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Opened 46 minutes ago
#20823 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.7.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000032337f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000322373000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000321367000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032035b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031f34f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031e343000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d337000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031c32b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031b31f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a313000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000319307000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001eeb8a240 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, 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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 61)
{"app_name":"ChimeraX","timestamp":"2026-08-05 17:37:47.00 +0200","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.7.4 (24G517)","roots_installed":0,"name":"ChimeraX","incident_id":"1AE5B21A-E7F5-4C08-BC94-A6B0B91EA3AD"}
{
"uptime" : 590000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 82201,
"osVersion" : {
"train" : "macOS 15.7.4",
"build" : "24G517",
"releaseType" : "User"
},
"captureTime" : "2026-08-05 17:37:42.9281 +0200",
"codeSigningMonitor" : 1,
"incident" : "1AE5B21A-E7F5-4C08-BC94-A6B0B91EA3AD",
"pid" : 36147,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-08-02 00:32:53.8328 +0200",
"procStartAbsTime" : 12890070446647,
"procExitAbsTime" : 14268729618981,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1285D59A-DC79-5D40-B366-2F3C3C4E451C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "31E19731-CFC0-05F8-DC37-45557C23533F",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "48393D59-CAE8-4E60-A91B-8B6619FF5ADA",
"wakeTime" : 7612,
"sleepWakeUUID" : "AA8FD552-F66E-4217-B565-DF2F2A347D70",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4371759080\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10493c000-104940000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":36147},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4371759080\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10493c000-104940000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7XBZ
Summary of feedback from opening 7XBZ fetched from pdb
---
notes | Fetching compressed mmCIF 7xbz from http://files.rcsb.org/download/7xbz.cif
Fetching CCD D4E from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/D4E/D4E.cif
7xbz title:
Crystal structure of Staphylococcus aureus ClpP in complex with R-ZG197 [more
info...]
Chain information for 7xbz #1
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195
Non-standard residues in 7xbz #1
---
D4E —
(6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
MG — magnesium ion
MPD — (4S)-2-methyl-2,4-pentanediol
49 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> set bgColor white
> open 7WGS
Summary of feedback from opening 7WGS fetched from pdb
---
notes | Fetching compressed mmCIF 7wgs from http://files.rcsb.org/download/7wgs.cif
Fetching CCD 9A2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/9A2/9A2.cif
7wgs title:
Structure of ClpP from Staphylococcus aureus in complex with (S)-ZG197 [more
info...]
Chain information for 7wgs #2
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195
Non-standard residues in 7wgs #2
---
9A2 —
(6S,9aS)-6-[(2R)-butan-2-yl]-8-[(1S)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
MPD — (4S)-2-methyl-2,4-pentanediol
> open "/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
> Models/Pdb/D7_deposition/D7_model2.deposit_000.cif"
Summary of feedback from opening
/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
Models/Pdb/D7_deposition/D7_model2.deposit_000.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 359
Skipping entity category: Missing column 'type' on line 42418
Missing entity information. Treating each chain as a separate entity.
Invalid sheet range for struct_sheet_range "B 5" on line 223
Invalid sheet range for struct_sheet_range "D 1": invalid entity "B", on line
227
Invalid sheet range for struct_sheet_range "D 2": invalid entity "B", on line
228
Invalid sheet range for struct_sheet_range "E 1": invalid entity "B", on line
229
Invalid sheet range for struct_sheet_range "E 2": invalid entity "B", on line
230
72 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 43004
Chain information for D7_model2.deposit_000.cif #3
---
Chain | Description
A B C D E F G H I J K L M N | No description available
> ui tool show Matchmaker
> matchmaker #!1-2 to #3
Computing secondary structure
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 D7_model2.deposit_000.cif, chain A (#3) with 7xbz, chain B (#1),
sequence alignment score = 737.9
RMSD between 181 pruned atom pairs is 0.724 angstroms; (across all 186 pairs:
0.828)
Matchmaker D7_model2.deposit_000.cif, chain A (#3) with 7wgs, chain H (#2),
sequence alignment score = 739.1
RMSD between 185 pruned atom pairs is 0.726 angstroms; (across all 187 pairs:
0.875)
> matchmaker #!1-2 to #3
Computing secondary structure
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 D7_model2.deposit_000.cif, chain A (#3) with 7xbz, chain B (#1),
sequence alignment score = 737.9
RMSD between 181 pruned atom pairs is 0.724 angstroms; (across all 186 pairs:
0.828)
Matchmaker D7_model2.deposit_000.cif, chain A (#3) with 7wgs, chain H (#2),
sequence alignment score = 739.1
RMSD between 185 pruned atom pairs is 0.726 angstroms; (across all 187 pairs:
0.875)
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
80180 atoms, 81002 bonds, 41 pseudobonds, 7731 residues, 6 models selected
> hide sel atoms
> show sel cartoons
> select ::name="HOH"
1230 atoms, 1230 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select ::name="KHS"
658 atoms, 672 bonds, 14 residues, 1 model selected
> hide sel
> select add #3
42014 atoms, 42350 bonds, 14 pseudobonds, 2646 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!1-2 to #3
Computing secondary structure
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 D7_model2.deposit_000.cif, chain A (#3) with 7xbz, chain B (#1),
sequence alignment score = 737.9
RMSD between 181 pruned atom pairs is 0.724 angstroms; (across all 186 pairs:
0.828)
Matchmaker D7_model2.deposit_000.cif, chain A (#3) with 7wgs, chain H (#2),
sequence alignment score = 739.1
RMSD between 185 pruned atom pairs is 0.726 angstroms; (across all 187 pairs:
0.875)
> matchmaker #!1-2 to #3
Computing secondary structure
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 D7_model2.deposit_000.cif, chain A (#3) with 7xbz, chain B (#1),
sequence alignment score = 737.9
RMSD between 181 pruned atom pairs is 0.724 angstroms; (across all 186 pairs:
0.828)
Matchmaker D7_model2.deposit_000.cif, chain A (#3) with 7wgs, chain H (#2),
sequence alignment score = 739.1
RMSD between 185 pruned atom pairs is 0.726 angstroms; (across all 187 pairs:
0.875)
> select add #1
19894 atoms, 20150 bonds, 38 pseudobonds, 2581 residues, 3 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel byhetero
> select subtract #1
Nothing selected
> select add #2
20170 atoms, 20450 bonds, 13 pseudobonds, 2586 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle
> color sel byhetero
> select add #1
40064 atoms, 40600 bonds, 51 pseudobonds, 5167 residues, 5 models selected
> select subtract #1
20170 atoms, 20450 bonds, 13 pseudobonds, 2586 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #3
42014 atoms, 42350 bonds, 14 pseudobonds, 2646 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tan
> color sel burly wood
> color sel tan
> select clear
> select #2/G:9A2
38 atoms, 41 bonds, 1 residue, 1 model selected
> select #1/G:34
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/G:9A2, #1/M:D4E
Expected an objects specifier or a keyword
> select #2/G:9A2, #1/M:D4E
Expected an objects specifier or a keyword
> select #2/G:9A2, #1/M:D4E
Expected an objects specifier or a keyword
> select #2/G:9A2
38 atoms, 41 bonds, 1 residue, 1 model selected
> select add #1/M:D4E
76 atoms, 82 bonds, 2 residues, 2 models selected
> select sel : undo
> select sel : hide ~sel cartoons, atoms
> show sel atoms
> style sel stick
Changed 1036 atom styles
> select @H*
21014 atoms, 2646 residues, 1 model selected
> hide sel
> select #3/M:301@FAD
1 atom, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 1 residue, 1 model selected
> hide sel
> select #2/G:9A2
38 atoms, 41 bonds, 1 residue, 1 model selected
> select #2/G:9A2
38 atoms, 41 bonds, 1 residue, 1 model selected
> hide ~sel & #1 cartoons, atoms
> select add #1/M:D4E
76 atoms, 82 bonds, 2 residues, 2 models selected
> hide ~sel & #1 cartoons, atoms
> hide ~sel & #2 cartoons, atoms
> select clear
> select #3/M:106
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/M:125
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
2954 atoms, 2977 bonds, 188 residues, 1 model selected
> select down
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2954 atoms, 2977 bonds, 188 residues, 1 model selected
> select down
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/M:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:126
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:37
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
2954 atoms, 2977 bonds, 188 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:36
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:41
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:43
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:44
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/M:203
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select #3/M:203
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel
> hide sel cartoons
> select #3/M:126
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
2954 atoms, 2977 bonds, 188 residues, 1 model selected
> select down
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/M:125
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/M:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/L:66
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> lighting simple
> select #2/G:201@C38
1 atom, 1 residue, 1 model selected
> select #2/G:201@C38
1 atom, 1 residue, 1 model selected
> select #2/G:201@C38
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
38 atoms, 41 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:40@CD
1 atom, 1 residue, 1 model selected
> select #3/M:40
15 atoms, 14 bonds, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> select #3/M:42
16 atoms, 15 bonds, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> select #3/M:41
24 atoms, 23 bonds, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> select #3/M:73
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> select #3/M:72
12 atoms, 11 bonds, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> select #3/M:75@CA
1 atom, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> select clear
> select #3/M:206@CD
1 atom, 1 residue, 1 model selected
> select #3/M:206@CA
1 atom, 1 residue, 1 model selected
> select #3/M:206
24 atoms, 23 bonds, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> transparency sel 70 cartoons, atoms
> select #3/M:104
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/M:103
14 atoms, 13 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/M:102
11 atoms, 10 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/M:101
16 atoms, 15 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/M:75
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/M:43
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/M:42
16 atoms, 15 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/M:43
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/M:44
20 atoms, 20 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select clear
> select #3/L:62
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select clear
> select #3/L:62
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select clear
> cd "/Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac"
Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main
Project/ZG_ProBac
> save tyr76_Rzg197_clash1.png width 4000 supersample 4
> open spin_movie.cxc
> movie record size 3840,2160
> turn y 2 180
> wait 180
> movie stop
> movie encode output my_movie.mp4 quality highest
Movie saved to my_movie.mp4
executed spin_movie.cxc
> open spin_movie.cxc
> movie record size 3840,2160
> turn y 2 180
> wait 180
> movie stop
> movie encode output my_movie.mp4 quality highest
Movie saved to my_movie.mp4
executed spin_movie.cxc
> select #2/G:9A2
38 atoms, 41 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1/M:D4E
76 atoms, 82 bonds, 2 residues, 2 models selected
> hide sel atoms
> undo
> select #1/M:D4E
38 atoms, 41 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:104
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select #3/M:103
14 atoms, 13 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select #3/M:102
11 atoms, 10 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select #3/M:101
16 atoms, 15 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select clear
> select #3/M:73
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:72
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/M:73
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select #3/M:72
12 atoms, 11 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select clear
> select #3/M:75
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select clear
> select #3/M:206
24 atoms, 23 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select clear
> select #3/M:40
15 atoms, 14 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select clear
> save S_zg197.png width 4000 supersample 4
> open spin_movie.cxc
> movie record size 3840,2160
> turn y 2 180
> wait 180
> movie stop
> movie encode output my_movie.mp4 quality highest
Movie saved to my_movie.mp4
executed spin_movie.cxc
> select #1/M:D4E
38 atoms, 41 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3/M:206@CA
1 atom, 1 residue, 1 model selected
> select #3/M:206@CA
1 atom, 1 residue, 1 model selected
> select #3/M:206@CA
1 atom, 1 residue, 1 model selected
> select #3/M:206
24 atoms, 23 bonds, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> select clear
> select #3/M:104
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select clear
> select #3/L:96
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/M:206
24 atoms, 23 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> hide sel atoms
> save S_R_zg197.png width 4000 supersample 4
> open spin_movie.cxc
> movie record size 3840,2160
> turn y 2 180
> wait 180
> movie stop
> movie encode output my_movie.mp4 quality highest
Movie saved to my_movie.mp4
executed spin_movie.cxc
> save "/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ZG_ProBac/ZG197_EcClpP_compare.cxs"
> select clear
> close #1-3
> open 7XBZ
7xbz title:
Crystal structure of Staphylococcus aureus ClpP in complex with R-ZG197 [more
info...]
Chain information for 7xbz #1
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195
Non-standard residues in 7xbz #1
---
D4E —
(6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
MG — magnesium ion
MPD — (4S)-2-methyl-2,4-pentanediol
49 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 7WGS
7wgs title:
Structure of ClpP from Staphylococcus aureus in complex with (S)-ZG197 [more
info...]
Chain information for 7wgs #2
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195
Non-standard residues in 7wgs #2
---
9A2 —
(6S,9aS)-6-[(2R)-butan-2-yl]-8-[(1S)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
MPD — (4S)-2-methyl-2,4-pentanediol
> hide #!1 models
> show #!1 models
> open 6tty
Summary of feedback from opening 6tty fetched from pdb
---
note | Fetching compressed mmCIF 6tty from http://files.rcsb.org/download/6tty.cif
6tty title:
Structure of ClpP from Staphylococcus aureus (apo, closed state) [more
info...]
Chain information for 6tty #3
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A077UUA2_STAAU 1-195
70 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!1-2 to #3
Computing secondary structure
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 6tty, chain E (#3) with 7xbz, chain H (#1), sequence alignment
score = 980.2
RMSD between 185 pruned atom pairs is 0.407 angstroms; (across all 185 pairs:
0.407)
Matchmaker 6tty, chain E (#3) with 7wgs, chain B (#2), sequence alignment
score = 980.2
RMSD between 184 pruned atom pairs is 0.477 angstroms; (across all 185 pairs:
0.507)
> matchmaker #!1-2 to #3
Computing secondary structure
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 6tty, chain E (#3) with 7xbz, chain H (#1), sequence alignment
score = 980.2
RMSD between 185 pruned atom pairs is 0.407 angstroms; (across all 185 pairs:
0.407)
Matchmaker 6tty, chain E (#3) with 7wgs, chain B (#2), sequence alignment
score = 980.2
RMSD between 184 pruned atom pairs is 0.477 angstroms; (across all 185 pairs:
0.507)
> select ::name="HOH"
3203 atoms, 3203 residues, 3 models selected
> delete atoms sel
> delete bonds sel
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
59427 atoms, 60200 bonds, 31 pseudobonds, 7765 residues, 6 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select add #3
20603 atoms, 20876 bonds, 4 pseudobonds, 2666 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tan
> select clear
> select add #2
20170 atoms, 20450 bonds, 13 pseudobonds, 2586 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle
> select add #1
40064 atoms, 40600 bonds, 51 pseudobonds, 5167 residues, 5 models selected
> select subtract #2
19894 atoms, 20150 bonds, 38 pseudobonds, 2581 residues, 3 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel byhetero
> select subtract #1
Nothing selected
> select add #2
20170 atoms, 20450 bonds, 13 pseudobonds, 2586 residues, 2 models selected
> color (#!2 & sel) byhetero
> select clear
> select #1/E:D4E
76 atoms, 82 bonds, 2 residues, 1 model selected
> select add #2/K:9A2
114 atoms, 123 bonds, 3 residues, 2 models selected
> select sel : select clear
> select #1/E:D4E
76 atoms, 82 bonds, 2 residues, 1 model selected
> select add #2/K:9A2
114 atoms, 123 bonds, 3 residues, 2 models selected
> select #1/I:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/E:201@F41
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 41 bonds, 1 residue, 1 model selected
> select add #2/K:9A2
76 atoms, 82 bonds, 2 residues, 2 models selected
> select sel : select sel : hide ~sel cartoons, atoms
> select clear
Drag select of 76 atoms, 77 residues, 82 bonds
> show sel atoms
> style sel stick
Changed 734 atom styles
> select clear
> undo
> select clear
> select #2/K:63
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/K:63
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #2/K:63
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #1/E:63
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select clear
> open spin_movie.cxc
> movie record size 3840,2160
> turn y 2 180
> wait 180
> movie stop
> movie encode output my_movie.mp4 quality highest
Movie saved to my_movie.mp4
executed spin_movie.cxc
> lighting simple
> open spin_movie.cxc
> movie record size 3840,2160
> turn y 2 180
> wait 180
> movie stop
> movie encode output my_movie.mp4 quality highest
Movie saved to my_movie.mp4
executed spin_movie.cxc
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting flat
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select #2/J:52
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 13 residues
> hide sel cartoons
> select clear
Drag select of 3 residues
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
> save apo_zg197.png width 4000 supersample 4
> select #2/K:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> open 6tty
6tty title:
Structure of ClpP from Staphylococcus aureus (apo, closed state) [more
info...]
Chain information for 6tty #4
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A077UUA2_STAAU 1-195
70 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #4
> open 1YG6
Summary of feedback from opening 1YG6 fetched from pdb
---
note | Fetching compressed mmCIF 1yg6 from http://files.rcsb.org/download/1yg6.cif
1yg6 title:
ClpP [more info...]
Chain information for 1yg6 #4
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI 1-193
Non-standard residues in 1yg6 #4
---
MPD — (4S)-2-methyl-2,4-pentanediol
Drag select of 10 residues
> select clear
Drag select of 8 residues
> select clear
Drag select of 1 residues
Drag select of 5 residues
Drag select of 8 residues
> select clear
> select #3/K:31
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/K:31
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 9 residues
> select clear
Drag select of 5 residues
Drag select of 9 atoms, 15 residues, 9 bonds
> select clear
> select #2/K:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/K:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
32 atoms, 31 bonds, 4 residues, 1 model selected
> select up
1467 atoms, 1486 bonds, 190 residues, 1 model selected
> select down
32 atoms, 31 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #2/K:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
32 atoms, 31 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #1/E:31
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/E:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 13 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 9 residues
> hide sel cartoons
Drag select of 10 residues
> hide sel cartoons
> save apo2_zg197.png width 4000 supersample 4
> save apo3_zg197.png width 4000 supersample 4
> select #2/K:61
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> save apo4_zg197.png width 4000 supersample 4
> save "/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ZG_ProBac/apo_zg_compare.cxs"
> close #1-3
> open "/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
> Models/Pdb/D7_deposition/D7_model2.deposit_000.cif"
Summary of feedback from opening
/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
Models/Pdb/D7_deposition/D7_model2.deposit_000.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 359
Skipping entity category: Missing column 'type' on line 42418
Missing entity information. Treating each chain as a separate entity.
Invalid sheet range for struct_sheet_range "B 5" on line 223
Invalid sheet range for struct_sheet_range "D 1": invalid entity "B", on line
227
Invalid sheet range for struct_sheet_range "D 2": invalid entity "B", on line
228
Invalid sheet range for struct_sheet_range "E 1": invalid entity "B", on line
229
Invalid sheet range for struct_sheet_range "E 2": invalid entity "B", on line
230
72 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 43004
Chain information for D7_model2.deposit_000.cif #1
---
Chain | Description
A B C D E F G H I J K L M N | No description available
> ui tool show Matchmaker
> matchmaker #!1 to #4
Computing secondary structure
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 1yg6, chain I (#4) with D7_model2.deposit_000.cif, chain A (#1),
sequence alignment score = 934.6
RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs:
2.818)
> matchmaker #!1 to #4
Computing secondary structure
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 1yg6, chain I (#4) with D7_model2.deposit_000.cif, chain A (#1),
sequence alignment score = 934.6
RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs:
2.818)
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
61831 atoms, 62481 bonds, 14 pseudobonds, 5250 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select ::name="HOH"
953 atoms, 953 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/C:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select add #4
20587 atoms, 20901 bonds, 2632 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tan
> select subtract #4
Nothing selected
> select add #1
42014 atoms, 42350 bonds, 14 pseudobonds, 2646 residues, 2 models selected
> ui tool show "Color Actions"
> color sel sky blue
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 1 residue, 1 model selected
> select sel : hide ~sel cartoons, atoms
> show sel atoms
> style sel stick
Changed 427 atom styles
> select @H*
21014 atoms, 2646 residues, 1 model selected
> hide sel
> open 7XBZ format mmcif fromDatabase pdb
7xbz title:
Crystal structure of Staphylococcus aureus ClpP in complex with R-ZG197 [more
info...]
Chain information for 7xbz #2
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195
Non-standard residues in 7xbz #2
---
D4E —
(6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
MG — magnesium ion
MPD — (4S)-2-methyl-2,4-pentanediol
49 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select clear
> select ::name="KHS"
658 atoms, 672 bonds, 14 residues, 1 model selected
> hide sel
> ui tool show Matchmaker
> matchmaker #!2 to #4
Computing secondary structure
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 1yg6, chain A (#4) with 7xbz, chain C (#2), sequence alignment
score = 751.1
RMSD between 181 pruned atom pairs is 0.725 angstroms; (across all 185 pairs:
0.910)
> matchmaker #!2 to #4
Computing secondary structure
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 1yg6, chain A (#4) with 7xbz, chain C (#2), sequence alignment
score = 751.1
RMSD between 181 pruned atom pairs is 0.725 angstroms; (across all 185 pairs:
0.910)
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
81137 atoms, 82034 bonds, 28 pseudobonds, 7792 residues, 5 models selected
> hide sel atoms
> show sel cartoons
> select ::name="HOH"
491 atoms, 491 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!2 models
> show #!2 models
> select ::name="KHS"
658 atoms, 672 bonds, 14 residues, 1 model selected
> show sel atoms
> select #1/M:301@CAC
1 atom, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
38 atoms, 41 bonds, 1 residue, 1 model selected
> select sel : hide ~sel cartoons, atoms
> select @H*
21014 atoms, 2646 residues, 1 model selected
> hide sel
> show sel atoms
> style sel stick
Changed 21014 atom styles
> undo
> select clear
Drag select of 64 residues, 57 atoms, 61 bonds
> show sel atoms
> style sel stick
Changed 828 atom styles
> select @H*
21014 atoms, 2646 residues, 1 model selected
> hide sel
> ui tool show Matchmaker
> ui tool show "Show Sequence Viewer"
> select clear
> select add #4
20587 atoms, 20901 bonds, 2632 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #2
19894 atoms, 20150 bonds, 38 pseudobonds, 2581 residues, 3 models selected
> ui tool show "Color Actions"
> color sel dark sea green
> color sel byhetero
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #4/B
Alignment identifier is 4/B
> select #4/B:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!2 models
> select #4/B:62
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/B:62
12 atoms, 12 bonds, 1 residue, 1 model selected
> show #!2 models
> select add #4
20587 atoms, 20901 bonds, 2632 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #2
19894 atoms, 20150 bonds, 38 pseudobonds, 2581 residues, 3 models selected
> ui tool show "Color Actions"
> color sel thistle
> color sel byhetero
> select clear
> select #4/B:62
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/N:76
33 atoms, 33 bonds, 2 residues, 2 models selected
> select add #2/D:63
45 atoms, 45 bonds, 3 residues, 3 models selected
> select add #2/C:D4E
83 atoms, 86 bonds, 4 residues, 3 models selected
> select add #1/N:KHS
130 atoms, 134 bonds, 5 residues, 3 models selected
> hide ~sel cartoons, atoms
> select clear
> select #1/N:301@FAD
1 atom, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 1 residue, 1 model selected
> hide sel
> lighting full
> lighting soft
> lighting simple
> save apo_EcClpP.png width 4000 supersample 4
> select #2/C:201@F42
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 41 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select #2/C:201@F42
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 41 bonds, 1 residue, 1 model selected
> color sel purple
> color sel byhetero
> select clear
> save apo_EcClpP.png width 4000 supersample 4
> select add #4
20587 atoms, 20901 bonds, 2632 residues, 1 model selected
> color sel byhetero
> select subtract #4
Nothing selected
> save apo_EcClpP.png width 4000 supersample 4
> select #2/C:201@F42
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 41 bonds, 1 residue, 1 model selected
> hide sel
> save apo2_EcClpP.png width 4000 supersample 4
> cd "/Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac"
Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main
Project/ZG_ProBac
> save "/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ZG_ProBac/apo_EcClpP_compare.cxs"
QPainter::begin: Paint device returned engine == 0, type: 2
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ZG_ProBac/SaClpP_EcClpP_ZG180_compare_Ayo.cxs"
Log from Sat Aug 1 19:27:04 2026UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ZG_ProBac/Comparison of SaClpP_7WID with our ClpP C1_model.cxs"
Log from Fri Jul 24 19:28:48 2026UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/mklimecka/Downloads/7WID.cif
Summary of feedback from opening C:/Users/mklimecka/Downloads/7WID.cif
---
warnings | Unable to fetch template for '9DF': might have incorrect bonds
Unable to fetch template for 'MG': might have incorrect bonds
Unable to fetch template for 'MPD': might have incorrect bonds
7WID.cif title:
Crystal structure of Staphylococcus aureus ClpP in complex with ZG180 [more
info...]
Chain information for 7WID.cif #1
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU
Non-standard residues in 7WID.cif #1
---
9DF —
(6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
MG — magnesium ion
MPD — (4S)-2-methyl-2,4-pentanediol
> hide surfaces
> select #1
22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected
> hide sel surfaces
> style sel stick
Changed 22004 atom styles
> show sel cartoons
> hide sel atoms
> ~select #1
Nothing selected
> open C:/Users/mklimecka/Downloads/C1_model.cif
Summary of feedback from opening C:/Users/mklimecka/Downloads/C1_model.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 1376
Missing entity information. Treating each chain as a separate entity.
Unable to fetch template for 'KHS': might have incorrect bonds
Bad residue range for struct_conf "7" near line 164
Invalid residue range for struct_conf "8": invalid entity "B", near line 165
Invalid residue range for struct_conf "9": invalid entity "B", near line 166
Invalid residue range for struct_conf "10": invalid entity "B", near line 167
Invalid residue range for struct_conf "11": invalid entity "B", near line 168
Invalid residue range for struct_conf "12": invalid entity "B", near line 169
2 messages similar to the above omitted
Bad residue range for struct_conf "21" near line 178
Invalid residue range for struct_conf "22": invalid entity "D", near line 179
Invalid residue range for struct_conf "23": invalid entity "D", near line 180
Invalid residue range for struct_conf "24": invalid entity "D", near line 181
Invalid residue range for struct_conf "25": invalid entity "D", near line 182
Invalid residue range for struct_conf "26": invalid entity "D", near line 183
2 messages similar to the above omitted
Bad residue range for struct_conf "35" near line 192
Invalid residue range for struct_conf "36": invalid entity "F", near line 193
Invalid residue range for struct_conf "37": invalid entity "F", near line 194
Invalid residue range for struct_conf "38": invalid entity "F", near line 195
Invalid residue range for struct_conf "39": invalid entity "F", near line 196
Invalid residue range for struct_conf "40": invalid entity "F", near line 197
2 messages similar to the above omitted
Bad residue range for struct_conf "49" near line 206
Invalid residue range for struct_conf "50": invalid entity "H", near line 207
Invalid residue range for struct_conf "51": invalid entity "H", near line 208
Invalid residue range for struct_conf "52": invalid entity "H", near line 209
Invalid residue range for struct_conf "53": invalid entity "H", near line 210
Invalid residue range for struct_conf "54": invalid entity "H", near line 211
2 messages similar to the above omitted
Bad residue range for struct_conf "63" near line 220
Invalid residue range for struct_conf "64": invalid entity "J", near line 221
Invalid residue range for struct_conf "65": invalid entity "J", near line 222
Invalid residue range for struct_conf "66": invalid entity "J", near line 223
Invalid residue range for struct_conf "67": invalid entity "J", near line 224
Invalid residue range for struct_conf "68": invalid entity "J", near line 225
2 messages similar to the above omitted
Bad residue range for struct_conf "77" near line 234
Invalid residue range for struct_conf "78": invalid entity "L", near line 235
Invalid residue range for struct_conf "79": invalid entity "L", near line 236
Invalid residue range for struct_conf "80": invalid entity "L", near line 237
Invalid residue range for struct_conf "81": invalid entity "L", near line 238
Invalid residue range for struct_conf "82": invalid entity "L", near line 239
2 messages similar to the above omitted
Bad residue range for struct_conf "91" near line 248
Invalid residue range for struct_conf "92": invalid entity "N", near line 249
Invalid residue range for struct_conf "93": invalid entity "N", near line 250
Invalid residue range for struct_conf "94": invalid entity "N", near line 251
Invalid residue range for struct_conf "95": invalid entity "N", near line 252
Invalid residue range for struct_conf "96": invalid entity "N", near line 253
2 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "10 1" near line 1244
Invalid sheet range for struct_sheet_range "11 1": invalid entity "B", near
line 1245
Invalid sheet range for struct_sheet_range "12 1": invalid entity "B", near
line 1246
Invalid sheet range for struct_sheet_range "13 1": invalid entity "B", near
line 1247
Invalid sheet range for struct_sheet_range "14 1": invalid entity "B", near
line 1248
72 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 43979
Chain information for C1_model.cif #2
---
Chain | Description
A B C D E F G H I J K L M N | No description available
> select #2
41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected
> style sel stick
Changed 41972 atom styles
> show sel cartoons
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #!2 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 7WID.cif, chain H (#1) with C1_model.cif, chain F (#2), sequence
alignment score = 740.3
RMSD between 185 pruned atom pairs is 0.785 angstroms; (across all 188 pairs:
0.931)
> ~select #2
Nothing selected
> show atoms
> show surfaces
> hide #!1 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C #1/D #1/E #1/F #1/G #1/H #1/I #1/J #1/K #1/L
> #1/M #1/N
Alignment identifier is 1
> select #1
22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected
> color sel bychain
> select #2
41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected
> ~select #2
14 models selected
> select #1
22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected
> ~select #1
14 models selected
> select #2
41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected
> color sel bychain
> ~select #2
14 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 cartoons
> select #1
22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> select #2
41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected
> show #!2 models
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> ui tool show Matchmaker
> show sel atoms
> hide sel cartoons
> show sel surfaces
> select #1
22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected
> hide sel cartoons
> show sel surfaces
> show sel atoms
> ~select #1
14 models selected
> select #2
41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected
> hide sel atoms
> hide #!2 models
> show #!2 models
> transparency sel 50
> ui tool show Matchmaker
> ~select #2
14 models selected
> save
> "C:/Users/mklimecka/WORK/Projekty/CnBCh/Protacs/CryoEM/PROTAC2/Comparison of
> our model C1_model_with ZG180_7WID_in yellow.cxs"
> save
> "C:/Users/mklimecka/WORK/Projekty/CnBCh/Protacs/CryoEM/PROTAC2/Comparison of
> our model C1_model_with ZG180_7WID_in yellow.tif" width 1325 height 818
> supersample 3
> hide #!2 models
> show #!2 models
> show atoms
> hide atoms
> undo
> select #2
41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected
> hide sel atoms
> ~select #2
14 models selected
> select #1
22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected
> show sel cartoons
> hide sel surfaces
> select #2
41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected
> hide sel surfaces
> show sel cartoons
> ~select #2
14 models selected
> hide #!2 models
> ui mousemode right select
> select #1/K:201@C6
1 atom, 1 residue, 1 model selected
> select #1/K:201@O33
1 atom, 1 residue, 1 model selected
> color sel byhetero
> ui mousemode right translate
> select ::name="9DF"
518 atoms, 560 bonds, 14 residues, 1 model selected
> color sel byhetero
> show #!2 models
> show sel surfaces
> hide sel surfaces
> select #1
22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected
> ~select #1
28 models selected
> select #2
41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected
> show sel surfaces
> show sel atoms
> select ::name="KHS"
658 atoms, 672 bonds, 14 residues, 1 model selected
> color sel byhetero
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C #1/D #1/E #1/F #1/G #1/H #1/I #1/J #1/K #1/L
> #1/M #1/N
Alignment identifier is 1
> select #1/C-D,G-I,K-N:193
73 atoms, 64 bonds, 9 residues, 1 model selected
> select #1/C-D,G-I,K-N:193
73 atoms, 64 bonds, 9 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B #2/C #2/D #2/E #2/F #2/G #2/H #2/I #2/J #2/K #2/L
> #2/M #2/N
Alignment identifier is 2
> select #2/A-N:206
336 atoms, 322 bonds, 14 residues, 1 model selected
> select #2/A-N:206
336 atoms, 322 bonds, 14 residues, 1 model selected
> hide #!1 models
> color (#!2 & sel) byhetero
> select ::name="KHS"
658 atoms, 672 bonds, 14 residues, 1 model selected
> hide sel atoms
> select ::name="9DF"
518 atoms, 560 bonds, 14 residues, 1 model selected
> show #!1 models
> toolshed show
Downloading bundle chimerax_cryozeta-0.3.6-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\1.3\site-packages
sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\site-packages
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\1.3\site-packages
sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\site-packages
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils:
C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\Python39\Include\chimerax-
cryozeta
sysconfig:
C:\Users\mklimecka\AppData\Roaming\Python\Python39\Include\chimerax-cryozeta
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\Python39\Scripts
sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\Scripts
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX
sysconfig: C:\Users\mklimecka\AppData\Roaming\Python
WARNING: Additional context:
user = True
home = None
root = None
prefix = None
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils:
C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\Python39\Include\UNKNOWN
sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\Include\UNKNOWN
WARNING: You are using pip version 21.2.4; however, version 26.0.1 is
available.
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.3\bin\ChimeraX.exe -m pip install --upgrade pip' command.
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing c:\users\mklimecka\downloads\chimerax_cryozeta-0.3.6-py3-none-
any.whl
Requirement already satisfied: ChimeraX-Core~=1.1 in c:\program files\chimerax
1.3\bin\lib\site-packages (from chimerax-cryozeta==0.3.6) (1.3)
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program files\chimerax
1.3\bin\lib\site-packages (from chimerax-cryozeta==0.3.6) (1.13.7)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.0->chimerax-
cryozeta==0.3.6) (1.1)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.0->chimerax-
cryozeta==0.3.6) (1.0)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.0->chimerax-
cryozeta==0.3.6) (1.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.0->chimerax-cryozeta==0.3.6) (1.1)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.0->chimerax-cryozeta==0.3.6) (1.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->chimerax-cryozeta==0.3.6) (1.0)
Installing collected packages: chimerax-cryozeta
Successfully installed chimerax-cryozeta-0.3.6
\---
Successfully installed chimerax-cryozeta-0.3.6
No change in list of installed bundles
> hide #!2 models
> show #!2 models
> save
> "C:/Users/mklimecka/WORK/Projekty/CnBCh/Protacs/CryoEM/PROTAC2/Comparison of
> SaClpP_7WID with our ClpP C1_model.cxs"
——— End of log from Fri Jul 24 19:28:48 2026 ———
opened ChimeraX session
> set bgColor white
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> close
Unsupported scale factor (0.000000) detected on Display0
[Repeated 3 time(s)]
> open "/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
> Models/Pdb/D7_deposition/D7_model2.deposit_000.cif"
Summary of feedback from opening
/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
Models/Pdb/D7_deposition/D7_model2.deposit_000.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 359
Skipping entity category: Missing column 'type' on line 42418
Missing entity information. Treating each chain as a separate entity.
Invalid sheet range for struct_sheet_range "B 5" on line 223
Invalid sheet range for struct_sheet_range "D 1": invalid entity "B", on line
227
Invalid sheet range for struct_sheet_range "D 2": invalid entity "B", on line
228
Invalid sheet range for struct_sheet_range "E 1": invalid entity "B", on line
229
Invalid sheet range for struct_sheet_range "E 2": invalid entity "B", on line
230
72 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 43004
Chain information for D7_model2.deposit_000.cif #1
---
Chain | Description
A B C D E F G H I J K L M N | No description available
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
41356 atoms, 41678 bonds, 14 pseudobonds, 2632 residues, 2 models selected
> select ::name="KHS"
658 atoms, 672 bonds, 14 residues, 1 model selected
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
41356 atoms, 41678 bonds, 14 pseudobonds, 2632 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select ::name="KHS"
658 atoms, 672 bonds, 14 residues, 1 model selected
> hide sel
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> open 7wh5
Summary of feedback from opening 7wh5 fetched from pdb
---
notes | Fetching compressed mmCIF 7wh5 from http://files.rcsb.org/download/7wh5.cif
Fetching CCD 9DF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/9DF/9DF.cif
7wh5 title:
Crystal structure of human ClpP in complex with ZG180 [more info...]
Chain information for 7wh5 #2
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit, mitochondrial | CLPP_HUMAN 57-277
Non-standard residues in 7wh5 #2
---
9DF —
(6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
MG — magnesium ion
> open 7wid
Summary of feedback from opening 7wid fetched from pdb
---
note | Fetching compressed mmCIF 7wid from http://files.rcsb.org/download/7wid.cif
7wid title:
Crystal structure of Staphylococcus aureus ClpP in complex with ZG180 [more
info...]
Chain information for 7wid #3
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195
Non-standard residues in 7wid #3
---
9DF —
(6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
MG — magnesium ion
MPD — (4S)-2-methyl-2,4-pentanediol
59 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Computing secondary structure
[Repeated 2 time(s)] 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 D7_model2.deposit_000.cif, chain A (#1) with 7wh5, chain I (#2),
sequence alignment score = 636.9
RMSD between 168 pruned atom pairs is 0.766 angstroms; (across all 176 pairs:
1.243)
Matchmaker D7_model2.deposit_000.cif, chain A (#1) with 7wid, chain H (#3),
sequence alignment score = 740.3
RMSD between 181 pruned atom pairs is 0.720 angstroms; (across all 188 pairs:
0.949)
> matchmaker #!2-3 to #1
Computing secondary structure
[Repeated 2 time(s)] 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 D7_model2.deposit_000.cif, chain A (#1) with 7wh5, chain I (#2),
sequence alignment score = 636.9
RMSD between 168 pruned atom pairs is 0.766 angstroms; (across all 176 pairs:
1.243)
Matchmaker D7_model2.deposit_000.cif, chain A (#1) with 7wid, chain H (#3),
sequence alignment score = 740.3
RMSD between 181 pruned atom pairs is 0.720 angstroms; (across all 188 pairs:
0.949)
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
79445 atoms, 80372 bonds, 52 pseudobonds, 7630 residues, 6 models selected
> hide sel atoms
> show sel cartoons
> select ::name="HOH"
1809 atoms, 1809 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> hide #!1 models
> hide #!2 models
> select add #3
20449 atoms, 20718 bonds, 36 pseudobonds, 2642 residues, 3 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> select ::name="9DF"
1036 atoms, 1120 bonds, 28 residues, 2 models selected
> color (#!3 & sel) byhetero
> select clear
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select add #1
42014 atoms, 42350 bonds, 14 pseudobonds, 2646 residues, 2 models selected
> ui tool show "Color Actions"
> color sel burly wood
> select clear
> show #!2 models
> hide #!3 models
> hide #!1 models
> select add #2
18818 atoms, 19208 bonds, 30 pseudobonds, 2414 residues, 3 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> color sel thistle
> select clear
> select ::name="9DF"
1036 atoms, 1120 bonds, 28 residues, 2 models selected
> select add #3
20967 atoms, 21278 bonds, 36 pseudobonds, 2656 residues, 4 models selected
> select subtract #3
518 atoms, 560 bonds, 14 residues, 1 model selected
> color sel byhetero
> select clear
> show #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #2/A:146
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:146
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show Matchmaker
> matchmaker #!3 to #2
Computing secondary structure
[Repeated 1 time(s)] 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 7wh5, chain B (#2) with 7wid, chain C (#3), sequence alignment
score = 614.7
RMSD between 164 pruned atom pairs is 0.705 angstroms; (across all 172 pairs:
1.166)
> matchmaker #!3 to #2
Computing secondary structure
[Repeated 1 time(s)] 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 7wh5, chain B (#2) with 7wid, chain C (#3), sequence alignment
score = 614.7
RMSD between 164 pruned atom pairs is 0.705 angstroms; (across all 172 pairs:
1.166)
> show sel atoms
> hide sel atoms
> style sel stick
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> show sel atoms
> select #3/A:91
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:91
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> hide #!2 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!3 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 D7_model2.deposit_000.cif, chain A (#1) with 7wid, chain H (#3),
sequence alignment score = 740.3
RMSD between 181 pruned atom pairs is 0.720 angstroms; (across all 188 pairs:
0.949)
> matchmaker #!3 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 D7_model2.deposit_000.cif, chain A (#1) with 7wid, chain H (#3),
sequence alignment score = 740.3
RMSD between 181 pruned atom pairs is 0.720 angstroms; (across all 188 pairs:
0.949)
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> select sel :< 5
917 atoms, 896 bonds, 69 residues, 3 models selected
> select sel :< 5
3537 atoms, 3526 bonds, 3 pseudobonds, 319 residues, 6 models selected
> hide ~selected cartoons, atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~selected cartoons atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~selected cartoons atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~selected cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~selected cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~select cartoons atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~select cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~sel cartoons atoms
Expected ',' or a keyword
> hide ~sel cartoons, atoms
> show sel & #!1,3 atoms
> style sel & #!1,3 stick
Changed 2660 atom styles
> select :@H*
Expected an objects specifier or a keyword
> select @H*
21014 atoms, 2646 residues, 1 model selected
> hide sel
> select #1/D:301@FAD
1 atom, 1 residue, 1 model selected
> select #1/D:301@FAD
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
47 atoms, 48 bonds, 1 residue, 1 model selected
> hide sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
> color sel purple
> color sel byhetero
> select #3/L:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
62 atoms, 63 bonds, 7 residues, 1 model selected
> hide ~sel & #3 cartoons
> hide ~sel & #3 cartoons, atoms
> select add ::name="9DF"
1098 atoms, 1183 bonds, 35 residues, 2 models selected
> show sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> select up
1457 atoms, 1476 bonds, 188 residues, 1 model selected
> select down
37 atoms, 40 bonds, 1 residue, 1 model selected
> select add sel :< 3 & ~sel
427 atoms, 426 bonds, 22 residues, 3 models selected
> select add sel :< 3 & ~sel
1782 atoms, 1747 bonds, 144 residues, 3 models selected
> hide ~sel cartoons, atoms
> select clear
> select #1/E:66
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
388 atoms, 392 bonds, 26 residues, 1 model selected
> select up
2836 atoms, 2859 bonds, 181 residues, 1 model selected
> hide sel atoms
> select #1/D:33
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
301 atoms, 302 bonds, 18 residues, 1 model selected
> select up
2954 atoms, 2977 bonds, 188 residues, 1 model selected
> select down
301 atoms, 302 bonds, 18 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/D:105
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
307 atoms, 308 bonds, 22 residues, 1 model selected
> hide sel atoms
> select #1/D:33
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
301 atoms, 302 bonds, 18 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/D:128@CG
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
44 atoms, 44 bonds, 3 residues, 1 model selected
> hide sel cartoons, atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel cartoons, atoms
> select #1/D:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons, atoms
> select #1/D:20
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel cartoons, atoms
> select #1/D:33
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
301 atoms, 302 bonds, 18 residues, 1 model selected
> select down
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons, atoms
> select #1/D:34
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons, atoms
> select #1/E:96
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 6 residues, 1 model selected
> select up
2836 atoms, 2859 bonds, 181 residues, 1 model selected
> select down
99 atoms, 99 bonds, 6 residues, 1 model selected
> select clear
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> label #1,3 text "{0.name} {0.number}{0.insertion_code}"
> ~label #1,3 residues
> select clear
> select #1/D:106
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
307 atoms, 308 bonds, 22 residues, 1 model selected
> hide sel cartoons, atoms
> select #1/D:202@CG1
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
799 atoms, 802 bonds, 50 residues, 1 model selected
> select up
2836 atoms, 2859 bonds, 181 residues, 1 model selected
> select down
799 atoms, 802 bonds, 50 residues, 1 model selected
> transparency sel 70 cartoons
> transparency sel 70 cartoons, atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
56 atoms, 56 bonds, 3 residues, 1 model selected
> transparency sel 70 cartoons, atoms
> select #1/E:92
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 6 residues, 1 model selected
> select up
2836 atoms, 2859 bonds, 181 residues, 1 model selected
> select down
99 atoms, 99 bonds, 6 residues, 1 model selected
> transparency sel 70 cartoons, atoms
> select #1/E:98
22 atoms, 21 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select clear
> select #1/D:46
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
95 atoms, 95 bonds, 6 residues, 1 model selected
> select up
2836 atoms, 2859 bonds, 181 residues, 1 model selected
> select down
95 atoms, 95 bonds, 6 residues, 1 model selected
> transparency sel 70 cartoons, atoms
> select #1/E:94
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons, atoms
> select #1/E:98
22 atoms, 21 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons, atoms
> select #1/D:202@CB
1 atom, 1 residue, 1 model selected
> select #1/D:202@CD1
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
799 atoms, 802 bonds, 50 residues, 1 model selected
> select up
2836 atoms, 2859 bonds, 181 residues, 1 model selected
> select down
799 atoms, 802 bonds, 50 residues, 1 model selected
> transparency sel 0 cartoons, atoms
> select #1/D:205
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
56 atoms, 56 bonds, 3 residues, 1 model selected
> transparency sel 0 cartoons, atoms
> select clear
> select #1/E:94
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 6 residues, 1 model selected
> hide sel cartoons, atoms
> select #1/E:98
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons, atoms
> select #1/D:41
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
80 atoms, 79 bonds, 4 residues, 1 model selected
> transparency sel 70 cartoons, atoms
> select clear
[Repeated 1 time(s)]
> select #1/D:74@CB
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
388 atoms, 392 bonds, 26 residues, 1 model selected
> select down
21 atoms, 21 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #1/D:73
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/L:61@CB
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select #3/L:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons, atoms
> select clear
> select #1/D:205
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
56 atoms, 56 bonds, 3 residues, 1 model selected
> transparency sel 50 cartoons, atoms
> select clear
[Repeated 1 time(s)]
> select #1/D:203@CG
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency sel 50 cartoons, atoms
> select clear
[Repeated 1 time(s)]
> select #1/E:66
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
388 atoms, 392 bonds, 26 residues, 1 model selected
> select down
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
388 atoms, 392 bonds, 26 residues, 1 model selected
> select up
2836 atoms, 2859 bonds, 181 residues, 1 model selected
> transparency sel 50 cartoons, atoms
> select clear
[Repeated 1 time(s)]
> cd /Users/ayomidefasemire/Documents/Doctoral
Current working directory is: /Users/ayomidefasemire/Documents/Doctoral
> cd "/Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac"
Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main
Project/ZG_ProBac
> save tyr76_clash1.png width 4000 supersample 4
> save tyr76_clash2.png width 4000 supersample 4
> save tyr76_clash3.png width 4000 supersample 4
> save "/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ZG_ProBac/SaClpP_EcClpP_ZG180_compare_Ayo.cxs"
——— End of log from Sat Aug 1 19:27:04 2026 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MXCV3ZE/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.4 (24G517)
Kernel Version: Darwin 24.6.0
Time since boot: 29 days, 18 hours, 52 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 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
P24h-2L:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
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