residues, 4 models selected  

> show sel cartoons

> hide sel atoms

> hide #!14 models

> hide #!15 models

> close #15

> select subtract #14

Nothing selected  

> show #!17 models

> hide #!17 models

> open /Users/oswanson/Downloads/cryosparc_P605_J23_class_00_final_volume.mrc

Opened cryosparc_P605_J23_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 2.9, shown at level 0.115, step 1, values float32  

> select add #14

10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected  

> select add #16

46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 4 models selected  

> select add #17

46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 6 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.28748,0.86499,0.41127,16.771,0.95617,0.23429,0.17561,44.158,0.055546,0.44373,-0.89444,263.76,#16,1,0,0,135.5,0,1,0,277.63,0,0,1,187.37,#17,1,0,0,135.5,0,1,0,277.63,0,0,1,187.37

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.18687,0.24553,0.95121,-76.618,0.83833,0.46491,-0.2847,108.53,-0.51213,0.85063,-0.11895,196.06,#16,0.54986,0.40325,-0.73147,138.69,0.044048,0.86052,0.50751,275.9,0.8341,-0.31128,0.4554,187.63,#17,0.54986,0.40325,-0.73147,138.69,0.044048,0.86052,0.50751,275.9,0.8341,-0.31128,0.4554,187.63

> volume #1 level 0.2269

> volume #1 level 0.1301

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.18687,0.24553,0.95121,-30.788,0.83833,0.46491,-0.2847,26.758,-0.51213,0.85063,-0.11895,210.32,#16,0.54986,0.40325,-0.73147,184.52,0.044048,0.86052,0.50751,194.12,0.8341,-0.31128,0.4554,201.88,#17,0.54986,0.40325,-0.73147,184.52,0.044048,0.86052,0.50751,194.12,0.8341,-0.31128,0.4554,201.88

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.12079,0.25201,0.96015,23.371,0.64731,0.75331,-0.11629,-0.5835,-0.7526,0.60747,-0.25413,305.87,#16,0.6476,0.11216,-0.75368,184.02,0.41769,0.77501,0.47423,193.72,0.6373,-0.62192,0.45505,201.57,#17,0.6476,0.11216,-0.75368,184.02,0.41769,0.77501,0.47423,193.72,0.6373,-0.62192,0.45505,201.57

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.12079,0.25201,0.96015,17.372,0.64731,0.75331,-0.11629,-0.15817,-0.7526,0.60747,-0.25413,290.4,#16,0.6476,0.11216,-0.75368,178.02,0.41769,0.77501,0.47423,194.15,0.6373,-0.62192,0.45505,186.1,#17,0.6476,0.11216,-0.75368,178.02,0.41769,0.77501,0.47423,194.15,0.6373,-0.62192,0.45505,186.1

> transparency #1.1 50

> ui tool show "Fit in Map"

> fitmap #14 inMap #17

Fit molecule 6qwl (#14) to map fold_lee_rdrp_trimer_dimer_model_0.cif map 8
(#17) using 10408 atoms  
average map value = 0.2949, steps = 52  
shifted from previous position = 2.8  
rotated from previous position = 3.66 degrees  
atoms outside contour = 973, contour level = 0.091911  
  
Position of 6qwl (#14) relative to fold_lee_rdrp_trimer_dimer_model_0.cif map
8 (#17) coordinates:  
Matrix rotation and translation  
-0.26601820 0.86761118 0.42010137 -122.48682198  
0.96396267 0.24087630 0.11293618 -224.65998238  
-0.00320777 0.43500512 -0.90042227 84.96204885  
Axis 0.59580861 0.78309703 0.17824460  
Axis point 35.35475112 0.00000000 66.57258889  
Rotation angle (degrees) 164.31913872  
Shift along axis -233.76524286  
  

> fitmap #14 inMap #1

Fit molecule 6qwl (#14) to map cryosparc_P605_J23_class_00_final_volume.mrc
(#1) using 10408 atoms  
average map value = 0.1799, steps = 200  
shifted from previous position = 21.9  
rotated from previous position = 74.3 degrees  
atoms outside contour = 3991, contour level = 0.1301  
  
Position of 6qwl (#14) relative to
cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.60115416 -0.46274634 0.65152091 74.63506249  
0.78882591 0.21309401 -0.57649340 125.49176200  
0.12793501 0.86049798 0.49312866 20.61803554  
Axis 0.72713451 0.26494062 0.63331026  
Axis point 0.00000000 83.73335535 57.16462029  
Rotation angle (degrees) 81.15926345  
Shift along axis 100.57520736  
  

> fitmap #16 inMap #1

Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 35830 atoms  
average map value = 0.1462, steps = 80  
shifted from previous position = 14.2  
rotated from previous position = 7.6 degrees  
atoms outside contour = 19724, contour level = 0.1301  
  
Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.64553227 0.15603228 -0.74762425 188.80351799  
0.47289373 0.68702028 0.55170161 187.23326867  
0.59971628 -0.70968801 0.36970707 192.28999636  
Axis -0.67358407 -0.71948199 0.16920452  
Axis point -224.98972481 0.00000000 152.57508207  
Rotation angle (degrees) 69.44356542  
Shift along axis -229.34967086  
  

> volume #1 level 0.1887

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.65777,0.35349,-0.66512,321.14,-0.567,0.34891,0.74617,136.4,0.49583,0.86793,-0.029068,32.827,#16,-0.73375,-0.11951,0.66882,185.61,-0.032984,-0.97698,-0.21076,187.23,0.67862,-0.17671,0.71292,192.09,#17,-0.73654,-0.090736,0.67028,196.56,0.033703,-0.99465,-0.097612,178.17,0.67555,-0.049305,0.73566,192.58

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.65777,0.35349,-0.66512,319.91,-0.567,0.34891,0.74617,141.42,0.49583,0.86793,-0.029068,31.088,#16,-0.73375,-0.11951,0.66882,184.37,-0.032984,-0.97698,-0.21076,192.24,0.67862,-0.17671,0.71292,190.35,#17,-0.73654,-0.090736,0.67028,195.33,0.033703,-0.99465,-0.097612,183.18,0.67555,-0.049305,0.73566,190.84

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.74976,0.28884,-0.59534,331.34,-0.64787,-0.13743,0.74925,206.52,0.1346,0.94746,0.29017,33.245,#16,-0.80043,-0.17992,0.57178,184.62,-0.25408,-0.76212,-0.5955,193.91,0.54291,-0.62193,0.56431,190.19,#17,-0.79743,-0.16606,0.58011,194.68,-0.19374,-0.84002,-0.50679,184.4,0.57146,-0.51652,0.63768,186.94

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.74976,0.28884,-0.59534,331.45,-0.64787,-0.13743,0.74925,197.96,0.1346,0.94746,0.29017,40.397,#16,-0.80043,-0.17992,0.57178,184.73,-0.25408,-0.76212,-0.5955,185.35,0.54291,-0.62193,0.56431,197.34,#17,-0.79743,-0.16606,0.58011,194.79,-0.19374,-0.84002,-0.50679,175.84,0.57146,-0.51652,0.63768,194.09

> fitmap #16 inMap #1

Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 35830 atoms  
average map value = 0.15, steps = 292  
shifted from previous position = 5.36  
rotated from previous position = 54.4 degrees  
atoms outside contour = 24089, contour level = 0.18871  
  
Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.74059655 -0.66117825 -0.11983354 184.20616119  
0.24333744 -0.09766510 -0.96501213 188.58923260  
0.62634147 -0.74384464 0.23321986 194.00978837  
Axis 0.18534914 -0.62533104 0.75802823  
Axis point 18.57115180 211.97461864 0.00000000  
Rotation angle (degrees) 143.37150914  
Shift along axis 63.27664874  
  

> vop flip #1

Opened cryosparc_P605_J23_class_00_final_volume.mrc z flip as #2, grid size
128,128,128, pixel 2.9, shown at step 1, values float32  

> fitmap #16 inMap #2

Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) using 35830 atoms  
average map value = 0.1442, steps = 120  
shifted from previous position = 22.3  
rotated from previous position = 13.4 degrees  
atoms outside contour = 24593, contour level = 0.18871  
  
Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
-0.76940695 -0.57566756 -0.27680282 185.63600251  
0.42188903 -0.13261273 -0.89689660 187.73379770  
0.47960670 -0.80685855 0.34490098 171.96023011  
Axis 0.07173535 -0.60264858 0.79477590  
Axis point 38.45425971 199.68363632 0.00000000  
Rotation angle (degrees) 141.12885946  
Shift along axis 36.84900469  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.20753,0.35524,-0.91145,232.73,-0.91446,-0.26044,-0.30972,368.73,-0.3474,0.89776,0.2708,112.41,#16,-0.69418,-0.24771,0.67584,183.35,-0.66486,-0.13916,-0.7339,188.3,0.27584,-0.95879,-0.06809,173.1,#17,-0.16546,0.59462,0.78679,200.35,-0.97326,-0.22734,-0.032866,180.69,0.15933,-0.77119,0.61634,192.29

> view matrix models
> #14,0.87363,0.2703,0.40461,-4.3424,0.4065,0.05162,-0.91219,232.85,-0.26745,0.96139,-0.064779,135.31,#16,0.7382,0.11433,0.66482,182.59,-0.67451,0.11071,0.72992,184.5,0.0098543,-0.98725,0.15884,172.66,#17,0.99092,0.13415,-0.0092278,189.53,-0.10914,0.84245,0.5276,194.59,0.078551,-0.5218,0.84944,196.43

> view matrix models
> #14,0.86818,-0.2967,0.39778,46.324,0.47562,0.2688,-0.83757,195.92,0.14158,0.91636,0.37449,32.278,#16,0.6312,0.62944,0.45321,184.13,-0.54308,-0.058522,0.83764,183.79,0.55376,-0.77484,0.3049,172.06,#17,0.79169,0.37475,-0.48249,176.8,0.056498,0.74147,0.6686,199.04,0.60831,-0.55658,0.56584,192.76

> volume #2 level 0.08303

> view matrix models
> #14,0.88761,-0.18414,0.42218,31.08,0.45951,0.41684,-0.78428,179.04,-0.031558,0.89013,0.45461,48.68,#16,0.68024,0.5349,0.50116,183.79,-0.47455,-0.1997,0.85727,183.44,0.55864,-0.82097,0.11799,172.51,#17,0.85733,0.32231,-0.40137,179.18,0.12,0.6331,0.76471,201.94,0.50058,-0.70378,0.5041,191.26

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.88761,-0.18414,0.42218,32.772,0.45951,0.41684,-0.78428,182.06,-0.031558,0.89013,0.45461,51.466,#16,0.68024,0.5349,0.50116,185.49,-0.47455,-0.1997,0.85727,186.45,0.55864,-0.82097,0.11799,175.3,#17,0.85733,0.32231,-0.40137,180.87,0.12,0.6331,0.76471,204.95,0.50058,-0.70378,0.5041,194.05

> view matrix models
> #14,0.88761,-0.18414,0.42218,23.115,0.45951,0.41684,-0.78428,185.33,-0.031558,0.89013,0.45461,47.88,#16,0.68024,0.5349,0.50116,175.83,-0.47455,-0.1997,0.85727,189.72,0.55864,-0.82097,0.11799,171.71,#17,0.85733,0.32231,-0.40137,171.21,0.12,0.6331,0.76471,208.23,0.50058,-0.70378,0.5041,190.46

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.86299,-0.34605,0.3681,46.814,0.49877,0.46748,-0.72986,169.24,0.080484,0.81346,0.57603,25.104,#16,0.59358,0.67207,0.44269,176.3,-0.40157,-0.22936,0.88664,189.52,0.69743,-0.70407,0.13374,171.72,#17,0.75616,0.41265,-0.50788,167.94,0.19549,0.59823,0.77712,209.02,0.62451,-0.68691,0.37168,188

> view matrix models
> #14,0.86747,-0.34312,0.36023,46.873,0.49054,0.46937,-0.7342,170.7,0.082836,0.81361,0.57548,24.836,#16,0.58855,0.67116,0.45072,176.28,-0.40824,-0.23449,0.88225,189.53,0.69782,-0.70325,0.13598,171.72,#17,0.75683,0.41946,-0.50125,168.07,0.18739,0.59546,0.78123,209.08,0.62617,-0.68519,0.37206,188.01

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.86747,-0.34312,0.36023,51.075,0.49054,0.46937,-0.7342,166.39,0.082836,0.81361,0.57548,26.91,#16,0.58855,0.67116,0.45072,180.49,-0.40824,-0.23449,0.88225,185.21,0.69782,-0.70325,0.13598,173.79,#17,0.75683,0.41946,-0.50125,172.27,0.18739,0.59546,0.78123,204.77,0.62617,-0.68519,0.37206,190.08

> fitmap #16 inMap #2

Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) using 35830 atoms  
average map value = 0.1527, steps = 196  
shifted from previous position = 10.3  
rotated from previous position = 52.9 degrees  
atoms outside contour = 14387, contour level = 0.083025  
  
Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.79116208 0.47083690 -0.39035262 189.77020175  
0.21834466 0.37874623 0.89937584 187.56612037  
0.57130392 -0.79678347 0.19684494 171.28797258  
Axis -0.86270884 -0.48912245 -0.12842384  
Axis point 0.00000000 134.63132621 35.34050310  
Rotation angle (degrees) 79.43349915  
Shift along axis -277.45669015  
  

> volume #2 level 0.1415

> select subtract #16

10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 5 models selected  

> select add #16

46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 6 models selected  

> select subtract #17

46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 4 models selected  

> select subtract #14

35830 atoms, 36512 bonds, 4496 residues, 1 model selected  

> color bfactor sel

35830 atoms, 4496 residues, atom bfactor range 19 to 94.1  

> hide #16 models

> show #!14 models

> fitmap #14 inMap #2

Fit molecule 6qwl (#14) to map cryosparc_P605_J23_class_00_final_volume.mrc z
flip (#2) using 10408 atoms  
average map value = 0.2296, steps = 172  
shifted from previous position = 24.9  
rotated from previous position = 29.8 degrees  
atoms outside contour = 3623, contour level = 0.14146  
  
Position of 6qwl (#14) relative to
cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.84866127 0.13336671 0.51184702 -23.71765426  
0.43643228 0.37015506 -0.82006835 194.27778117  
-0.29883258 0.91934680 0.25593073 86.01589402  
Axis 0.89529654 0.41726591 0.15599126  
Axis point 0.00000000 49.60474067 161.53558806  
Rotation angle (degrees) 76.26842446  
Shift along axis 73.24888814  
  

> select subtract #16

Nothing selected  

> select add #14

10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected  

> show #16 models

> hide #16 models

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.87735,0.17176,0.44806,-23.989,0.34241,0.43009,-0.83533,201.02,-0.33618,0.8863,0.31853,86.902

> volume #2 level 0.1999

> view matrix models
> #14,-0.97442,-0.15226,0.16529,311.43,-0.082037,-0.44376,-0.89238,385.87,0.20922,-0.88312,0.41992,239.92

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.97442,-0.15226,0.16529,227.79,-0.082037,-0.44376,-0.89238,431.33,0.20922,-0.88312,0.41992,236.53

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.12974,-0.15321,-0.97964,272.18,0.89189,0.41365,-0.18281,83.262,0.43323,-0.89745,0.082977,254.85

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.12974,-0.15321,-0.97964,351.43,0.89189,0.41365,-0.18281,35.006,0.43323,-0.89745,0.082977,278.16

> view matrix models
> #14,-0.12974,-0.15321,-0.97964,358.16,0.89189,0.41365,-0.18281,31.031,0.43323,-0.89745,0.082977,268.4

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.003597,-0.27496,-0.96145,355.08,0.85574,0.49662,-0.14523,19.411,0.5174,-0.82327,0.23351,225.91

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.003597,-0.27496,-0.96145,354.62,0.85574,0.49662,-0.14523,17.032,0.5174,-0.82327,0.23351,217.48

> fitmap #14 inMap #2

Fit molecule 6qwl (#14) to map cryosparc_P605_J23_class_00_final_volume.mrc z
flip (#2) using 10408 atoms  
average map value = 0.2172, steps = 100  
shifted from previous position = 8.52  
rotated from previous position = 14.8 degrees  
atoms outside contour = 5286, contour level = 0.1999  
  
Position of 6qwl (#14) relative to
cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.13567298 -0.47227038 -0.87094978 355.00638729  
0.86038618 0.49204153 -0.13278088 19.43382005  
0.49125194 -0.73133837 0.47309165 171.17570398  
Axis -0.29965963 -0.68196767 0.66717629  
Axis point 38.44526890 0.00000000 367.58717042  
Rotation angle (degrees) 87.11089207  
Shift along axis -5.42994726  
  

> fitmap #14 inMap #2

Fit molecule 6qwl (#14) to map cryosparc_P605_J23_class_00_final_volume.mrc z
flip (#2) using 10408 atoms  
average map value = 0.2172, steps = 44  
shifted from previous position = 0.0432  
rotated from previous position = 0.058 degrees  
atoms outside contour = 5294, contour level = 0.1999  
  
Position of 6qwl (#14) relative to
cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.13636012 -0.47157692 -0.87121818 354.83006149  
0.86025263 0.49250116 -0.13193943 19.24156614  
0.49129556 -0.73147646 0.47283281 171.21387534  
Axis -0.30015678 -0.68213925 0.66677729  
Axis point 38.31968328 0.00000000 367.40995255  
Rotation angle (degrees) 87.08542200  
Shift along axis -5.46855382  
  

> hide #!2 models

> show #16 models

> matchmaker #16 to #14

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6qwl, chain K (#14) with fold_lee_rdrp_trimer_dimer_model_0.cif,
chain C (#16), sequence alignment score = 3220.4  
RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs:
3.053)  
  

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.3317

> hide #!14 models

> show #!14 models

> hide #16 models

> volume #2 level 0.1962

> show #!17 models

> molmap #14 8

Opened 6qwl map 8 as #3, grid size 51,53,56, pixel 2.67, shown at level
0.0839, step 1, values float32  

> hide #!17 models

> hide #!14 models

> show #!14 models

> select subtract #14

Nothing selected  

> select add #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.12389,-0.51731,-0.84678,359.36,0.92551,0.36802,-0.089421,21.402,0.35789,-0.77263,0.52437,187.81

> fitmap #3 inMap #2

Fit map 6qwl map 8 in map cryosparc_P605_J23_class_00_final_volume.mrc z flip
using 12587 points  
correlation = 0.7629, correlation about mean = 0.09084, overlap = 759.9  
steps = 84, shift = 1.08, angle = 9.77 degrees  
  
Position of 6qwl map 8 (#3) relative to
cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.15606119 -0.44984957 -0.87936356 349.86982704  
0.85254165 0.51093661 -0.11007501 14.36108019  
0.49881623 -0.73251562 0.46325287 171.75362759  
Axis -0.31188241 -0.69055588 0.65258098  
Axis point 35.44588963 0.00000000 361.38339726  
Rotation angle (degrees) 86.26595020  
Shift along axis -6.95222053  
  

> hide #!14 models

> hide #!3 models

> show #16 models

> show #!14 models

> hide #!14 models

> show #!1 models

> hide #!2 models

> combine #14

> select subtract #3

Nothing selected  

> hide #16 models

> select add #4

10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.13636,-0.47158,-0.87122,406.48,0.86025,0.4925,-0.13194,-67.544,0.4913,-0.73148,0.47283,172.74

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.7157,-0.37195,-0.59113,469.87,0.59514,0.11815,-0.79489,111.74,0.3655,-0.9207,0.1368,262.37

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.7157,-0.37195,-0.59113,454.84,0.59514,0.11815,-0.79489,208.5,0.3655,-0.9207,0.1368,283.3

> view matrix models
> #4,-0.7157,-0.37195,-0.59113,419.53,0.59514,0.11815,-0.79489,213.45,0.3655,-0.9207,0.1368,289.75

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.69442,-0.3599,-0.6231,419.44,0.58127,0.22986,-0.78057,198.11,0.42415,-0.90423,0.04958,291.65

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.69442,-0.3599,-0.6231,418.63,0.58127,0.22986,-0.78057,183.26,0.42415,-0.90423,0.04958,291.57

> fitmap #4 inMap #1

Fit molecule copy of 6qwl (#4) to map
cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 10408 atoms  
average map value = 0.2096, steps = 144  
shifted from previous position = 6.47  
rotated from previous position = 64.2 degrees  
atoms outside contour = 4629, contour level = 0.18871  
  
Position of copy of 6qwl (#4) relative to
cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.14347824 -0.98911909 0.03251793 336.65894023  
0.42613730 -0.09140306 -0.90002915 264.97601036  
0.89320826 -0.11527749 0.43461489 61.69787383  
Axis 0.42814429 -0.46957486 0.77213465  
Axis point 25.50671173 281.72175705 0.00000000  
Rotation angle (degrees) 113.58650590  
Shift along axis 67.35159673  
  

> volume #1 level 0.3031

> volume #1 color #76765d80

> volume #1 color #807f6480

> volume #1 color #807f645d

> volume #1 color #d6d6d6

> volume #1 color silver

> volume #1 color #c0c0c08c

> volume #1 color #76d6ff

> volume #1 color #76d6ff43

> volume #1 color darkgrey

> volume #1 color #a9a9a987

> volume #1 color #a9a9a98f

> lighting soft

> lighting simple

> volume #1 level 0.2683

> fitmap #4 inMap #1

Fit molecule copy of 6qwl (#4) to map
cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 10408 atoms  
average map value = 0.2096, steps = 44  
shifted from previous position = 0.0604  
rotated from previous position = 0.0648 degrees  
atoms outside contour = 7386, contour level = 0.26829  
  
Position of copy of 6qwl (#4) relative to
cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.14358010 -0.98907322 0.03345021 336.54517646  
0.42657360 -0.09235260 -0.89972549 264.94152825  
0.89298360 -0.11491370 0.43517252 61.59581517  
Axis 0.42822749 -0.46899885 0.77243854  
Axis point 25.58148056 281.48695698 0.00000000  
Rotation angle (degrees) 113.60194188  
Shift along axis 67.43960578  
  

> combine #16

> matchmaker #5 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of 6qwl, chain K (#4) with copy of
fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#5), sequence alignment score
= 3220.4  
RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs:
3.053)  
  

> fitmap #5 inMap #1

Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#5) to map
cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 35830 atoms  
average map value = 0.08176, steps = 132  
shifted from previous position = 7.76  
rotated from previous position = 5.08 degrees  
atoms outside contour = 32465, contour level = 0.26829  
  
Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#5) relative to
cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.80899717 -0.29911248 -0.50601906 198.65812349  
-0.58098274 0.27603427 0.76567887 194.08321522  
-0.08934550 0.91342039 -0.39709013 277.46996867  
Axis 0.28178569 -0.79471666 -0.53760789  
Axis point 121.61319452 0.00000000 95.61507287  
Rotation angle (degrees) 164.80219121  
Shift along axis -247.43219487  
  

> hide #!4 models

> volume #1 level 0.1367

> open pdb:3J9B

Summary of feedback from opening 3J9B fetched from pdb  
---  
note | Fetching compressed mmCIF 3j9b from http://files.rcsb.org/download/3j9b.cif  
  
3j9b title:  
Electron cryo-microscopy of an RNA polymerase [more info...]  
  
Chain information for 3j9b #6  
---  
Chain | Description | UniProt  
A H | Polymerase | Q91R78_9INFA 259-716  
B I | RNA-directed RNA polymerase catalytic subunit | RDRP_I96A0 1-24  
C J | Polymerase basic protein 2 |   
D K | RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') |   
E | RNA (5'-R(*UP*UP*UP*UP*UP*A)-3') |   
L | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') |   
  

> matchmaker #!6 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of fold_lee_rdrp_trimer_dimer_model_0.cif, chain A (#5) with
3j9b, chain A (#6), sequence alignment score = 1181.1  
RMSD between 246 pruned atom pairs is 1.151 angstroms; (across all 454 pairs:
4.689)  
  

> hide #!6 models

> show #!6 models

> select add #6

23262 atoms, 23718 bonds, 31 pseudobonds, 3244 residues, 5 models selected  

> select clear

> select add #6

12854 atoms, 13050 bonds, 7 pseudobonds, 1974 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> hide #!1 models

> show #!1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> open /Users/oswanson/Downloads/cryosparc_P605_J45_class_00_final_volume.mrc

Opened cryosparc_P605_J45_class_00_final_volume.mrc as #7, grid size
256,256,256, pixel 1.45, shown at level 0.0414, step 1, values float32  

> transparency #7.1 50

> volume #7 level 0.1009

> volume #7 level 0.1726

> hide #5 models

> volume #7 level 0.1498

> show #5 models

> fitmap #5 inMap #7

Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#5) to map
cryosparc_P605_J45_class_00_final_volume.mrc (#7) using 35830 atoms  
average map value = 0.05264, steps = 764  
shifted from previous position = 14  
rotated from previous position = 10.2 degrees  
atoms outside contour = 30732, contour level = 0.14976  
  
Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#5) relative to
cryosparc_P605_J45_class_00_final_volume.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.72693585 -0.40409826 -0.55521965 189.47473641  
-0.68191939 0.32950002 0.65300511 201.23646391  
-0.08093334 0.85330788 -0.51508782 269.53556139  
Axis 0.34238374 -0.81071233 -0.47488830  
Axis point 122.28388606 0.00000000 100.44646883  
Rotation angle (degrees) 162.99158906  
Shift along axis -226.27109781  
  

> show #16 models

> select clear

> select add #16

35830 atoms, 36512 bonds, 4496 residues, 1 model selected  

> view matrix models
> #16,-0.80542,-0.1331,0.57757,92.095,0.12444,0.91477,0.38433,139.56,-0.5795,0.38142,-0.72021,113.29

> view matrix models
> #16,-0.80542,-0.1331,0.57757,165.41,0.12444,0.91477,0.38433,167.11,-0.5795,0.38142,-0.72021,104.45

> fitmap #16 inMap #7

Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
cryosparc_P605_J45_class_00_final_volume.mrc (#7) using 35830 atoms  
average map value = 0.05062, steps = 2000  
shifted from previous position = 25.2  
rotated from previous position = 30.1 degrees  
atoms outside contour = 31031, contour level = 0.14976  
  
Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
cryosparc_P605_J45_class_00_final_volume.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.45526558 -0.47379441 0.75382498 189.36681218  
0.00872221 0.84424206 0.53589109 169.24944743  
-0.89031296 0.25054779 -0.38022182 98.42982751  
Axis -0.16426646 0.94649747 0.27777521  
Axis point 126.23588556 0.00000000 -41.59599197  
Rotation angle (degrees) 119.71081820  
Shift along axis 156.42892503  
  

> fitmap #16 inMap #7

Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
cryosparc_P605_J45_class_00_final_volume.mrc (#7) using 35830 atoms  
average map value = 0.05056, steps = 2000  
shifted from previous position = 0.55  
rotated from previous position = 0.731 degrees  
atoms outside contour = 31068, contour level = 0.14976  
  
Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
cryosparc_P605_J45_class_00_final_volume.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.45390691 -0.47418558 0.75439814 189.45692177  
0.02001012 0.84100233 0.54066133 169.71982871  
-0.89082440 0.26050551 -0.37224826 98.18257195  
Axis -0.16095929 0.94523772 0.28393266  
Axis point 125.64106046 0.00000000 -42.66603170  
Rotation angle (degrees) 119.51006315  
Shift along axis 157.80797159  
  

> select clear

> ui mousemode right select

Drag select of 2294 residues, 7 cryosparc_P605_J45_class_00_final_volume.mrc  

> select up

21255 atoms, 21646 bonds, 2671 residues, 4 models selected  

> select up

35830 atoms, 36512 bonds, 4496 residues, 4 models selected  

> select up

71660 atoms, 73024 bonds, 8992 residues, 4 models selected  

> select down

35830 atoms, 36512 bonds, 4496 residues, 4 models selected  

> combine selection

Expected a keyword  

> combine sel name Lee_init

Remapping chain ID 'A' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'G'  
Remapping chain ID 'B' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'H'  
Remapping chain ID 'C' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'I'  
Remapping chain ID 'D' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'J'  
Remapping chain ID 'E' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'K'  
Remapping chain ID 'F' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'L'  

> hide #5 models

> hide #16 models

> select clear

> select #8/I:535

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 899 residues  

> select up

8410 atoms, 8550 bonds, 1056 residues, 1 model selected  

> select up

17915 atoms, 18256 bonds, 2248 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

Drag select of 1990 residues  

> select up

16641 atoms, 16952 bonds, 2086 residues, 1 model selected  

> select up

17915 atoms, 18256 bonds, 2248 residues, 1 model selected  

> select up

53745 atoms, 54768 bonds, 6744 residues, 1 model selected  

> select down

17915 atoms, 18256 bonds, 2248 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> color #8 bychain

> hide #!7 models

> show #!7 models

> select #8/L:270

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

130 atoms, 129 bonds, 16 residues, 1 model selected  

> select up

6170 atoms, 6275 bonds, 770 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> show #!4 models

> hide #!4 models

> show #!6 models

> hide #!6 models

> sequence chain #16/E #16/F #5/E #5/F #8/E #8/L

Alignment identifier is 1  

> select #16/E-F:770 #5/E-F:770 #8/E,L:770

42 atoms, 36 bonds, 6 residues, 3 models selected  

> select #16/E-F #5/E-F #8/E,L

37020 atoms, 37650 bonds, 4620 residues, 3 models selected  
. [ID: 1] region 6 chains [1-770] RMSD: 123.980  
  

> select clear

> hide #8 models

> show #8 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  

Window position QRect(2319,365 600x300) outside any known screen, using
primary screen  

OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  


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

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,13
      Model Number: Z1BP0006TLL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 13822.1.2

Software:

    System Software Overview:

      System Version: macOS 26.0.1 (25A362)
      Kernel Version: Darwin 25.0.0
      Time since boot: 26 days, 9 hours, 8 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2880 x 1864 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 4 weeks 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 Tom Goddard, 4 weeks ago

Resolution: → duplicate
Status: assigned → closed

The ChimeraX bug report panel said what we know about this crash:
"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."

The ChimeraX daily builds use a newer Qt version (6.9) and we have not seen this crash with this newer Qt.

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