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Opened 4 weeks ago
Last modified 4 weeks ago
#19299 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-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" : {
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"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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===== Log before crash start =====
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
> select up
1459 atoms, 1497 bonds, 181 residues, 1 model selected
> ui tool show "Color Actions"
> color sel blue
> color sel royal blue
> show #6 models
> hide #6 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #4 models
> select clear
> hide #2 models
> select #4/A:71
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
150 atoms, 151 bonds, 9 residues, 1 model selected
> select up
2813 atoms, 2852 bonds, 174 residues, 1 model selected
> color sel dark sea green
> color sel olive drab
> color sel medium sea green
> color sel forest green
> select clear
> show #5 models
> hide #4 models
> select #5/A:70
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
155 atoms, 156 bonds, 9 residues, 1 model selected
> select up
2845 atoms, 2882 bonds, 174 residues, 1 model selected
> color sel sienna
> color sel indian red
> color sel saddle brown
> color sel maroon
> select clear
> hide #5 models
> show #6 models
> show #7 models
> hide #6 models
> select #7/G:81
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #7/H:21
28 atoms, 26 bonds, 2 residues, 1 model selected
> select up
183 atoms, 182 bonds, 12 residues, 1 model selected
> select up
3494 atoms, 3537 bonds, 236 residues, 1 model selected
> color sel silver
> select #7/A:104
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
147 atoms, 147 bonds, 8 residues, 1 model selected
> select up
2806 atoms, 2845 bonds, 174 residues, 1 model selected
> color sel midnight blue
> select clear
> show #!1 models
> hide #7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #!1 models
> show #6 models
> hide #6 models
> show #!1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #4 models
> show #5 models
> show #!3 models
> hide #!3 models
> show #2 models
> hide #2 models
> hide #4 models
> hide #!1 models
> show #2 models
> show #6 models
> hide #5 models
> hide #2 models
> show #5 models
> show #7 models
> hide #6 models
> show #6 models
> show #4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> tile
4 models tiled
> hide #5 models
> show #5 models
> select clear
> select #5/G:124
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #5/H:67
25 atoms, 23 bonds, 2 residues, 1 model selected
> select up
161 atoms, 160 bonds, 11 residues, 1 model selected
> select up
3494 atoms, 3537 bonds, 236 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4,6-7#!1 to #5 & 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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #4 models
> hide #6 models
> hide #7 models
> show #7 models
> matchmaker #4,6-7#!1 to #5 & 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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #7 models
> show #6 models
> matchmaker #4,6-7#!1 to #5 & 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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #6 models
> show #4 models
> matchmaker #4,6-7#!1 to #5 & 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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #4 models
> show #!1 models
> matchmaker #4,6-7#!1 to #5 & 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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> matchmaker #4,6-7#!1 to #5 & 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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #5 models
> select #1/L:106
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/H:112C
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #1/H:110
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add #1/H:59
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #1/H:35
35 atoms, 30 bonds, 5 residues, 1 model selected
> select up
307 atoms, 318 bonds, 39 residues, 1 model selected
> select up
3334 atoms, 3411 bonds, 444 residues, 1 model selected
> select down
307 atoms, 318 bonds, 39 residues, 1 model selected
> select add #1/H:38
319 atoms, 330 bonds, 40 residues, 1 model selected
> select up
331 atoms, 344 bonds, 41 residues, 1 model selected
> select add #1/H:40
341 atoms, 354 bonds, 42 residues, 1 model selected
> select add #1/H:67
353 atoms, 366 bonds, 43 residues, 1 model selected
> select up
417 atoms, 434 bonds, 50 residues, 1 model selected
> show #5 models
> matchmaker #!1 & sel to #5 & sel
No 'to' model specified
> matchmaker #!1 & sel to #5 & sel
No 'to' model specified
> matchmaker #!1 & sel to #5 & sel
No 'to' model specified
> matchmaker #!1 & sel 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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 227.4
RMSD between 42 pruned atom pairs is 0.783 angstroms; (across all 42 pairs:
0.783)
> select add #5/G:109
428 atoms, 444 bonds, 51 residues, 2 models selected
> select up
744 atoms, 770 bonds, 72 residues, 2 models selected
> select add #5/G:72
768 atoms, 793 bonds, 73 residues, 2 models selected
> select up
841 atoms, 866 bonds, 78 residues, 2 models selected
> select up
5259 atoms, 5364 bonds, 570 residues, 2 models selected
> select down
841 atoms, 866 bonds, 78 residues, 2 models selected
> select add #5/G:80
862 atoms, 887 bonds, 79 residues, 2 models selected
> select up
937 atoms, 962 bonds, 84 residues, 2 models selected
> select add #5/G:75
948 atoms, 972 bonds, 85 residues, 2 models selected
> select up
992 atoms, 1018 bonds, 88 residues, 2 models selected
> matchmaker #!1 & sel 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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 227.4
RMSD between 42 pruned atom pairs is 0.783 angstroms; (across all 42 pairs:
0.783)
> select add #5/G:56
999 atoms, 1024 bonds, 89 residues, 2 models selected
> select subtract #5/G:56
992 atoms, 1018 bonds, 88 residues, 2 models selected
> select clear
> select #1/H:111C
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #5/G:102
31 atoms, 30 bonds, 2 residues, 2 models selected
> select up
508 atoms, 526 bonds, 44 residues, 2 models selected
> matchmaker #!1 & sel to #5 & 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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 121.6
RMSD between 22 pruned atom pairs is 0.765 angstroms; (across all 22 pairs:
0.765)
> matchmaker #!1 & sel to #5 & 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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 121.6
RMSD between 22 pruned atom pairs is 0.765 angstroms; (across all 22 pairs:
0.765)
Desktop color scheme is dark
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(2345,363 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.
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.
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.
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.
Desktop color scheme is light
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/gui.py", line 873, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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/gui.py", line 172, in _update_color_scheme
self.session.logger.status(msg)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
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.
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.
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.
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.
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.
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.
Desktop color scheme is light
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/gui.py", line 873, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
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.
> show #2 models
> hide #!1 models
> hide #5 models
> select add #1
4974 atoms, 5093 bonds, 7 pseudobonds, 630 residues, 4 models selected
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/model_panel/tool.py", line 475, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 120, in select_add
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select add #5
10986 atoms, 11176 bonds, 7 pseudobonds, 1018 residues, 4 models selected
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/model_panel/tool.py", line 475, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 120, in select_add
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select subtract #1
6339 atoms, 6419 bonds, 410 residues, 1 model selected
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/model_panel/tool.py", line 475, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 132, in select_subtract
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select subtract #5
Nothing selected
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/model_panel/tool.py", line 475, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 132, in select_subtract
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> view orient
> hide #2 models
> show #!1 models
> view orient
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.
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.
> show #4 models
> hide #4 models
> show #5 models
> hide #!1 models
> show #6 models
> show #7 models
> show #4 models
> show #!1 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,)
)
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.
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.
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.
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.
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/gui.py", line 172, in _update_color_scheme
self.session.logger.status(msg)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
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.
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.
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.
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.
Desktop color scheme is light
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/gui.py", line 873, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
> hide #!1 models
> hide #4 models
> hide #6 models
> hide #7 models
> show #6 models
> hide #6 models
> select clear
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/mouse_modes/mousemodes.py", line 656, in
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select
select_pick(session, pick, mode)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 227, in select_pick
session.logger.status('cleared selection')
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select #5/H:39
17 atoms, 16 bonds, 1 residue, 1 model selected
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/mouse_modes/mousemodes.py", line 656, in
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select
select_pick(session, pick, mode)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 241, in select_pick
run(session, 'select %s' % spec)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 62, in select
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select add #5/G:93
33 atoms, 31 bonds, 2 residues, 1 model selected
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/mouse_modes/mousemodes.py", line 656, in
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select
select_pick(session, pick, mode)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 245, in select_pick
run(session, 'select %s %s' % (operation, spec))
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 120, in select_add
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select up
218 atoms, 221 bonds, 13 residues, 1 model selected
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/gui.py", line 393, in forward_keystroke
run(self.session, 'select up')
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 145, in select_up
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select up
3494 atoms, 3537 bonds, 236 residues, 1 model selected
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/gui.py", line 393, in forward_keystroke
run(self.session, 'select up')
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 145, in select_up
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> show #6 models
> show #7 models
> show #4 models
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #4,6-7 to #5 & 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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
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/match_maker/tool.py", line 175, in
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 312, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 777, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 552, in match
logger.status("Matchmaker %s (#%s) with %s (#%s),"
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs
——— End of log from Fri Oct 31 13:49:15 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #4,6-7 to #5 & 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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
> select clear
> hide #5 models
> hide #4 models
> hide #6 models
> select #7/G:101
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
327 atoms, 336 bonds, 22 residues, 1 model selected
> select subtract #7/G:120
320 atoms, 329 bonds, 21 residues, 1 model selected
> select #7/G:23
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
118 atoms, 117 bonds, 8 residues, 1 model selected
> select up
1925 atoms, 1953 bonds, 126 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> select #7/H:22
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
87 atoms, 86 bonds, 6 residues, 1 model selected
> select up
1569 atoms, 1584 bonds, 110 residues, 1 model selected
> color sel cornsilk
> color sel floral white
> color sel light yellow
> select clear
Drag select of 1 residues
> select up
327 atoms, 336 bonds, 22 residues, 1 model selected
> select subtract #7/G:113
313 atoms, 321 bonds, 21 residues, 1 model selected
> select subtract #7/G:114
293 atoms, 300 bonds, 20 residues, 1 model selected
> select subtract #7/G:116
272 atoms, 277 bonds, 19 residues, 1 model selected
> select subtract #7/G:115
260 atoms, 266 bonds, 18 residues, 1 model selected
> select subtract #7/G:117
236 atoms, 240 bonds, 17 residues, 1 model selected
> select subtract #7/G:118
229 atoms, 233 bonds, 16 residues, 1 model selected
> select subtract #7/G:120
222 atoms, 226 bonds, 15 residues, 1 model selected
> select add #7/G:113
236 atoms, 239 bonds, 16 residues, 1 model selected
> select add #7/G:114
256 atoms, 259 bonds, 17 residues, 1 model selected
> select add #7/G:115
268 atoms, 270 bonds, 18 residues, 1 model selected
> select add #7/G:116
289 atoms, 291 bonds, 19 residues, 1 model selected
> select add #7/G:117
313 atoms, 316 bonds, 20 residues, 1 model selected
> select add #7/G:98
337 atoms, 339 bonds, 21 residues, 1 model selected
> select subtract #7/G:119
320 atoms, 323 bonds, 20 residues, 1 model selected
> select subtract #7/G:117
296 atoms, 298 bonds, 19 residues, 1 model selected
> color sel royal blue
> color sel cornflower blue
> color sel deep sky blue
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting shadows false
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> ui tool show "Side View"
> color sel deep sky blue
> color sel light steel blue
> color sel sky blue
> color sel light sky blue
> color sel light cyan
> color sel sky blue
> select clear
> select #7/A:70
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
155 atoms, 156 bonds, 9 residues, 1 model selected
> select up
2806 atoms, 2845 bonds, 174 residues, 1 model selected
> show #!1 models
> hide #!1 models
> matchmaker #!1 to #5 & sel
No 'to' model specified
> matchmaker #!1 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 design_start.pdb, chain A (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1), sequence alignment
score = 709.7
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
1.402)
> show #!1 models
> hide #!1 models
> show #5 models
> hide #7 models
> select #5/G:5
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
69 atoms, 68 bonds, 4 residues, 1 model selected
> select up
1925 atoms, 1953 bonds, 126 residues, 1 model selected
> select up
6339 atoms, 6419 bonds, 410 residues, 1 model selected
> select down
1925 atoms, 1953 bonds, 126 residues, 1 model selected
> matchmaker #!1 to #5 & 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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> show #!1 models
> hide #5 models
> show #6 models
> show #7 models
> hide #7 models
> hide #6 models
> show #6 models
> show #7 models
> select clear
> select #6/A:130
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
167 atoms, 170 bonds, 10 residues, 1 model selected
> select up
2815 atoms, 2853 bonds, 174 residues, 1 model selected
> color sel pink
> hide #!1 models
> hide #7 models
> select #6/G:5
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
69 atoms, 68 bonds, 4 residues, 1 model selected
> select up
1925 atoms, 1953 bonds, 126 residues, 1 model selected
> color sel pale goldenrod
> select #6/H:22
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
87 atoms, 86 bonds, 6 residues, 1 model selected
> select up
1569 atoms, 1584 bonds, 110 residues, 1 model selected
> color sel light yellow
> select clear
> select #6/G:102
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
327 atoms, 336 bonds, 22 residues, 1 model selected
> select #6/G:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/G:103
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
327 atoms, 336 bonds, 22 residues, 1 model selected
> select subtract #6/G:120
320 atoms, 329 bonds, 21 residues, 1 model selected
> select subtract #6/G:119
303 atoms, 312 bonds, 20 residues, 1 model selected
> select subtract #6/G:118
296 atoms, 305 bonds, 19 residues, 1 model selected
> select subtract #6/G:117
272 atoms, 279 bonds, 18 residues, 1 model selected
> color sel sky blue
> select clear
> show #7 models
> hide #7 models
> select #6/G:98
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel sky blue
> select clear
> show #7 models
> hide #6 models
> show #6 models
> hide #7 models
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> show #7 models
> hide #6 models
> show #6 models
> hide #7 models
> hide #6 models
> show #4 models
> show #6 models
> hide #6 models
> select #4/G:47
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
75 atoms, 76 bonds, 4 residues, 1 model selected
> select up
1925 atoms, 1953 bonds, 126 residues, 1 model selected
> color sel pale goldenrod
> select #4/H:87
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
124 atoms, 126 bonds, 9 residues, 1 model selected
> select up
1569 atoms, 1584 bonds, 110 residues, 1 model selected
> color sel light yellow
> select clear
> select #4/G:101
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
327 atoms, 336 bonds, 22 residues, 1 model selected
> select #4/G:98
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> select #4/G:109
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
327 atoms, 336 bonds, 22 residues, 1 model selected
> select add #4/G:98
351 atoms, 359 bonds, 23 residues, 1 model selected
> select subtract #4/G:116
330 atoms, 336 bonds, 22 residues, 1 model selected
> select subtract #4/G:117
306 atoms, 310 bonds, 21 residues, 1 model selected
> select subtract #4/G:119
289 atoms, 292 bonds, 20 residues, 1 model selected
> select add #4/G:95
310 atoms, 313 bonds, 21 residues, 1 model selected
> select add #4/G:119
327 atoms, 329 bonds, 22 residues, 1 model selected
> select subtract #4/G:95
306 atoms, 308 bonds, 21 residues, 1 model selected
> select subtract #4/G:118
299 atoms, 302 bonds, 20 residues, 1 model selected
> select subtract #4/G:119
282 atoms, 286 bonds, 19 residues, 1 model selected
> select subtract #4/G:120
275 atoms, 280 bonds, 18 residues, 1 model selected
> color sel sky blue
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> select clear
> show #6 models
> hide #6 models
> show #!1 models
> show #6 models
> show #7 models
> hide #4 models
> hide #6 models
> show #6 models
> hide #!1 models
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> hide #7 models
> show #4 models
> hide #6 models
> show #6 models
> hide #4 models
> show #7 models
> hide #6 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #6 models
> select clear
> select #6/A:76
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
178 atoms, 180 bonds, 11 residues, 1 model selected
> select up
2815 atoms, 2853 bonds, 174 residues, 1 model selected
> select up
6309 atoms, 6390 bonds, 410 residues, 1 model selected
> select down
2815 atoms, 2853 bonds, 174 residues, 1 model selected
> matchmaker #7 to #6 & 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 RMSD4_NNK1.pdb, chain A (#6) with RMSD6_NNK1.pdb, chain A (#7),
sequence alignment score = 841.6
RMSD between 174 pruned atom pairs is 0.233 angstroms; (across all 174 pairs:
0.233)
> select clear
> hide #7 models
> hide #6 models
> show #7 models
> show #6 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> hide #7 models
> select clear
> select #6/G:105
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
327 atoms, 336 bonds, 22 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true color #ffd479 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
98 contacts
atom1 atom2 overlap distance
RMSD4_NNK1.pdb #6/G GLY 110 O RMSD4_NNK1.pdb #6/H LEU 34 3HD1 0.347 2.133
RMSD4_NNK1.pdb #6/G ASP 107 H RMSD4_NNK1.pdb #6/A GLU 79 OE1 0.259 1.821
RMSD4_NNK1.pdb #6/G PHE 114 H RMSD4_NNK1.pdb #6/H TYR 38 OH 0.241 1.859
RMSD4_NNK1.pdb #6/G PHE 114 H RMSD4_NNK1.pdb #6/H LEU 48 2HD1 0.178 1.822
RMSD4_NNK1.pdb #6/G PRO 112 O RMSD4_NNK1.pdb #6/H TYR 38 HH 0.172 1.908
RMSD4_NNK1.pdb #6/G TYR 111 CE2 RMSD4_NNK1.pdb #6/H LEU 34 CD2 0.152 3.248
RMSD4_NNK1.pdb #6/G TYR 106 CD2 RMSD4_NNK1.pdb #6/A LEU 70 1HD2 0.132 2.568
RMSD4_NNK1.pdb #6/G ASP 115 OD1 RMSD4_NNK1.pdb #6/H TYR 51 HH 0.130 1.950
RMSD4_NNK1.pdb #6/G GLY 110 O RMSD4_NNK1.pdb #6/H LEU 34 CD1 0.120 3.060
RMSD4_NNK1.pdb #6/G ASP 115 OD1 RMSD4_NNK1.pdb #6/H LEU 48 3HD1 0.112 2.368
RMSD4_NNK1.pdb #6/G TYR 111 CE2 RMSD4_NNK1.pdb #6/H LEU 34 1HD2 0.104 2.596
RMSD4_NNK1.pdb #6/G GLY 110 O RMSD4_NNK1.pdb #6/H TYR 93 1HB 0.064 2.416
RMSD4_NNK1.pdb #6/G TYR 111 OH RMSD4_NNK1.pdb #6/A VAL 77 3HG1 0.048 2.452
RMSD4_NNK1.pdb #6/G PHE 114 HD1 RMSD4_NNK1.pdb #6/H TYR 38 OH 0.047 2.453
RMSD4_NNK1.pdb #6/G ASP 115 CG RMSD4_NNK1.pdb #6/H TYR 51 OH 0.031 3.169
RMSD4_NNK1.pdb #6/G TRP 117 CZ3 RMSD4_NNK1.pdb #6/H PRO 46 CG 0.022 3.378
RMSD4_NNK1.pdb #6/G PHE 114 H RMSD4_NNK1.pdb #6/H LEU 48 CD1 0.008 2.692
RMSD4_NNK1.pdb #6/G PHE 114 CD1 RMSD4_NNK1.pdb #6/H TYR 38 OH -0.013 3.213
RMSD4_NNK1.pdb #6/G TRP 117 CE3 RMSD4_NNK1.pdb #6/H PRO 46 CG -0.014 3.414
RMSD4_NNK1.pdb #6/G TYR 106 CD2 RMSD4_NNK1.pdb #6/A LEU 70 CD2 -0.018 3.418
RMSD4_NNK1.pdb #6/G TYR 111 CD2 RMSD4_NNK1.pdb #6/H LEU 34 CD2 -0.019 3.419
RMSD4_NNK1.pdb #6/G TYR 111 CD2 RMSD4_NNK1.pdb #6/H LEU 34 2HD2 -0.019 2.719
RMSD4_NNK1.pdb #6/G PHE 114 N RMSD4_NNK1.pdb #6/H LEU 48 2HD1 -0.033 2.658
RMSD4_NNK1.pdb #6/G PHE 114 O RMSD4_NNK1.pdb #6/H TYR 38 HE2 -0.033 2.513
RMSD4_NNK1.pdb #6/G ASP 115 OD1 RMSD4_NNK1.pdb #6/H TYR 51 OH -0.033 2.613
RMSD4_NNK1.pdb #6/G PHE 114 N RMSD4_NNK1.pdb #6/H TYR 38 OH -0.042 2.767
RMSD4_NNK1.pdb #6/G TRP 117 CD2 RMSD4_NNK1.pdb #6/H PRO 46 1HG -0.046 2.746
RMSD4_NNK1.pdb #6/G ASP 115 CG RMSD4_NNK1.pdb #6/H TYR 51 HH -0.065 2.765
RMSD4_NNK1.pdb #6/G PHE 114 CE1 RMSD4_NNK1.pdb #6/H PHE 101 HZ -0.082 2.782
RMSD4_NNK1.pdb #6/G TYR 105 CE2 RMSD4_NNK1.pdb #6/A LEU 36 1HD2 -0.083 2.783
RMSD4_NNK1.pdb #6/G TYR 111 HH RMSD4_NNK1.pdb #6/A VAL 77 3HG1 -0.085 2.085
RMSD4_NNK1.pdb #6/G PHE 114 HE1 RMSD4_NNK1.pdb #6/H PHE 101 HZ -0.093 2.093
RMSD4_NNK1.pdb #6/G ASP 107 H RMSD4_NNK1.pdb #6/A GLU 79 CD -0.093 2.793
RMSD4_NNK1.pdb #6/G TRP 117 CE3 RMSD4_NNK1.pdb #6/H PRO 46 1HG -0.104 2.804
RMSD4_NNK1.pdb #6/G ASP 107 N RMSD4_NNK1.pdb #6/A GLU 79 OE1 -0.107 2.812
RMSD4_NNK1.pdb #6/G TYR 105 OH RMSD4_NNK1.pdb #6/A VAL 41 3HG1 -0.112 2.612
RMSD4_NNK1.pdb #6/G TYR 105 HE2 RMSD4_NNK1.pdb #6/A LEU 36 1HD2 -0.122 2.122
RMSD4_NNK1.pdb #6/G PHE 114 N RMSD4_NNK1.pdb #6/H LEU 48 CD1 -0.134 3.459
RMSD4_NNK1.pdb #6/G TYR 105 HE2 RMSD4_NNK1.pdb #6/A VAL 41 2HG2 -0.140 2.140
RMSD4_NNK1.pdb #6/G TYR 111 CZ RMSD4_NNK1.pdb #6/H LEU 34 1HD2 -0.146 2.846
RMSD4_NNK1.pdb #6/G GLY 110 CA RMSD4_NNK1.pdb #6/H TYR 93 CD1 -0.152 3.552
RMSD4_NNK1.pdb #6/G GLY 110 C RMSD4_NNK1.pdb #6/H LEU 34 3HD1 -0.156 2.856
RMSD4_NNK1.pdb #6/G PHE 114 HD1 RMSD4_NNK1.pdb #6/H TYR 38 CZ -0.169 2.869
RMSD4_NNK1.pdb #6/G TRP 117 CZ3 RMSD4_NNK1.pdb #6/H PRO 46 2HG -0.173 2.873
RMSD4_NNK1.pdb #6/G TRP 117 CE2 RMSD4_NNK1.pdb #6/H PRO 46 1HG -0.174 2.874
RMSD4_NNK1.pdb #6/G TYR 105 CE2 RMSD4_NNK1.pdb #6/A LEU 36 CD2 -0.174 3.574
RMSD4_NNK1.pdb #6/G GLY 110 O RMSD4_NNK1.pdb #6/H TYR 93 CB -0.182 3.362
RMSD4_NNK1.pdb #6/G TYR 111 OH RMSD4_NNK1.pdb #6/A VAL 77 CG1 -0.191 3.391
RMSD4_NNK1.pdb #6/G TYR 105 CD1 RMSD4_NNK1.pdb #6/A MET 49 CE -0.196 3.596
RMSD4_NNK1.pdb #6/G PRO 112 1HG RMSD4_NNK1.pdb #6/H SER 36 HG -0.205 2.205
RMSD4_NNK1.pdb #6/G PRO 112 O RMSD4_NNK1.pdb #6/H TYR 38 OH -0.208 2.788
RMSD4_NNK1.pdb #6/G ASN 113 OD1 RMSD4_NNK1.pdb #6/H TYR 51 CE1 -0.209 3.389
RMSD4_NNK1.pdb #6/G ASP 115 OD1 RMSD4_NNK1.pdb #6/H LEU 48 CD1 -0.215 3.395
RMSD4_NNK1.pdb #6/G GLY 110 2HA RMSD4_NNK1.pdb #6/H TYR 93 CE1 -0.217 2.917
RMSD4_NNK1.pdb #6/G TRP 117 CH2 RMSD4_NNK1.pdb #6/H PRO 46 CG -0.221 3.621
RMSD4_NNK1.pdb #6/G PRO 112 C RMSD4_NNK1.pdb #6/H TYR 38 HH -0.222 2.922
RMSD4_NNK1.pdb #6/G TYR 106 1HB RMSD4_NNK1.pdb #6/A GLU 79 OE1 -0.235 2.715
RMSD4_NNK1.pdb #6/G TYR 106 OH RMSD4_NNK1.pdb #6/A TYR 72 CD2 -0.240 3.440
RMSD4_NNK1.pdb #6/G PRO 112 1HG RMSD4_NNK1.pdb #6/H SER 36 OG -0.249 2.749
RMSD4_NNK1.pdb #6/G GLY 110 2HA RMSD4_NNK1.pdb #6/H TYR 93 CD1 -0.250 2.950
RMSD4_NNK1.pdb #6/G TYR 105 CE1 RMSD4_NNK1.pdb #6/A MET 49 SD -0.251 3.733
RMSD4_NNK1.pdb #6/G TYR 105 OH RMSD4_NNK1.pdb #6/A VAL 41 HA -0.257 2.757
RMSD4_NNK1.pdb #6/G PHE 114 CB RMSD4_NNK1.pdb #6/H TYR 38 OH -0.259 3.459
RMSD4_NNK1.pdb #6/G TRP 117 CZ3 RMSD4_NNK1.pdb #6/H PRO 46 1HG -0.276 2.976
RMSD4_NNK1.pdb #6/G ASP 107 CB RMSD4_NNK1.pdb #6/A GLU 79 OE1 -0.280 3.460
RMSD4_NNK1.pdb #6/G GLY 110 CA RMSD4_NNK1.pdb #6/H TYR 93 CE1 -0.281 3.681
RMSD4_NNK1.pdb #6/G TYR 111 CE2 RMSD4_NNK1.pdb #6/H LEU 34 2HD2 -0.282 2.982
RMSD4_NNK1.pdb #6/G ASN 113 HA RMSD4_NNK1.pdb #6/H LEU 48 CD1 -0.284 2.984
RMSD4_NNK1.pdb #6/G TRP 117 CD2 RMSD4_NNK1.pdb #6/H PRO 46 CG -0.287 3.687
RMSD4_NNK1.pdb #6/G TYR 111 HH RMSD4_NNK1.pdb #6/A VAL 77 CG1 -0.297 2.997
RMSD4_NNK1.pdb #6/G PHE 114 H RMSD4_NNK1.pdb #6/H TYR 38 HH -0.321 2.321
RMSD4_NNK1.pdb #6/G TYR 111 CZ RMSD4_NNK1.pdb #6/H LEU 34 CD2 -0.328 3.728
RMSD4_NNK1.pdb #6/G TYR 106 OH RMSD4_NNK1.pdb #6/A TYR 72 CE2 -0.329 3.529
RMSD4_NNK1.pdb #6/G TYR 106 CG RMSD4_NNK1.pdb #6/A LEU 70 1HD2 -0.332 3.032
RMSD4_NNK1.pdb #6/G TYR 105 CD1 RMSD4_NNK1.pdb #6/A MET 49 3HE -0.332 3.032
RMSD4_NNK1.pdb #6/G TYR 105 CG RMSD4_NNK1.pdb #6/A MET 49 CE -0.332 3.732
RMSD4_NNK1.pdb #6/G TRP 117 CE3 RMSD4_NNK1.pdb #6/H PRO 46 CD -0.334 3.734
RMSD4_NNK1.pdb #6/G PRO 112 O RMSD4_NNK1.pdb #6/H SER 36 HG -0.334 2.414
RMSD4_NNK1.pdb #6/G PHE 114 1HB RMSD4_NNK1.pdb #6/H TYR 38 OH -0.339 2.839
RMSD4_NNK1.pdb #6/G ASP 107 2HB RMSD4_NNK1.pdb #6/A GLU 79 OE1 -0.340 2.820
RMSD4_NNK1.pdb #6/G ASN 113 HA RMSD4_NNK1.pdb #6/H LEU 48 1HD1 -0.341 2.341
RMSD4_NNK1.pdb #6/G PHE 114 HE1 RMSD4_NNK1.pdb #6/H PHE 101 CZ -0.343 3.043
RMSD4_NNK1.pdb #6/G GLY 110 O RMSD4_NNK1.pdb #6/H TYR 93 CG -0.343 3.523
RMSD4_NNK1.pdb #6/G PHE 114 1HB RMSD4_NNK1.pdb #6/H TYR 38 CE2 -0.347 3.047
RMSD4_NNK1.pdb #6/G TYR 105 CE2 RMSD4_NNK1.pdb #6/A PHE 40 HE1 -0.349 3.049
RMSD4_NNK1.pdb #6/G TRP 117 HZ2 RMSD4_NNK1.pdb #6/H TYR 38 CE2 -0.360 3.060
RMSD4_NNK1.pdb #6/G TYR 105 HE2 RMSD4_NNK1.pdb #6/A LEU 36 CD2 -0.366 3.066
RMSD4_NNK1.pdb #6/G TRP 117 CE3 RMSD4_NNK1.pdb #6/H PRO 46 1HD -0.367 3.067
RMSD4_NNK1.pdb #6/G PHE 114 CA RMSD4_NNK1.pdb #6/H TYR 38 OH -0.368 3.568
RMSD4_NNK1.pdb #6/G TRP 117 CZ2 RMSD4_NNK1.pdb #6/H PRO 46 1HG -0.371 3.071
RMSD4_NNK1.pdb #6/G ASN 113 OD1 RMSD4_NNK1.pdb #6/H TYR 51 CD1 -0.372 3.552
RMSD4_NNK1.pdb #6/G PHE 114 H RMSD4_NNK1.pdb #6/H TYR 38 CZ -0.373 3.073
RMSD4_NNK1.pdb #6/G TYR 106 CE2 RMSD4_NNK1.pdb #6/A LEU 70 1HD2 -0.376 3.076
RMSD4_NNK1.pdb #6/G GLY 110 O RMSD4_NNK1.pdb #6/H TYR 93 CD1 -0.380 3.560
RMSD4_NNK1.pdb #6/G TYR 105 CZ RMSD4_NNK1.pdb #6/A MET 49 SD -0.388 3.870
RMSD4_NNK1.pdb #6/G TRP 117 CH2 RMSD4_NNK1.pdb #6/H PRO 46 2HG -0.391 3.091
RMSD4_NNK1.pdb #6/G GLY 110 C RMSD4_NNK1.pdb #6/H LEU 34 CD1 -0.398 3.798
RMSD4_NNK1.pdb #6/G TRP 117 CH2 RMSD4_NNK1.pdb #6/H PRO 46 1HG -0.399 3.099
98 contacts
> undo
> hide sel atoms
> select up
310 atoms, 302 bonds, 17 residues, 1 model selected
> hide sel atoms
> select add #6/G:111
331 atoms, 323 bonds, 18 residues, 1 model selected
> select up
1781 atoms, 1810 bonds, 112 residues, 1 model selected
> hide sel atoms
> select clear
> select #6/A:71
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
152 atoms, 154 bonds, 9 residues, 1 model selected
> select up
2815 atoms, 2853 bonds, 174 residues, 1 model selected
> contacts ignoreHiddenModels true color #ff2600
4408 contacts
> undo
> select #6/A:70
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
152 atoms, 154 bonds, 9 residues, 1 model selected
> select up
2815 atoms, 2853 bonds, 174 residues, 1 model selected
> contacts sel restrict cross ignoreHiddenModels true color #ff2600
57 contacts
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true color #ff2600 reveal true
57 contacts
> select up
400 atoms, 387 bonds, 24 residues, 1 model selected
> color sel byhetero
> show #!1 models
> show #7 models
> hide #7 models
> select #6/A:71
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
152 atoms, 154 bonds, 9 residues, 1 model selected
> select up
2815 atoms, 2853 bonds, 174 residues, 1 model selected
> matchmaker #!1 to #6 & 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 RMSD4_NNK1.pdb, chain A (#6) with
231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1), sequence alignment
score = 692.2
RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs:
1.442)
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #7 models
> select #7/A:70
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
155 atoms, 156 bonds, 9 residues, 1 model selected
> select up
2806 atoms, 2845 bonds, 174 residues, 1 model selected
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true color #ff2600 name contacts_RMSD6 reveal
> true
63 contacts
> select up
344 atoms, 338 bonds, 20 residues, 1 model selected
> color sel byhetero
> select clear
> hide #8 models
> hide #!7 models
> show #!1 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
> select up
4647 atoms, 4757 bonds, 608 residues, 1 model selected
> select down
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_poly310
> reveal true
64 contacts
> select up
237 atoms, 233 bonds, 27 residues, 1 model selected
> color sel byhetero
> hide #!1 models
> show #!1 models
> select clear
> select #1/H:126
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 5 residues, 1 model selected
> select up
1725 atoms, 1772 bonds, 228 residues, 1 model selected
> color sel pale goldenrod
> select #1/L:105
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
67 atoms, 69 bonds, 8 residues, 1 model selected
> select up
1609 atoms, 1639 bonds, 216 residues, 1 model selected
> color sel light yellow
> select clear
> select #1/H:111C
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
181 atoms, 190 bonds, 22 residues, 1 model selected
> select subtract #1/H:119
177 atoms, 185 bonds, 21 residues, 1 model selected
> select subtract #1/H:120
168 atoms, 176 bonds, 20 residues, 1 model selected
> select subtract #1/H:121
164 atoms, 173 bonds, 19 residues, 1 model selected
> select subtract #1/H:118
150 atoms, 157 bonds, 18 residues, 1 model selected
> select subtract #1/H:117
138 atoms, 144 bonds, 17 residues, 1 model selected
> color sel sky blue
> select add #1
4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected
> color sel byhetero
> select clear
> hide #!1 models
> show #!6 models
> select add #6
6309 atoms, 6390 bonds, 114 pseudobonds, 410 residues, 3 models selected
> select add #7
12609 atoms, 12772 bonds, 177 pseudobonds, 820 residues, 5 models selected
> show #!7 models
> select H
12439 atoms, 19 pseudobonds, 1640 residues, 7 models selected
> select clear
> select add #6
6309 atoms, 6390 bonds, 114 pseudobonds, 410 residues, 3 models selected
> select add #7
12609 atoms, 12772 bonds, 177 pseudobonds, 820 residues, 5 models selected
> select H
12439 atoms, 19 pseudobonds, 1640 residues, 7 models selected
> delete atoms (#!6-7 & sel)
> delete bonds (#!6-7 & sel)
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> show #!1 models
> show #2 models
> hide #2 models
> hide #!1 models
> select clear
> hide #!7 models
> show #!1 models
> hide #!6 models
> show #4 models
> hide #4 models
> show #!6 models
> hide #6.1 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> select #1/E:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
74 atoms, 76 bonds, 10 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
> show #5 models
> hide #5 models
> show #!6 models
> select clear
> show #!7 models
> hide #!7 models
> select #6/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
88 atoms, 91 bonds, 10 residues, 1 model selected
> select up
1416 atoms, 1454 bonds, 174 residues, 1 model selected
> show #8 models
> matchmaker #4 to #6 & 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 RMSD4_NNK1.pdb, chain A (#6) with Cluster2c_lib1.pdb, chain A (#4),
sequence alignment score = 808.5
RMSD between 174 pruned atom pairs is 0.223 angstroms; (across all 174 pairs:
0.223)
> hide #!6 models
> show #4 models
> hide #4 models
> hide #1.3 models
> hide #1.1 models
> show #1.3 models
> select #1/E:43
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
113 atoms, 114 bonds, 14 residues, 1 model selected
> select subtract #1/E:52
102 atoms, 102 bonds, 13 residues, 1 model selected
> select subtract #1/E:50
93 atoms, 92 bonds, 12 residues, 1 model selected
> select subtract #1/E:51
85 atoms, 85 bonds, 11 residues, 1 model selected
> select subtract #1/E:49
80 atoms, 80 bonds, 10 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/E:37
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/E:133
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/E:134
24 atoms, 22 bonds, 3 residues, 1 model selected
> select add #1/E:38
28 atoms, 25 bonds, 4 residues, 1 model selected
> select add #1/E:135
36 atoms, 32 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> hide #!1 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #6.1 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #6.1 models
> show #6.1 models
> hide #6.1 models
> hide #8 models
> show #8 models
> select add #8
21 pseudobonds, 1 model selected
> select add #6.1
42 pseudobonds, 2 models selected
> hide #!6 cartoons
> show #!6 cartoons
> hide #!6 atoms
> select clear
> hide #8 models
> show #!7 models
> select add #7
3204 atoms, 3286 bonds, 20 pseudobonds, 410 residues, 2 models selected
> hide sel atoms
> select clear
> hide #1.3 models
> hide #1.2 models
> hide #!6 models
> hide #7.1 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> lighting soft
> hide #!6 models
> lighting gentle
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> save view init_design
Cannot determine format for 'view'
> view name init_design
> view list
Named views: init_design, session-start
> show #!6 models
> hide #!7 models
> select #6/A:68
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
78 atoms, 80 bonds, 9 residues, 1 model selected
> select up
1416 atoms, 1454 bonds, 174 residues, 1 model selected
> color sel pink
> color sel pale violet red
> color sel dark sea green
> color sel salmon
> color sel dark salmon
> color sel coral
> color sel pale violet red
> select clear
> select #6/H:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 6 residues, 1 model selected
> select up
797 atoms, 812 bonds, 110 residues, 1 model selected
> color sel pale goldenrod
> select #6/G:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
33 atoms, 32 bonds, 4 residues, 1 model selected
> select up
990 atoms, 1018 bonds, 126 residues, 1 model selected
> color sel burly wood
> color sel goldenrod
> color sel dark goldenrod
> select clear
> select #6/G:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/G:107
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
181 atoms, 190 bonds, 22 residues, 1 model selected
> select subtract #6/G:115
173 atoms, 181 bonds, 21 residues, 1 model selected
> select add #6/G:97
178 atoms, 185 bonds, 22 residues, 1 model selected
> select subtract #6/G:97
173 atoms, 181 bonds, 21 residues, 1 model selected
> select subtract #6/G:116
161 atoms, 168 bonds, 20 residues, 1 model selected
> select subtract #6/G:117
147 atoms, 152 bonds, 19 residues, 1 model selected
> select subtract #6/G:118
143 atoms, 148 bonds, 18 residues, 1 model selected
> select subtract #6/G:119
134 atoms, 139 bonds, 17 residues, 1 model selected
> select subtract #6/G:120
130 atoms, 136 bonds, 16 residues, 1 model selected
> color sel navy
> color sel steel blue
> color sel teal
> color sel dark cyan
> select clear
> show #!7 models
> hide #!6 models
> select #7/H:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
33 atoms, 32 bonds, 4 residues, 1 model selected
> select up
797 atoms, 812 bonds, 110 residues, 1 model selected
> color sel pale goldenrod
> select #7/G:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 5 residues, 1 model selected
> select up
990 atoms, 1018 bonds, 126 residues, 1 model selected
> select up
3204 atoms, 3286 bonds, 410 residues, 1 model selected
> select down
990 atoms, 1018 bonds, 126 residues, 1 model selected
> color sel goldenrod
> select clear
> select #7/G:101
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
181 atoms, 190 bonds, 22 residues, 1 model selected
> select add #7/G:98
192 atoms, 200 bonds, 23 residues, 1 model selected
> select subtract #7/G:116
180 atoms, 186 bonds, 22 residues, 1 model selected
> select subtract #7/G:117
166 atoms, 170 bonds, 21 residues, 1 model selected
> select subtract #7/G:118
162 atoms, 166 bonds, 20 residues, 1 model selected
> select subtract #7/G:119
153 atoms, 157 bonds, 19 residues, 1 model selected
> select subtract #7/G:120
149 atoms, 154 bonds, 18 residues, 1 model selected
> color sel dark cyan
> select clear
> view list
Named views: init_design, session-start
> view init_design
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> select #7/A:68
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
77 atoms, 78 bonds, 9 residues, 1 model selected
> select up
1417 atoms, 1456 bonds, 174 residues, 1 model selected
> color sel olive drab
> color sel dark khaki
> color sel dark sea green
> color sel light green
> color sel pale green
> color sel green yellow
> color sel forest green
> color sel green
> color sel lime
> color sel lawn green
> color sel blue
> color sel medium blue
> color sel dark blue
> color sel medium sea green
> color sel sea green
> color sel olive drab
> color sel green
> color sel dark blue
> color sel navy
> color sel indigo
> color sel navy
> color sel dark blue
> color sel navy
> color sel medium blue
> select clear
> select #7/A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
90 atoms, 92 bonds, 11 residues, 1 model selected
> select up
1417 atoms, 1456 bonds, 174 residues, 1 model selected
> color sel dark blue
> select clear
> show #!6 models
> hide #!7 models
> select #6/A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
90 atoms, 92 bonds, 11 residues, 1 model selected
> select up
1416 atoms, 1454 bonds, 174 residues, 1 model selected
> show sel surfaces
> transparency sel 50
> transparency sel 70
> select clear
> show #!7 models
> hide #!6 models
> select #7/A:36
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
74 atoms, 76 bonds, 10 residues, 1 model selected
> select up
1417 atoms, 1456 bonds, 174 residues, 1 model selected
> volume style surface
No volumes specified
> select clear
> select #7/A:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
90 atoms, 92 bonds, 11 residues, 1 model selected
> select up
1417 atoms, 1456 bonds, 174 residues, 1 model selected
> show sel surfaces
> transparency sel 50
> transparency sel 70
> select clear
> show #!6 models
> hide #6.2 models
> show #6.2 models
> hide #6.2 models
> hide #!7 models
> show #!7 models
> show #6.2 models
> hide #!7 models
> hide #6.2 models
> show #6.2 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select #7/A:108
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
67 atoms, 67 bonds, 8 residues, 2 models selected
> select up
1417 atoms, 1456 bonds, 174 residues, 2 models selected
> show sel surfaces
> show #!6 models
> hide #!7 models
> select #6/A:168
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
99 atoms, 101 bonds, 13 residues, 2 models selected
> select up
1416 atoms, 1454 bonds, 174 residues, 2 models selected
> show sel surfaces
> select clear
> show #!7 models
> hide #!6 models
> select #7/A:45@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
129 atoms, 133 bonds, 14 residues, 2 models selected
> select up
1417 atoms, 1456 bonds, 174 residues, 2 models selected
> hide sel surfaces
> color sel slate gray
> color sel dim gray
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> color sel dark orange
> color sel chocolate
> color sel dark red
> color sel maroon
> show sel surfaces
> transparency sel 70
> select clear
> show #!6 models
> hide #!7 models
> show #5 models
> hide #5 models
> show #!7 models
> hide #!6 models
> select #7/A:46@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
129 atoms, 133 bonds, 14 residues, 2 models selected
> select up
1417 atoms, 1456 bonds, 174 residues, 2 models selected
> color sel medium aquamarine
> transparency sel 70
> select clear
> select #7/G:98
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
58 atoms, 59 bonds, 7 residues, 1 model selected
> select up
990 atoms, 1018 bonds, 126 residues, 1 model selected
> select down
58 atoms, 59 bonds, 7 residues, 1 model selected
> select #7/G:101
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
181 atoms, 190 bonds, 22 residues, 1 model selected
> select subtract #7/G:116
169 atoms, 176 bonds, 21 residues, 1 model selected
> select subtract #7/G:117
155 atoms, 160 bonds, 20 residues, 1 model selected
> select subtract #7/G:118
151 atoms, 156 bonds, 19 residues, 1 model selected
> select subtract #7/G:119
142 atoms, 147 bonds, 18 residues, 1 model selected
> select subtract #7/G:120
138 atoms, 144 bonds, 17 residues, 1 model selected
> select add #7/G:98
149 atoms, 154 bonds, 18 residues, 1 model selected
> color sel navy
> color sel dark blue
> color sel medium aquamarine
> color sel blue
> color sel medium blue
> color sel dark blue
> color sel navy
> color sel indigo
> color sel midnight blue
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> select #6/G:107
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
181 atoms, 190 bonds, 22 residues, 1 model selected
> select subtract #6/G:120
177 atoms, 186 bonds, 21 residues, 1 model selected
> select subtract #6/G:119
168 atoms, 177 bonds, 20 residues, 1 model selected
> select subtract #6/G:118
164 atoms, 173 bonds, 19 residues, 1 model selected
> select subtract #6/G:117
150 atoms, 157 bonds, 18 residues, 1 model selected
> select subtract #6/G:115
142 atoms, 148 bonds, 17 residues, 1 model selected
> select subtract #6/G:116
130 atoms, 136 bonds, 16 residues, 1 model selected
> color sel midnight blue
> show #!7 models
> hide #!7 models
> select clear
> show #!7 models
> hide #!6 models
> select #7/G:108
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/G:109
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/G:110
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #7/G:111
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #7/G:112
23 atoms, 22 bonds, 3 residues, 1 model selected
> select add #7/G:113
31 atoms, 29 bonds, 4 residues, 1 model selected
> select add #7/G:114
42 atoms, 40 bonds, 5 residues, 1 model selected
> select add #7/G:115
50 atoms, 47 bonds, 6 residues, 1 model selected
> select add #7/G:98
61 atoms, 57 bonds, 7 residues, 1 model selected
> select add #7/G:99
65 atoms, 60 bonds, 8 residues, 1 model selected
> select add #7/G:100
69 atoms, 63 bonds, 9 residues, 1 model selected
> select add #7/G:101
83 atoms, 78 bonds, 10 residues, 1 model selected
> select add #7/G:102
91 atoms, 85 bonds, 11 residues, 1 model selected
> select add #7/G:103
97 atoms, 90 bonds, 12 residues, 1 model selected
> select add #7/G:104
105 atoms, 97 bonds, 13 residues, 1 model selected
> color sel goldenrod
> select clear
> show #!6 models
> hide #!7 models
> name view init_des2
"init_des2": invalid atom specifier
> view name init_des2
> show #!7 models
> hide #!7 models
> select add #6/G:114
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #6/G:99
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #6/G:100
19 atoms, 17 bonds, 3 residues, 1 model selected
> select add #6/G:101
33 atoms, 32 bonds, 4 residues, 1 model selected
> select add #6/G:102
41 atoms, 39 bonds, 5 residues, 1 model selected
> select add #6/G:105
53 atoms, 51 bonds, 6 residues, 1 model selected
> select subtract #6/G:105
41 atoms, 39 bonds, 5 residues, 1 model selected
Drag select of RMSD4_NNK1.pdb_A SES surface, 12 of 169006 triangles, 1
residues
> select add #6/G:104
55 atoms, 46 bonds, 7 residues, 1 model selected
> select add #6/G:110
59 atoms, 49 bonds, 8 residues, 1 model selected
> select add #6/G:111
71 atoms, 61 bonds, 9 residues, 1 model selected
> select add #6/G:112
78 atoms, 68 bonds, 10 residues, 1 model selected
> select add #6/G:113
86 atoms, 75 bonds, 11 residues, 1 model selected
> color sel goldenrod
> select clear
> select #6/G:98
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
58 atoms, 59 bonds, 7 residues, 1 model selected
> select up
990 atoms, 1018 bonds, 126 residues, 1 model selected
> select subtract #6/G:109
984 atoms, 1011 bonds, 125 residues, 1 model selected
> select subtract #6/G:108
978 atoms, 1005 bonds, 124 residues, 1 model selected
> select subtract #6/G:107
970 atoms, 997 bonds, 123 residues, 1 model selected
> select subtract #6/G:105
958 atoms, 983 bonds, 122 residues, 1 model selected
> select subtract #6/G:106
946 atoms, 971 bonds, 121 residues, 1 model selected
> color sel goldenrod
> select clear
> view init_des2
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> view init_des2
> hide #!6 models
> select clear
> show #!6 models
> hide #!7 models
> save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
> show #!1 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #1.2 models
> show #1.3 models
> select add #1.3
64 pseudobonds, 1 model selected
> show #!1 atoms
> select up
71 pseudobonds, 3 models selected
> select #1/E:36@CA
1 atom, 1 residue, 1 model selected
> select #1/E:36
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/H:111B
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #1/E:50
29 atoms, 27 bonds, 1 pseudobond, 3 residues, 2 models selected
> select add #1/E:49
34 atoms, 31 bonds, 1 pseudobond, 4 residues, 2 models selected
> select add #1/H:111C
46 atoms, 43 bonds, 1 pseudobond, 5 residues, 2 models selected
> select add #1/H:109
60 atoms, 58 bonds, 1 pseudobond, 6 residues, 2 models selected
> select add #1/E:128
68 atoms, 65 bonds, 1 pseudobond, 7 residues, 2 models selected
> select add #1/E:68
76 atoms, 72 bonds, 1 pseudobond, 8 residues, 2 models selected
> select add #1/H:59
84 atoms, 79 bonds, 1 pseudobond, 9 residues, 2 models selected
> select add #1/H:62
90 atoms, 84 bonds, 1 pseudobond, 10 residues, 2 models selected
> select add #1/H:110
98 atoms, 91 bonds, 1 pseudobond, 11 residues, 2 models selected
> select add #1/E:72
105 atoms, 98 bonds, 1 pseudobond, 12 residues, 2 models selected
> select add #1/H:66
113 atoms, 105 bonds, 1 pseudobond, 13 residues, 2 models selected
> select add #1/E:74
122 atoms, 113 bonds, 1 pseudobond, 14 residues, 2 models selected
> select add #1/H:112D
130 atoms, 120 bonds, 1 pseudobond, 15 residues, 2 models selected
> select add #1/E:52
141 atoms, 131 bonds, 1 pseudobond, 16 residues, 2 models selected
> select add #1/H:111A
149 atoms, 138 bonds, 1 pseudobond, 17 residues, 2 models selected
> select ~sel & ##selected
4498 atoms, 4613 bonds, 41 pseudobonds, 591 residues, 4 models selected
> hide sel atoms
> undo
> redo
> select clear
> select #1/H:111C
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #1.3
64 pseudobonds, 1 model selected
> select add #1.2
70 pseudobonds, 2 models selected
> view orient
> select subtract #1.3
6 pseudobonds, 1 model selected
> select subtract #1.2
Nothing selected
> select #1/H:111C
12 atoms, 12 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
> style sel sphere
Changed 1725 atom styles
> select up
4647 atoms, 4757 bonds, 608 residues, 1 model selected
> style sel sphere
Changed 4647 atom styles
> style sel ball
Changed 4647 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 4647 atom styles
> hide #1.3 models
> open
> /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json
Failed opening file
/Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_model_0.cif
Chain information for fold_y513_gspy_uca3_notags_model_0.cif #9
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> open
> /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/poly310_uca3/fold_poly310_uca3_model_0.cif
Chain information for fold_poly310_uca3_model_0.cif #10
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> open
> /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/poly28_uca3/fold_poly28_uca3_model_0.cif
Chain information for fold_poly28_uca3_model_0.cif #11
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> ui tool show Matchmaker
> select #1/E:132
9 atoms, 8 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
> matchmaker #9-11 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
fold_y513_gspy_uca3_notags_model_0.cif, chain A (#9), sequence alignment score
= 675.4
RMSD between 152 pruned atom pairs is 0.658 angstroms; (across all 164 pairs:
1.656)
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
fold_poly310_uca3_model_0.cif, chain A (#10), sequence alignment score = 803.4
RMSD between 153 pruned atom pairs is 0.635 angstroms; (across all 164 pairs:
1.380)
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
fold_poly28_uca3_model_0.cif, chain A (#11), sequence alignment score = 766
RMSD between 157 pruned atom pairs is 0.633 angstroms; (across all 164 pairs:
1.406)
> hide #9 models
> hide #11 models
> show #11 models
> hide #10 models
> show #!6 models
> hide #!6 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #9 models
> hide #11 models
> show #2 models
> matchmaker #2 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 #5 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
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)
> show #5 models
> hide #2 models
> hide #9 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!1 models
> show #11 models
> hide #11 models
> show #9 models
> hide #9 models
> show #!1 models
> show #2 models
> hide #!1 models
> hide #5 models
> show #9 models
> hide #1.2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> select #9/A:85
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
93 atoms, 96 bonds, 11 residues, 1 model selected
> select up
1449 atoms, 1487 bonds, 184 residues, 1 model selected
> color bfactor sel
1449 atoms, 184 residues, atom bfactor range 15.7 to 97.6
> select clear
> select #9/A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
129 atoms, 134 bonds, 18 residues, 1 model selected
> select subtract #9/A:18
122 atoms, 126 bonds, 17 residues, 1 model selected
> select subtract #9/A:17
115 atoms, 118 bonds, 16 residues, 1 model selected
> select subtract #9/A:16
110 atoms, 113 bonds, 15 residues, 1 model selected
> select subtract #9/A:15
103 atoms, 105 bonds, 14 residues, 1 model selected
> select subtract #9/A:14
95 atoms, 97 bonds, 13 residues, 1 model selected
> select subtract #9/A:13
90 atoms, 92 bonds, 12 residues, 1 model selected
> hide sel cartoons
> select #9/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
93 atoms, 96 bonds, 11 residues, 1 model selected
> select up
1449 atoms, 1487 bonds, 184 residues, 1 model selected
> ui tool show Contacts
> 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
116 contacts
atom1 atom2 overlap distance
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 O 1.315 1.985
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CD1 0.992 2.188
fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CB 0.884 2.766
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 ND2 fold_y513_gspy_uca3_notags_model_0.cif #9/B ASN 113 ND2 0.667 2.613
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA 0.633 3.127
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2 0.606 2.914
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C 0.598 2.892
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 CA fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH 0.541 2.799
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 O 0.531 2.769
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O 0.504 2.156
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2 0.481 3.039
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2 0.470 3.170
fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CH2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD1 0.459 3.061
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH 0.413 2.287
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA 0.412 2.928
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2 0.393 3.127
fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CH2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE1 0.383 3.137
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 NE1 0.355 2.305
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE1 0.313 3.327
fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2 0.258 3.142
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2 0.199 3.441
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CZ 0.198 3.292
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1 0.193 3.147
fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 74 SD fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2 0.177 3.473
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C 0.135 3.355
fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1 0.116 3.374
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2 fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2 0.112 3.408
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ 0.093 3.157
fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1 fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CG 0.089 3.671
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ 0.084 3.286
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH 0.078 2.402
fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CZ2 0.067 3.573
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA 0.063 3.697
fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 ND1 fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1 0.055 3.465
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CD fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2 0.053 3.587
fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CZ2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD1 0.052 3.468
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 CB 0.044 3.716
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O 0.040 3.260
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 CD fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2 0.039 3.451
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 C 0.037 3.213
fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CG 0.035 3.345
fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 CZ fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2 0.033 3.337
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH 0.022 3.318
fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1 0.008 3.752
fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1 fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 OD2 -0.019 3.319
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CB fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1 -0.022 3.782
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CD1 -0.034 3.404
fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2 -0.048 3.688
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CA -0.055 3.815
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 N -0.060 3.580
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CZ3 -0.069 3.709
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 OH -0.088 3.428
fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CD2 fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1 -0.089 3.729
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2 -0.090 3.490
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CG fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1 -0.107 3.867
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH -0.120 3.460
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 27 CA -0.128 3.888
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C -0.128 3.198
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 N -0.140 3.420
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 N -0.140 3.660
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 89 CZ fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH -0.142 3.362
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1 -0.147 3.487
fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NE fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2 -0.147 3.547
fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CZ2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE1 -0.149 3.669
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 OE1 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2 -0.154 3.334
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B GLY 57 CA -0.158 3.918
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CG fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE2 -0.161 3.801
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CZ3 -0.165 3.805
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2 -0.167 3.687
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B ASN 113 ND2 -0.180 3.430
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CD fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1 -0.183 3.943
fold_y513_gspy_uca3_notags_model_0.cif #9/A ALA 13 CB fold_y513_gspy_uca3_notags_model_0.cif #9/C ASN 33 ND2 -0.184 3.704
fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 CE fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CB -0.186 3.946
fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 CB fold_y513_gspy_uca3_notags_model_0.cif #9/C GLU 52 OE2 -0.194 3.494
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CB -0.200 3.960
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 N -0.204 3.724
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CD fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O -0.208 3.508
fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH2 fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 CB -0.210 3.730
fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CZ2 -0.214 3.854
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 NE1 -0.215 3.465
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH -0.218 2.918
fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CE1 fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1 -0.219 3.859
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B GLY 57 CA -0.234 3.994
fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2 -0.237 3.767
fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1 fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CB -0.243 4.003
fold_y513_gspy_uca3_notags_model_0.cif #9/A ALA 5 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 O -0.254 3.554
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 CE1 -0.255 3.895
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 CA -0.257 3.777
fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH1 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 111 CE2 -0.262 3.662
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH -0.269 3.489
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 C -0.270 3.520
fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 9 O fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O -0.271 3.111
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE2 -0.272 3.912
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 OE1 fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2 -0.274 3.574
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 CD fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH -0.286 3.356
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CA fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 51 CE2 -0.290 3.930
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ -0.296 3.666
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 N fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH -0.298 2.998
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 CG2 -0.300 4.060
fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD1 fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2 -0.301 3.941
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 O fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CB -0.304 3.604
fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2 -0.308 3.948
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CG -0.310 3.340
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH -0.314 3.384
fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH1 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 111 CD2 -0.323 3.723
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 CB -0.334 3.854
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CB fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 51 CE2 -0.336 3.976
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CD1 -0.339 3.979
fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2 -0.347 4.107
fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 C -0.368 3.438
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 CA -0.375 3.895
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 CA fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 CZ -0.383 3.873
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 CB fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH -0.384 3.724
fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 89 CE1 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH -0.393 3.613
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CZ -0.396 3.426
fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 O fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 CE1 -0.400 3.580
116 contacts
> select up
373 atoms, 366 bonds, 41 residues, 1 model selected
> show sel cartoons
> select clear
> select #9/A:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
129 atoms, 134 bonds, 18 residues, 1 model selected
> select subtract #9/A:13
124 atoms, 128 bonds, 17 residues, 1 model selected
> select subtract #9/A:14
116 atoms, 120 bonds, 16 residues, 1 model selected
> select subtract #9/A:15
109 atoms, 112 bonds, 15 residues, 1 model selected
> select subtract #9/A:16
104 atoms, 107 bonds, 14 residues, 1 model selected
> select subtract #9/A:17
97 atoms, 99 bonds, 13 residues, 1 model selected
> select subtract #9/A:18
90 atoms, 92 bonds, 12 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #9/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
73 atoms, 74 bonds, 9 residues, 1 model selected
> select up
1449 atoms, 1487 bonds, 184 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:
9 fold_y513_gspy_uca3_notags_model_0.cif
12 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH no hydrogen 2.918 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 OD1 no hydrogen 3.757 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 OG no hydrogen 3.788 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O no hydrogen 3.089 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O no hydrogen 2.156 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2 fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH no hydrogen 2.287 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 N fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 O no hydrogen 3.544 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1 fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 OD1 no hydrogen 2.990 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1 fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 OD2 no hydrogen 2.993 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2 no hydrogen 2.402 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 N fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 9 O no hydrogen 3.520 N/A
fold_y513_gspy_uca3_notags_model_0.cif #9/C LYS 55 NZ fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 O no hydrogen 3.388 N/A
12 hydrogen bonds found
> hide #9.1 models
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
26 atoms, 24 bonds, 3 residues, 1 model selected
> hide sel atoms
> show #2 models
> select #2/B:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
150 atoms, 152 bonds, 21 residues, 1 model selected
> show sel atoms
> select clear
> hide #2 models
> hide #!9 models
> show #10 models
> select #10/A:74
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
70 atoms, 71 bonds, 8 residues, 1 model selected
> select up
1533 atoms, 1572 bonds, 191 residues, 1 model selected
> color bfactor sel
1533 atoms, 191 residues, atom bfactor range 23 to 97.7
> select clear
> select #10/A:33
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
74 atoms, 76 bonds, 10 residues, 1 model selected
> select up
1533 atoms, 1572 bonds, 191 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:
10 fold_poly310_uca3_model_0.cif
27 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2 fold_poly310_uca3_model_0.cif #10/B ASN 54 O no hydrogen 3.290 N/A
fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ fold_poly310_uca3_model_0.cif #10/B THR 74 O no hydrogen 2.445 N/A
fold_poly310_uca3_model_0.cif #10/A THR 50 OG1 fold_poly310_uca3_model_0.cif #10/B TYR 105 OH no hydrogen 3.816 N/A
fold_poly310_uca3_model_0.cif #10/A LYS 70 NZ fold_poly310_uca3_model_0.cif #10/B TYR 116 OH no hydrogen 3.243 N/A
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1 no hydrogen 2.708 N/A
fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1 fold_poly310_uca3_model_0.cif #10/B GLY 103 O no hydrogen 1.975 N/A
fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1 fold_poly310_uca3_model_0.cif #10/B TYR 106 O no hydrogen 3.125 N/A
fold_poly310_uca3_model_0.cif #10/A ASN 125 ND2 fold_poly310_uca3_model_0.cif #10/B THR 58 O no hydrogen 3.150 N/A
fold_poly310_uca3_model_0.cif #10/A GLU 189 N fold_poly310_uca3_model_0.cif #10/C GLU 52 OE1 no hydrogen 3.690 N/A
fold_poly310_uca3_model_0.cif #10/B THR 28 OG1 fold_poly310_uca3_model_0.cif #10/A ASP 43 OD1 no hydrogen 3.445 N/A
fold_poly310_uca3_model_0.cif #10/B THR 28 OG1 fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2 no hydrogen 2.892 N/A
fold_poly310_uca3_model_0.cif #10/B THR 30 OG1 fold_poly310_uca3_model_0.cif #10/A GLU 40 OE1 no hydrogen 2.847 N/A
fold_poly310_uca3_model_0.cif #10/B THR 30 OG1 fold_poly310_uca3_model_0.cif #10/A GLU 40 OE2 no hydrogen 3.309 N/A
fold_poly310_uca3_model_0.cif #10/B TYR 33 OH fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1 no hydrogen 2.574 N/A
fold_poly310_uca3_model_0.cif #10/B TYR 33 OH fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2 no hydrogen 3.482 N/A
fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2 fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2 no hydrogen 2.754 N/A
fold_poly310_uca3_model_0.cif #10/B ASN 54 ND2 fold_poly310_uca3_model_0.cif #10/A ALA 36 O no hydrogen 2.530 N/A
fold_poly310_uca3_model_0.cif #10/B SER 55 OG fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2 no hydrogen 3.777 N/A
fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2 fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2 no hydrogen 3.406 N/A
fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1 fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2 no hydrogen 2.768 N/A
fold_poly310_uca3_model_0.cif #10/B ARG 98 NH2 fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2 no hydrogen 3.151 N/A
fold_poly310_uca3_model_0.cif #10/B TYR 105 OH fold_poly310_uca3_model_0.cif #10/A THR 50 OG1 no hydrogen 3.816 N/A
fold_poly310_uca3_model_0.cif #10/B TYR 105 OH fold_poly310_uca3_model_0.cif #10/A ASP 64 OD1 no hydrogen 3.083 N/A
fold_poly310_uca3_model_0.cif #10/B TYR 105 OH fold_poly310_uca3_model_0.cif #10/A ASP 64 OD2 no hydrogen 3.375 N/A
fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ fold_poly310_uca3_model_0.cif #10/A TRP 187 O no hydrogen 3.072 N/A
fold_poly310_uca3_model_0.cif #10/C TYR 93 OH fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2 no hydrogen 1.879 N/A
fold_poly310_uca3_model_0.cif #10/C SER 97 N fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2 no hydrogen 3.403 N/A
27 hydrogen bonds found
> show #!1 models
> show #1.2 models
> hide #1.2 models
> hide #!1 models
> select #10/A:119
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
72 atoms, 74 bonds, 9 residues, 1 model selected
> select up
1533 atoms, 1572 bonds, 191 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
149 contacts
atom1 atom2 overlap distance
fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2 fold_poly310_uca3_model_0.cif #10/B TYR 111 OH 1.410 1.930
fold_poly310_uca3_model_0.cif #10/A ARG 77 NH2 fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1 0.724 2.676
fold_poly310_uca3_model_0.cif #10/A LEU 32 CD2 fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1 0.708 3.052
fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1 fold_poly310_uca3_model_0.cif #10/B GLY 103 O 0.685 1.975
fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1 fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1 0.681 2.719
fold_poly310_uca3_model_0.cif #10/A MET 73 SD fold_poly310_uca3_model_0.cif #10/B TRP 101 CE3 0.672 2.858
fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2 fold_poly310_uca3_model_0.cif #10/C TYR 93 OH 0.601 1.879
fold_poly310_uca3_model_0.cif #10/A ARG 123 CD fold_poly310_uca3_model_0.cif #10/B TYR 106 O 0.432 2.868
fold_poly310_uca3_model_0.cif #10/A LEU 32 CD1 fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1 0.425 3.335
fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1 fold_poly310_uca3_model_0.cif #10/B TYR 106 CD1 0.423 3.217
fold_poly310_uca3_model_0.cif #10/A ASP 96 CG fold_poly310_uca3_model_0.cif #10/C TYR 93 OH 0.406 2.934
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B ASP 107 CG 0.401 3.119
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B GLY 110 N 0.359 2.921
fold_poly310_uca3_model_0.cif #10/A GLU 186 CG fold_poly310_uca3_model_0.cif #10/C TYR 51 OH 0.353 2.987
fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1 fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1 0.336 3.064
fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2 fold_poly310_uca3_model_0.cif #10/B LEU 104 CB 0.324 3.436
fold_poly310_uca3_model_0.cif #10/A PHE 48 CZ fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1 0.314 3.326
fold_poly310_uca3_model_0.cif #10/A LEU 90 CD2 fold_poly310_uca3_model_0.cif #10/B TYR 105 O 0.283 3.017
fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2 fold_poly310_uca3_model_0.cif #10/B TYR 105 CD2 0.271 3.369
fold_poly310_uca3_model_0.cif #10/A PHE 48 CE1 fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1 0.262 3.378
fold_poly310_uca3_model_0.cif #10/A ASP 96 CG fold_poly310_uca3_model_0.cif #10/C SER 96 N 0.249 3.271
fold_poly310_uca3_model_0.cif #10/A LYS 94 CB fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2 0.241 3.399
fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2 fold_poly310_uca3_model_0.cif #10/B TYR 111 CZ 0.239 3.251
fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2 fold_poly310_uca3_model_0.cif #10/B THR 28 CA 0.220 3.080
fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ fold_poly310_uca3_model_0.cif #10/B THR 74 O 0.215 2.445
fold_poly310_uca3_model_0.cif #10/A LYS 94 CD fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ 0.147 3.343
fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2 fold_poly310_uca3_model_0.cif #10/B THR 28 CG2 0.144 3.156
fold_poly310_uca3_model_0.cif #10/A ALA 36 O fold_poly310_uca3_model_0.cif #10/B ASN 54 ND2 0.130 2.530
fold_poly310_uca3_model_0.cif #10/A ARG 77 CZ fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1 0.120 3.250
fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2 fold_poly310_uca3_model_0.cif #10/B THR 28 CB 0.119 3.181
fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1 fold_poly310_uca3_model_0.cif #10/B GLY 103 C 0.107 3.143
fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1 fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2 0.102 2.558
fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1 fold_poly310_uca3_model_0.cif #10/B TYR 106 CB 0.100 3.420
fold_poly310_uca3_model_0.cif #10/A MET 73 SD fold_poly310_uca3_model_0.cif #10/B TRP 101 CB 0.095 3.555
fold_poly310_uca3_model_0.cif #10/A LYS 94 CD fold_poly310_uca3_model_0.cif #10/C TYR 93 OH 0.094 3.246
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B SER 109 OG 0.092 2.608
fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1 fold_poly310_uca3_model_0.cif #10/B TYR 106 CB 0.058 3.702
fold_poly310_uca3_model_0.cif #10/A PRO 68 CG fold_poly310_uca3_model_0.cif #10/B TYR 32 OH 0.044 3.296
fold_poly310_uca3_model_0.cif #10/A ASN 92 OD1 fold_poly310_uca3_model_0.cif #10/B ASP 107 CB 0.034 3.266
fold_poly310_uca3_model_0.cif #10/A ARG 123 CG fold_poly310_uca3_model_0.cif #10/B ASP 107 CG 0.031 3.729
fold_poly310_uca3_model_0.cif #10/A ARG 123 CZ fold_poly310_uca3_model_0.cif #10/B GLY 103 O 0.025 3.005
fold_poly310_uca3_model_0.cif #10/A ARG 77 NH2 fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1 0.014 3.386
fold_poly310_uca3_model_0.cif #10/A ARG 123 CD fold_poly310_uca3_model_0.cif #10/B ASP 107 CA 0.014 3.746
fold_poly310_uca3_model_0.cif #10/A LYS 94 CD fold_poly310_uca3_model_0.cif #10/C TYR 93 CE1 0.012 3.628
fold_poly310_uca3_model_0.cif #10/A ARG 123 CG fold_poly310_uca3_model_0.cif #10/B ASP 107 CB -0.004 3.764
fold_poly310_uca3_model_0.cif #10/A LYS 94 CE fold_poly310_uca3_model_0.cif #10/B ASP 107 CG -0.012 3.772
fold_poly310_uca3_model_0.cif #10/A LEU 32 CG fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1 -0.028 3.788
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B SER 109 N -0.035 3.315
fold_poly310_uca3_model_0.cif #10/A ARG 123 O fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2 -0.042 2.882
fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1 fold_poly310_uca3_model_0.cif #10/B TYR 106 CG -0.044 3.534
fold_poly310_uca3_model_0.cif #10/A PHE 119 CD2 fold_poly310_uca3_model_0.cif #10/B TYR 105 CB -0.044 3.684
fold_poly310_uca3_model_0.cif #10/A LYS 94 CE fold_poly310_uca3_model_0.cif #10/B GLY 110 N -0.046 3.566
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1 -0.048 2.708
fold_poly310_uca3_model_0.cif #10/A LEU 190 CG fold_poly310_uca3_model_0.cif #10/B TYR 111 OH -0.059 3.399
fold_poly310_uca3_model_0.cif #10/A ARG 77 CZ fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1 -0.059 3.429
fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ fold_poly310_uca3_model_0.cif #10/B SER 75 CA -0.066 3.586
fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2 fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ -0.069 3.099
fold_poly310_uca3_model_0.cif #10/A ASP 124 CG fold_poly310_uca3_model_0.cif #10/B TYR 33 OH -0.070 3.410
fold_poly310_uca3_model_0.cif #10/A GLU 40 CD fold_poly310_uca3_model_0.cif #10/B THR 30 OG1 -0.076 3.416
fold_poly310_uca3_model_0.cif #10/A PRO 68 CB fold_poly310_uca3_model_0.cif #10/B TYR 32 OH -0.077 3.417
fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2 fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2 -0.078 3.378
fold_poly310_uca3_model_0.cif #10/A MET 73 SD fold_poly310_uca3_model_0.cif #10/B TRP 101 CD2 -0.082 3.462
fold_poly310_uca3_model_0.cif #10/A ARG 123 CG fold_poly310_uca3_model_0.cif #10/B ASP 107 CA -0.083 3.843
fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2 fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2 -0.094 2.754
fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1 fold_poly310_uca3_model_0.cif #10/B TYR 33 OH -0.094 2.574
fold_poly310_uca3_model_0.cif #10/A LEU 99 CD2 fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2 -0.107 3.407
fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2 fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1 -0.108 2.768
fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1 fold_poly310_uca3_model_0.cif #10/B TYR 111 CE2 -0.110 3.510
fold_poly310_uca3_model_0.cif #10/A HIS 188 CE1 fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2 -0.121 3.301
fold_poly310_uca3_model_0.cif #10/A ARG 123 CD fold_poly310_uca3_model_0.cif #10/B TYR 106 C -0.122 3.612
fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2 fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2 -0.126 3.406
fold_poly310_uca3_model_0.cif #10/A ARG 77 CD fold_poly310_uca3_model_0.cif #10/B TYR 106 CB -0.136 3.896
fold_poly310_uca3_model_0.cif #10/A GLU 40 OE2 fold_poly310_uca3_model_0.cif #10/B THR 30 CG2 -0.141 3.441
fold_poly310_uca3_model_0.cif #10/A ASP 64 OD2 fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1 -0.143 3.323
fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1 fold_poly310_uca3_model_0.cif #10/B TYR 106 CD2 -0.145 3.545
fold_poly310_uca3_model_0.cif #10/A LYS 94 CB fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ -0.146 3.636
fold_poly310_uca3_model_0.cif #10/A LYS 94 CG fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2 -0.154 3.794
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B SER 109 CB -0.164 3.684
fold_poly310_uca3_model_0.cif #10/A MET 73 CE fold_poly310_uca3_model_0.cif #10/B TRP 101 CB -0.167 3.927
fold_poly310_uca3_model_0.cif #10/A MET 73 SD fold_poly310_uca3_model_0.cif #10/B TRP 101 CZ3 -0.172 3.702
fold_poly310_uca3_model_0.cif #10/A ASP 43 CG fold_poly310_uca3_model_0.cif #10/B THR 28 OG1 -0.172 3.512
fold_poly310_uca3_model_0.cif #10/A ASP 64 CG fold_poly310_uca3_model_0.cif #10/B TYR 105 OH -0.181 3.521
fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2 fold_poly310_uca3_model_0.cif #10/C SER 96 CA -0.184 3.484
fold_poly310_uca3_model_0.cif #10/A MET 73 CG fold_poly310_uca3_model_0.cif #10/B TRP 101 CE3 -0.188 3.828
fold_poly310_uca3_model_0.cif #10/A ASP 69 CB fold_poly310_uca3_model_0.cif #10/B TYR 32 OH -0.189 3.529
fold_poly310_uca3_model_0.cif #10/A ASP 69 CG fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2 -0.190 3.950
fold_poly310_uca3_model_0.cif #10/A LYS 70 CE fold_poly310_uca3_model_0.cif #10/B TYR 116 OH -0.194 3.534
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B SER 109 CA -0.198 3.718
fold_poly310_uca3_model_0.cif #10/A HIS 188 CE1 fold_poly310_uca3_model_0.cif #10/B ASN 113 ND2 -0.198 3.598
fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2 fold_poly310_uca3_model_0.cif #10/C SER 96 N -0.207 2.867
fold_poly310_uca3_model_0.cif #10/A ASP 69 CG fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1 -0.208 3.728
fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2 fold_poly310_uca3_model_0.cif #10/B TYR 106 OH -0.210 3.550
fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1 fold_poly310_uca3_model_0.cif #10/B ILE 102 CG2 -0.212 3.732
fold_poly310_uca3_model_0.cif #10/A ILE 93 CG2 fold_poly310_uca3_model_0.cif #10/B TYR 111 OH -0.216 3.556
fold_poly310_uca3_model_0.cif #10/A ARG 123 O fold_poly310_uca3_model_0.cif #10/B ASP 107 CG -0.221 3.521
fold_poly310_uca3_model_0.cif #10/A LYS 94 CB fold_poly310_uca3_model_0.cif #10/C TYR 93 OH -0.227 3.567
fold_poly310_uca3_model_0.cif #10/A TRP 187 C fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ -0.229 3.479
fold_poly310_uca3_model_0.cif #10/A TYR 102 CE2 fold_poly310_uca3_model_0.cif #10/B TYR 105 C -0.234 3.604
fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1 fold_poly310_uca3_model_0.cif #10/B TYR 106 CE1 -0.237 3.877
fold_poly310_uca3_model_0.cif #10/A LEU 99 CD1 fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2 -0.238 3.538
fold_poly310_uca3_model_0.cif #10/A SER 95 N fold_poly310_uca3_model_0.cif #10/C TYR 32 CE1 -0.239 3.639
fold_poly310_uca3_model_0.cif #10/A GLU 189 CG fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ -0.242 3.762
fold_poly310_uca3_model_0.cif #10/A ASP 96 OD1 fold_poly310_uca3_model_0.cif #10/C GLY 95 CA -0.242 3.542
fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2 fold_poly310_uca3_model_0.cif #10/B LEU 104 O -0.244 3.544
fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2 fold_poly310_uca3_model_0.cif #10/B TRP 101 CZ3 -0.245 3.885
fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ fold_poly310_uca3_model_0.cif #10/B GLY 110 CA -0.247 3.767
fold_poly310_uca3_model_0.cif #10/A PHE 119 CE2 fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1 -0.250 3.770
fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ fold_poly310_uca3_model_0.cif #10/B THR 74 C -0.254 3.504
fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2 fold_poly310_uca3_model_0.cif #10/B TYR 106 CZ -0.257 3.747
fold_poly310_uca3_model_0.cif #10/A HIS 1 CD2 fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2 -0.261 3.661
fold_poly310_uca3_model_0.cif #10/A LYS 94 CG fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ -0.264 3.754
fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2 fold_poly310_uca3_model_0.cif #10/B TYR 106 CE2 -0.266 3.906
fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1 fold_poly310_uca3_model_0.cif #10/C GLU 52 CD -0.267 3.787
fold_poly310_uca3_model_0.cif #10/A ASP 43 CG fold_poly310_uca3_model_0.cif #10/B THR 28 CG2 -0.271 4.031
fold_poly310_uca3_model_0.cif #10/A ASP 96 CG fold_poly310_uca3_model_0.cif #10/C GLY 95 CA -0.279 4.039
fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1 fold_poly310_uca3_model_0.cif #10/B TYR 105 C -0.281 3.531
fold_poly310_uca3_model_0.cif #10/A ASP 124 CG fold_poly310_uca3_model_0.cif #10/B TRP 50 CH2 -0.282 3.922
fold_poly310_uca3_model_0.cif #10/A TRP 187 O fold_poly310_uca3_model_0.cif #10/C LYS 55 CD -0.284 3.584
fold_poly310_uca3_model_0.cif #10/A PRO 68 CB fold_poly310_uca3_model_0.cif #10/B TRP 101 NE1 -0.286 3.806
fold_poly310_uca3_model_0.cif #10/A LYS 94 CD fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2 -0.293 3.933
fold_poly310_uca3_model_0.cif #10/A LYS 94 CE fold_poly310_uca3_model_0.cif #10/B ASP 107 O -0.297 3.597
fold_poly310_uca3_model_0.cif #10/A ILE 93 CG2 fold_poly310_uca3_model_0.cif #10/B TYR 111 CE1 -0.297 3.937
fold_poly310_uca3_model_0.cif #10/A ASP 96 CG fold_poly310_uca3_model_0.cif #10/C SER 96 CA -0.298 4.058
fold_poly310_uca3_model_0.cif #10/A LYS 94 CA fold_poly310_uca3_model_0.cif #10/C TYR 32 CE1 -0.310 3.950
fold_poly310_uca3_model_0.cif #10/A PHE 119 CE2 fold_poly310_uca3_model_0.cif #10/B TYR 105 CG -0.310 3.680
fold_poly310_uca3_model_0.cif #10/A LYS 94 CE fold_poly310_uca3_model_0.cif #10/B GLY 110 CA -0.322 4.082
fold_poly310_uca3_model_0.cif #10/A TRP 187 CB fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ -0.333 3.853
fold_poly310_uca3_model_0.cif #10/A LYS 94 CE fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1 -0.334 3.634
fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ fold_poly310_uca3_model_0.cif #10/B SER 75 C -0.350 3.600
fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2 fold_poly310_uca3_model_0.cif #10/B ARG 98 CZ -0.354 3.384
fold_poly310_uca3_model_0.cif #10/A GLU 186 CG fold_poly310_uca3_model_0.cif #10/C TYR 51 CZ -0.355 3.845
fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2 fold_poly310_uca3_model_0.cif #10/B TYR 111 CE2 -0.365 4.005
fold_poly310_uca3_model_0.cif #10/A ASP 124 CG fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2 -0.366 3.886
fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1 fold_poly310_uca3_model_0.cif #10/B TYR 33 CE1 -0.366 3.546
fold_poly310_uca3_model_0.cif #10/A HIS 188 CA fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2 -0.367 3.667
fold_poly310_uca3_model_0.cif #10/A GLU 40 OE1 fold_poly310_uca3_model_0.cif #10/B THR 30 OG1 -0.367 2.847
fold_poly310_uca3_model_0.cif #10/A LYS 42 CE fold_poly310_uca3_model_0.cif #10/B THR 74 O -0.369 3.669
fold_poly310_uca3_model_0.cif #10/A HIS 188 CA fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ -0.371 3.891
fold_poly310_uca3_model_0.cif #10/A PHE 119 CZ fold_poly310_uca3_model_0.cif #10/B TYR 105 CD2 -0.375 3.895
fold_poly310_uca3_model_0.cif #10/A ASP 69 OD1 fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2 -0.375 3.675
fold_poly310_uca3_model_0.cif #10/A ASP 43 CG fold_poly310_uca3_model_0.cif #10/B THR 28 CB -0.379 4.139
fold_poly310_uca3_model_0.cif #10/A TYR 102 CE2 fold_poly310_uca3_model_0.cif #10/B TYR 105 O -0.381 3.561
fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1 fold_poly310_uca3_model_0.cif #10/B TYR 105 O -0.381 3.041
fold_poly310_uca3_model_0.cif #10/A ASP 124 CB fold_poly310_uca3_model_0.cif #10/B TRP 50 CH2 -0.382 4.022
fold_poly310_uca3_model_0.cif #10/A PHE 119 CZ fold_poly310_uca3_model_0.cif #10/B TYR 105 CE2 -0.384 3.904
fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2 fold_poly310_uca3_model_0.cif #10/B ASN 52 CB -0.386 3.686
fold_poly310_uca3_model_0.cif #10/A VAL 75 CG1 fold_poly310_uca3_model_0.cif #10/B TYR 106 CE2 -0.393 4.033
fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1 fold_poly310_uca3_model_0.cif #10/B GLY 103 N -0.393 3.673
fold_poly310_uca3_model_0.cif #10/A PHE 119 CD2 fold_poly310_uca3_model_0.cif #10/B TYR 105 CG -0.399 3.769
149 contacts
> hide #10.2 models
> hide #!10 models
> select add #10
3324 atoms, 3406 bonds, 176 pseudobonds, 428 residues, 3 models selected
> select subtract #10
Nothing selected
> show #11 models
> select #11/A:35
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
74 atoms, 76 bonds, 10 residues, 1 model selected
> select up
1590 atoms, 1630 bonds, 197 residues, 1 model selected
> color bfactor sel
1590 atoms, 197 residues, atom bfactor range 14.1 to 97.5
> 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:
11 fold_poly28_uca3_model_0.cif
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
fold_poly28_uca3_model_0.cif #11/A SER 7 OG fold_poly28_uca3_model_0.cif #11/C ASN 33 OD1 no hydrogen 3.348 N/A
fold_poly28_uca3_model_0.cif #11/B THR 28 OG1 fold_poly28_uca3_model_0.cif #11/A SER 101 O no hydrogen 3.603 N/A
fold_poly28_uca3_model_0.cif #11/B ASN 54 ND2 fold_poly28_uca3_model_0.cif #11/A TYR 80 O no hydrogen 3.294 N/A
fold_poly28_uca3_model_0.cif #11/B LEU 104 N fold_poly28_uca3_model_0.cif #11/A GLU 81 OE2 no hydrogen 3.487 N/A
fold_poly28_uca3_model_0.cif #11/C TYR 32 OH fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1 no hydrogen 2.872 N/A
fold_poly28_uca3_model_0.cif #11/C TYR 51 OH fold_poly28_uca3_model_0.cif #11/A ASN 131 O no hydrogen 2.250 N/A
fold_poly28_uca3_model_0.cif #11/C SER 54 OG fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1 no hydrogen 2.636 N/A
fold_poly28_uca3_model_0.cif #11/C SER 96 N fold_poly28_uca3_model_0.cif #11/A GLU 46 OE2 no hydrogen 3.304 N/A
8 hydrogen bonds found
> select #11/A:138
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
76 atoms, 77 bonds, 9 residues, 1 model selected
> 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
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