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Opened 6 months ago
Last modified 6 months ago
#17963 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-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x0000000324d4b000 (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 0x0000000323d3f000 (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 0x0000000322d33000 (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 0x0000000321d27000 (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 0x0000000320d1b000 (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 0x000000031fd0f000 (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 0x000000031ed03000 (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 0x000000031dcf7000 (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 0x000000031cceb000 (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 0x000000031bcdf000 (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 0x000000031acd3000 (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 0x00000001f259df00 (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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 57)
{"app_name":"ChimeraX","timestamp":"2025-06-11 11:49:30.00 +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 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"2716AF47-0EF1-4544-B048-143854704255"}
{
"uptime" : 210000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 1197,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-06-11 11:38:00.0771 +0200",
"codeSigningMonitor" : 1,
"incident" : "2716AF47-0EF1-4544-B048-143854704255",
"pid" : 6531,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-10 15:54:00.1052 +0200",
"procStartAbsTime" : 4599329544027,
"procExitAbsTime" : 5146662798269,
"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":"9BDB9CDB-E58F-5068-BDC9-9BA0DAE3F595","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CAD67506-F537-BEEC-A425-4A7CBCD2B0A6",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage"]},
"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" : "33B6B639-59EB-4F8C-AD95-C2265621EDE4",
"wakeTime" : 9127,
"sleepWakeUUID" : "D6E75A66-85D7-44AB-A368-DAE2D964C60C",
"sip" : "enabled",
"vmRegionInfo" : "0x6e036ccb3658 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, 0x00006e036ccb3658","rawCodes":[1,120960989214296],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00006e036ccb3658"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":6531},
"vmregioninfo" : "0x6e036ccb3658 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",
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"faultingThread" : 0,
"threads" : 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"name" : "AppKit",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> close session
> cd Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Cryo-
> EM/250205-Krios
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> windowsize width 1000 height 1000
> set bgColor white
> lighting soft
> graphics silhouettes true
> lighting shadows true intensity 0.5
> open 8p5e
8p5e title:
S. cerevisiae nexus-sCMGE after DNA replication initiation [more info...]
Chain information for 8p5e #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
A | DNA (19-MER) |
B | DNA (7-MER) |
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F | DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
G | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
H | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
I | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213
Non-standard residues in 8p5e #1
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> hide atoms
> show cartoons
> select #1/A,B
539 atoms, 608 bonds, 14 pseudobonds, 26 residues, 2 models selected
> color sel grey
> select #1/H,C,D,I
6676 atoms, 6804 bonds, 4 pseudobonds, 814 residues, 2 models selected
> color sel light sky blue
> clear sel
Unknown command: clear sel
> select #1/E
4282 atoms, 4364 bonds, 4 pseudobonds, 549 residues, 2 models selected
> color sel teal
> clear sel
Unknown command: clear sel
> select #1/2-7
30906 atoms, 31390 bonds, 46 pseudobonds, 3911 residues, 3 models selected
> color sel royal blue
> select #1/G
6630 atoms, 6770 bonds, 14 pseudobonds, 827 residues, 3 models selected
> color sel green
> clear self
Unknown command: clear self
> select #1/F
4381 atoms, 4476 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color sel lawn green
> select #2:ATP,ADP
Nothing selected
> show sel atoms
> color sel light grey
> style sel stick
Changed 0 atom styles
> color sel byhetero
> select clear
> select #2/B
Nothing selected
> style sel cartoons
Expected a keyword
> hide sel atoms
> select clear
> open
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Predictions/Pif1-AFpulldown-
> models/Pif1-cdc45-unrelaxed-model4.pdb
Chain information for Pif1-cdc45-unrelaxed-model4.pdb #2
---
Chain | Description
B | No description available
C | No description available
> matchmaker #2 to #1/E pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 8p5e, chain E (#1) with Pif1-cdc45-unrelaxed-model4.pdb, chain C
(#2), sequence alignment score = 3024.3
RMSD between 513 pruned atom pairs is 0.991 angstroms; (across all 549 pairs:
1.259)
> undo
> close session
> close session
> cd Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Cryo-
> EM/250205-Krios
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> windowsize width 1000 height 1000
> set bgColor white
> lighting soft
> graphics silhouettes true
> lighting shadows true intensity 0.5
> open 8p5e
8p5e title:
S. cerevisiae nexus-sCMGE after DNA replication initiation [more info...]
Chain information for 8p5e #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
A | DNA (19-MER) |
B | DNA (7-MER) |
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
E | Cell division control protein 45 | CDC45_YEAST 1-650
F | DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
G | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
H | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
I | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213
Non-standard residues in 8p5e #1
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> hide atoms
> show cartoons
> select #1/A,B
539 atoms, 608 bonds, 14 pseudobonds, 26 residues, 2 models selected
> color sel grey
> select #1/H,C,D,I
6676 atoms, 6804 bonds, 4 pseudobonds, 814 residues, 2 models selected
> color sel light sky blue
> clear sel
Unknown command: clear sel
> select #1/E
4282 atoms, 4364 bonds, 4 pseudobonds, 549 residues, 2 models selected
> color sel teal
> clear sel
Unknown command: clear sel
> select #1/2-7
30906 atoms, 31390 bonds, 46 pseudobonds, 3911 residues, 3 models selected
> color sel royal blue
> select #1/G
6630 atoms, 6770 bonds, 14 pseudobonds, 827 residues, 3 models selected
> color sel green
> clear self
Unknown command: clear self
> select #1/F
4381 atoms, 4476 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color sel lawn green
> select #2:ATP,ADP
Nothing selected
> show sel atoms
> color sel light grey
> style sel stick
Changed 0 atom styles
> color sel byhetero
> select clear
> select #2/B
Nothing selected
> style sel cartoons
Expected a keyword
> hide sel atoms
> select clear
> getcrd the Pif1-Cdc45 model 5
Missing or invalid "atoms" argument: invalid atom specifier
> open
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Predictions/Pif1-AFpulldown-
> models/Pif1-cdc45-unrelaxed-model4.pdb
Chain information for Pif1-cdc45-unrelaxed-model4.pdb #2
---
Chain | Description
B | No description available
C | No description available
> matchmaker #1/E to #2/B pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 Pif1-cdc45-unrelaxed-model4.pdb, chain B (#2) with 8p5e, chain E
(#1), sequence alignment score = 79.4
RMSD between 5 pruned atom pairs is 1.252 angstroms; (across all 417 pairs:
50.037)
> select #2/B,C
11768 atoms, 11970 bonds, 1470 residues, 1 model selected
> hide sel cartoons
> clear sel
Unknown command: clear sel
> select #2/B:155-170
130 atoms, 131 bonds, 16 residues, 1 model selected
> show sel cartoons
> color sel orange red
> select clear
> ui tool show Matchmaker
> select clear
> matchmaker #2 to #1/E pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 8p5e, chain E (#1) with Pif1-cdc45-unrelaxed-model4.pdb, chain C
(#2), sequence alignment score = 3024.3
RMSD between 513 pruned atom pairs is 0.991 angstroms; (across all 549 pairs:
1.259)
> select clear
> open
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Predictions/Pif1-AFpulldown-
> models/Pif1-Dpb2-unrelaxed-model5.pdb
Chain information for Pif1-Dpb2-unrelaxed-model5.pdb #3
---
Chain | Description
B | No description available
C | No description available
> matchmaker #3 to #1/F pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 8p5e, chain F (#1) with Pif1-Dpb2-unrelaxed-model5.pdb, chain C
(#3), sequence alignment score = 3153.4
RMSD between 401 pruned atom pairs is 0.962 angstroms; (across all 548 pairs:
11.367)
> select #3/B,C
12051 atoms, 12284 bonds, 1509 residues, 1 model selected
> hide sel cartoons
> clear sel
Unknown command: clear sel
> select #3/B:21-39
155 atoms, 157 bonds, 19 residues, 1 model selected
> show sel cartoons
> color sel orange red
> select clear
> open
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Predictions/Pif1-AFpulldown-
> models/Rrm3(1-80)CMGE.pdb
Chain information for Rrm3(1-80)CMGE.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
> select add #4
13293 atoms, 13554 bonds, 1649 residues, 1 model selected
> select subtract #4
Nothing selected
> select #4/B:80-130
395 atoms, 400 bonds, 51 residues, 1 model selected
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/G
Alignment identifier is 4/G
> view sel
> view
> select add #4
13293 atoms, 13554 bonds, 1649 residues, 1 model selected
> ui tool show Matchmaker
Alignment identifier is 4/B
Alignment identifier is 4/C
Alignment identifier is 4/D
Alignment identifier is 4/E
Alignment identifier is 4/F
Alignment identifier is 4/G
> ui tool show Matchmaker
> select clear
> matchmaker #4 to #1
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 8p5e, chain F (#1) with Rrm3(1-80)CMGE.pdb, chain G (#4), sequence
alignment score = 3153.4
RMSD between 409 pruned atom pairs is 0.824 angstroms; (across all 548 pairs:
2.582)
> matchmaker #4 to #1
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 8p5e, chain F (#1) with Rrm3(1-80)CMGE.pdb, chain G (#4), sequence
alignment score = 3153.4
RMSD between 409 pruned atom pairs is 0.824 angstroms; (across all 548 pairs:
2.582)
> select #4
13293 atoms, 13554 bonds, 1649 residues, 1 model selected
> hide sel cartoons
> select #4/G
5513 atoms, 5634 bonds, 689 residues, 1 model selected
> show sel cartoons
> color sel orange
> select clear
> select #4
13293 atoms, 13554 bonds, 1649 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> show sel cartoons
> color sel orange
> select clear
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> color sel #ff2600ff
> color sel #ea3115ff
> color sel #ea3114ff
> color sel #ea3015ff
> color sel #ea2f15ff
> color sel #ea2e16ff
> color sel #ea2918ff
> color sel #ea2518ff
> color sel #ea2318ff
> color sel #ea2019ff
> color sel #ea1c1aff
> color sel #ea1a1fff
> color sel #ea1a27ff
> color sel #ea192dff
> color sel #ea1931ff
> color sel #ea1833ff
> color sel #ea1834ff
> color sel #ea1835ff
> color sel #ea173aff
> color sel #ea163eff
> color sel #ea1445ff
> color sel #ea154eff
> color sel #ea1a5cff
> color sel #ea1e60ff
> color sel #ea2164ff
> color sel #ea2467ff
> color sel #ea2669ff
> color sel #ea2769ff
> color sel #ea286cff
> color sel #ea2974ff
> color sel #ea297eff
> color sel #ea2883ff
> color sel #ea2886ff
> color sel #ea2889ff
> color sel #ea288cff
> color sel #ea2989ff
> color sel #ea2885ff
> color sel #ea2884ff
> color sel #ea2681ff
> color sel #ea2580ff
> color sel #ea247fff
> color sel #ea227dff
> color sel #ea217cff
> color sel #ea1f7bff
> color sel #ea1e7aff
> color sel #ea1c79ff
> color sel #ea1a77ff
> color sel #ea166fff
> color sel #ea1263ff
> color sel #ea0f59ff
> color sel #ea0d55ff
> color sel #ea0b52ff
> color sel #ea0951ff
> color sel #ea0950ff
> color sel #ea084fff
> color sel #ea074eff
> color sel #ea064eff
> color sel orange
> select clear
> select #1/I
1591 atoms, 1624 bonds, 1 pseudobond, 190 residues, 2 models selected
> color sel light sky blue
> ui tool show "Color Actions"
> color sel cyan
> select #1/D
2014 atoms, 2056 bonds, 245 residues, 1 model selected
> ui tool show "Color Actions"
> color sel turquoise
> color sel medium turquoise
> select #1/C
1408 atoms, 1441 bonds, 2 pseudobonds, 175 residues, 2 models selected
> color sel light sky blue
> ui tool show "Color Actions"
> color sel powder blue
> select #1/2-7
30906 atoms, 31390 bonds, 46 pseudobonds, 3911 residues, 3 models selected
> select clear
> select add #1
53414 atoms, 54412 bonds, 85 pseudobonds, 6675 residues, 4 models selected
> show sel surfaces
> select clear
> view matrix
view matrix camera
-0.39023,-0.80478,-0.44727,-27.073,-0.28839,-0.3545,0.88947,732.38,-0.87439,0.47609,-0.09375,232.53
view matrix models
#1,-0.62133,-0.2275,0.7498,223.16,0.49404,-0.85648,0.14952,333.07,0.60817,0.46333,0.64455,-118.98,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.16784,0.17751,0.9697,31.655,-0.52249,0.81811,-0.2402,271.45,-0.83596,-0.54698,-0.044565,520.32,#3,-0.13634,0.19348,0.97159,22.213,-0.51505,0.82393,-0.23635,267.28,-0.84625,-0.53264,-0.01268,516.05,#4,0.49391,-0.82693,0.26877,165.61,0.83924,0.37251,-0.39613,303.27,0.22745,0.42121,0.87798,235.06
> turn x 90
> view
> turn x -90
> view matrix
view matrix camera
-0.3869,-0.80478,-0.45015,-229.46,-0.29498,-0.3545,0.88731,1120.3,-0.87367,0.47609,-0.10023,171.05
view matrix models
#1,-0.62133,-0.2275,0.7498,223.16,0.49404,-0.85648,0.14952,333.07,0.60817,0.46333,0.64455,-118.98,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.16784,0.17751,0.9697,31.655,-0.52249,0.81811,-0.2402,271.45,-0.83596,-0.54698,-0.044565,520.32,#3,-0.13634,0.19348,0.97159,22.213,-0.51505,0.82393,-0.23635,267.28,-0.84625,-0.53264,-0.01268,516.05,#4,0.49391,-0.82693,0.26877,165.61,0.83924,0.37251,-0.39613,303.27,0.22745,0.42121,0.87798,235.06
> turn x 90
> view name top
> turn 180
Expected an axis vector or a keyword
> turn y 180
> view name bottom
> turn 90
Expected an axis vector or a keyword
> turn x 90
> view side
Expected an objects specifier or a view name or a keyword
> view side
Expected an objects specifier or a view name or a keyword
> view matrix camera
> -0.3869,-0.80478,-0.45015,-229.46,-0.29498,-0.3545,0.88731,1120.3,-0.87367,0.47609,-0.10023,171.05
> view name side
> view top
> view side
> turn x 90
> turn x -90
> turn y -90
> view side
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> view sel
> select clear
> view
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> view sel
> ui tool show "Side View"
> lighting soft
> select clear
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figues/Pif1+Rrm3-CMGE_zoom.png
> width 766 height 681 supersample 3 transparentBackground true
> view side
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figues/Pif1+Rrm3-CMGE_side.png
> width 766 height 681 supersample 3
> bottom
Unknown command: bottom
> view bottom
> view front
Expected an objects specifier or a view name or a keyword
> view side
> turn y -90
> view name front
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figues/Pif1+Rrm3-CMGE_front.png
> width 766 height 681 supersample 3
> select add #2
11768 atoms, 11970 bonds, 1470 residues, 1 model selected
> view sel
> select clear
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figues/Pif1+Rrm3-CMGE_front-
> ZOOM.png width 766 height 681 supersample 3 transparentBackground true
> view
> view side
> select add #2
11768 atoms, 11970 bonds, 1470 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #3
12051 atoms, 12284 bonds, 1509 residues, 1 model selected
> view sel
> select add #4
25344 atoms, 25838 bonds, 3158 residues, 2 models selected
> view sel
> select clear
> view side
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_side.png
> width 766 height 681 supersample 3 transparentBackground true
> view front
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_front.png
> width 766 height 681 supersample 3 transparentBackground true
> view side
> view matrix
view matrix camera
-0.37766,-0.80634,-0.45517,-62.374,-0.3125,-0.35174,0.8824,782.55,-0.87162,0.47549,-0.11914,198.16
view matrix models
#1,-0.62133,-0.2275,0.7498,223.16,0.49404,-0.85648,0.14952,333.07,0.60817,0.46333,0.64455,-118.98,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.16784,0.17751,0.9697,31.655,-0.52249,0.81811,-0.2402,271.45,-0.83596,-0.54698,-0.044565,520.32,#3,-0.13634,0.19348,0.97159,22.213,-0.51505,0.82393,-0.23635,267.28,-0.84625,-0.53264,-0.01268,516.05,#4,0.49391,-0.82693,0.26877,165.61,0.83924,0.37251,-0.39613,303.27,0.22745,0.42121,0.87798,235.06
> view name side
> turn x 90
> view name top
> turn y 180
> view name bottom
> view side
> turn y -90
> view name front
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_front.png
> width 766 height 681 supersample 3 transparentBackground true
> view side
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_side.png
> width 766 height 681 supersample 3 transparentBackground true
> select add #4
13293 atoms, 13554 bonds, 1649 residues, 1 model selected
> view sel
> select #1/F:189@OE1
1 atom, 1 residue, 1 model selected
> select add #4
13294 atoms, 13554 bonds, 1650 residues, 3 models selected
> select add #3
25345 atoms, 25838 bonds, 3159 residues, 4 models selected
> select add #2
37113 atoms, 37808 bonds, 4629 residues, 5 models selected
> show sel atoms
> hide sel atoms
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 395 atom styles
> select #3/B:21-39
155 atoms, 157 bonds, 19 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 155 atom styles
> select #1/H:143@O
1 atom, 1 residue, 1 model selected
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_zoom.png
> width 766 height 681 supersample 3 transparentBackground true
> view front
> select #3/B:21-39
155 atoms, 157 bonds, 19 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 155 atom styles
> select #3/B:21-39
155 atoms, 157 bonds, 19 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 155 atom styles
> select #5/B:155-170
Nothing selected
> show sel atoms
> style sel stick
Changed 0 atom styles
> select #5/B:155-170
Nothing selected
> show sel atoms
> style sel stick
Changed 0 atom styles
> matchmaker #2 to #1/E pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 8p5e, chain E (#1) with Pif1-cdc45-unrelaxed-model4.pdb, chain C
(#2), sequence alignment score = 3024.3
RMSD between 513 pruned atom pairs is 0.991 angstroms; (across all 549 pairs:
1.259)
> select #2/B:155-170
130 atoms, 131 bonds, 16 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 130 atom styles
> view sel
> select clear
> view front
> matchmaker #2 to #1/E pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 8p5e, chain E (#1) with Pif1-cdc45-unrelaxed-model4.pdb, chain C
(#2), sequence alignment score = 3024.3
RMSD between 513 pruned atom pairs is 0.991 angstroms; (across all 549 pairs:
1.259)
> select #2/B:155-170
130 atoms, 131 bonds, 16 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 130 atom styles
> view sel
> select clear
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_front-
> ZOOM.png width 766 height 681 supersample 3 transparentBackground true
> select add #4
13293 atoms, 13554 bonds, 1649 residues, 1 model selected
> select subtract #4
Nothing selected
> view side
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> view side
> hide #3 models
> show #3 models
> hide #3 models
> select #4/B:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> select clear
> hide #2,4#!1 atoms
> interfaces #2,4#!1 & ~solvent
75 buried areas: #4/G #1/F 15496, #2/C #1/E 13818, #4/C #1/D 8225, #4/D #1/H
6788, #4/E #1/I 6546, #4/F #1/C 5556, #1/5 #1/3 4523, #1/2 #1/6 3968, #1/6
#1/4 3958, #1/7 #1/3 3424, #1/5 #1/2 3153, #4/C #1/H 2814, #1/G #1/F 2804,
#1/7 #1/4 2789, #1/G #4/G 2707, #4/C #1/I 2644, #4/C #4/E 2526, #4/G #4/D
2392, #1/D #1/I 2266, #4/C #4/D 2218, #1/D #1/H 2130, #4/E #1/C 1959, #4/G
#1/H 1944, #1/H #4/F 1878, #1/D #4/E 1523, #2/B #1/3 1522, #4/E #4/F 1490,
#4/D #4/F 1456, #1/F #4/D 1333, #1/I #1/C 1317, #4/G #4/B 1306, #1/F #1/H
1253, #1/H #1/C 1187, #1/5 #4/F 1128, #1/F #4/B 1094, #1/5 #4/E 1034, #1/G
#1/5 1034, #1/D #4/D 1024, #1/5 #2/C 1018, #2/C #1/H 950, #1/E #1/H 920, #2/C
#4/D 848, #1/E #4/D 797, #1/2 #1/E 789, #1/5 #1/E 688, #1/2 #2/C 646, #2/C
#4/C 639, #1/E #4/C 625, #2/B #2/C 618, #1/5 #1/C 617, #1/3 #1/C 615, #2/B
#1/E 614, #1/5 #1/I 564, #4/C #4/B 530, #4/E #1/H 524, #1/I #4/F 487, #1/3
#4/F 480, #1/5 #1/F 478, #2/B #1/5 474, #1/D #4/B 464, #1/G #1/2 463, #4/G
#1/5 458, #1/5 #1/A 430, #1/G #2/C 409, #2/B #4/E 390, #4/G #2/C 388, #4/E
#4/D 371, #1/6 #1/A 363, #4/D #1/C 356, #1/H #1/I 352, #4/G #4/C 350, #1/A
#1/B 331, #1/G #1/E 323, #2/B #1/7 304, #4/G #1/D 303
> hide #!1 models
> hide #2 models
> interfaces #4 & ~solvent
9 buried areas: C E 2526, G D 2392, C D 2218, E F 1490, D F 1456, G B 1306, C
B 530, E D 371, G C 350
> show #!1 models
> show sel atoms
> style sel stick
Changed 560 atom styles
> hide sel atoms
> select #1/F:77@CD1
1 atom, 1 residue, 1 model selected
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> ui tool show "Color Actions"
> color sel crimson
> color sel tomato
> color sel orange red
> color sel coral
> color sel fire brick
> color sel orange red
> select clear
> view side
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> view sel
> select clear
> select #4/B
395 atoms, 400 bonds, 51 residues, 1 model selected
> select #4/B:82
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/B:82
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/B:86
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:85-86
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #4/B:82
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/B:82
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:88
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:88-89
19 atoms, 19 bonds, 2 residues, 1 model selected
> show sel atoms
> select #4/B:120
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:120-121
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel cartoons
> select #4/B:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/B:112-118
61 atoms, 62 bonds, 7 residues, 1 model selected
> show sel atoms
> select #4/B:96
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/B:92-96
36 atoms, 36 bonds, 5 residues, 1 model selected
> show sel atoms
> select #4/B:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:100-101
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/B:101
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:101-102
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/B:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select #4/B:101
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:101-102
15 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> select #4/B:104
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/B:104-105
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> select #4/B:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/B:107-109
24 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> select #4/B:82, 88-89,92-96,99,101-102,104-105,107-109,112-118, 120-121
206 atoms, 203 bonds, 25 residues, 1 model selected
> select #1/H:52@OE2
1 atom, 1 residue, 1 model selected
> select clear
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Rrm3-CMGE_side.png
> width 874 height 681 supersample 3 transparentBackground true
> hide #4 models
> show #2 models
> show #3 models
> hide #2 models
> hide #!1 models
> show #2 models
> interfaces #2-3 & ~solvent
3 buried areas: #3/B #3/C 1003, #2/B #2/C 618, #3/B #2/C 555
Alignment identifier is 2/C
Alignment identifier is 3/B
Alignment identifier is 3/C
Alignment identifier is 2/C
Alignment identifier is 3/B
Alignment identifier is 3/C
> select add #3
12146 atoms, 12284 bonds, 1521 residues, 2 models selected
> select add #2
23819 atoms, 24254 bonds, 2979 residues, 2 models selected
> hide #2 models
> select subtract #2
12051 atoms, 12284 bonds, 1509 residues, 1 model selected
> hide #3 models
> show #3 models
> hide #3 models
> select subtract #3
Nothing selected
> show #2 models
> show #!1 models
> select add #1
53757 atoms, 54412 bonds, 85 pseudobonds, 6718 residues, 6 models selected
> open
> /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif
Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open
> /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif
Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open
> /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif
Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open
> /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif
Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open
> /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif
Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif #9
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> select add #5
86131 atoms, 87414 bonds, 85 pseudobonds, 10739 residues, 22 models selected
> select add #6
118505 atoms, 120416 bonds, 85 pseudobonds, 14760 residues, 23 models selected
> select add #7
150879 atoms, 153418 bonds, 85 pseudobonds, 18781 residues, 24 models selected
> select add #8
183253 atoms, 186420 bonds, 85 pseudobonds, 22802 residues, 25 models selected
> select add #9
215627 atoms, 219422 bonds, 85 pseudobonds, 26823 residues, 26 models selected
> ui tool show Matchmaker
> matchmaker #6-9 to #5
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 fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5) with
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif, chain G (#6), sequence alignment
score = 4699.3
RMSD between 870 pruned atom pairs is 0.413 angstroms; (across all 914 pairs:
0.829)
Matchmaker fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5) with
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif, chain G (#7), sequence alignment
score = 4707.1
RMSD between 882 pruned atom pairs is 0.800 angstroms; (across all 914 pairs:
0.983)
Matchmaker fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5) with
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif, chain G (#8), sequence alignment
score = 4707.7
RMSD between 827 pruned atom pairs is 0.790 angstroms; (across all 914 pairs:
2.042)
Matchmaker fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5) with
fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif, chain G (#9), sequence alignment
score = 4704.1
RMSD between 844 pruned atom pairs is 0.873 angstroms; (across all 914 pairs:
1.312)
> show sel & #2,5-9#!1 cartoons
> hide sel & #2,5-9#!1 surfaces
> hide sel & #2,5-9#!1 atoms
> select add #3
227610 atoms, 231706 bonds, 85 pseudobonds, 28323 residues, 26 models selected
> select add #2
239103 atoms, 243676 bonds, 85 pseudobonds, 29759 residues, 26 models selected
> select add #1
239103 atoms, 243676 bonds, 85 pseudobonds, 29759 residues, 27 models selected
> select subtract #1
185689 atoms, 189264 bonds, 23084 residues, 22 models selected
> select subtract #2
173921 atoms, 177294 bonds, 21614 residues, 6 models selected
> select subtract #3
161870 atoms, 165010 bonds, 20105 residues, 5 models selected
> select add #1
215284 atoms, 219422 bonds, 85 pseudobonds, 26780 residues, 10 models selected
> select add #2
227052 atoms, 231392 bonds, 85 pseudobonds, 28250 residues, 26 models selected
> select subtract #2
215284 atoms, 219422 bonds, 85 pseudobonds, 26780 residues, 25 models selected
> show sel surfaces
> select subtract #1
161870 atoms, 165010 bonds, 20105 residues, 60 models selected
> hide sel surfaces
> select clear
> matchmaker #5 to #1 bring #6-9
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 8p5e, chain G (#1) with
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5), sequence alignment
score = 4302.7
RMSD between 551 pruned atom pairs is 1.266 angstroms; (across all 825 pairs:
2.292)
> view
> select add #5
32374 atoms, 33002 bonds, 4021 residues, 1 model selected
> select add #6
64748 atoms, 66004 bonds, 8042 residues, 10 models selected
> select add #7
97122 atoms, 99006 bonds, 12063 residues, 19 models selected
> select add #9
129496 atoms, 132008 bonds, 16084 residues, 28 models selected
> select add #8
161870 atoms, 165010 bonds, 20105 residues, 37 models selected
> color sel bychain
> select subtract #7
129496 atoms, 132008 bonds, 16084 residues, 44 models selected
> select subtract #8
97122 atoms, 99006 bonds, 12063 residues, 35 models selected
> select subtract #9
64748 atoms, 66004 bonds, 8042 residues, 26 models selected
> select subtract #6
32374 atoms, 33002 bonds, 4021 residues, 17 models selected
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> select #5-9/A
34295 atoms, 34910 bonds, 4295 residues, 5 models selected
Alignment identifier is 1
> select clear
> select #1/F:387@CD2
1 atom, 1 residue, 1 model selected
> select #1/F:685@CB
1 atom, 1 residue, 1 model selected
> select #5/A:89
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:89 #6/A:89 #7/A:89 #8/A:89 #9/A:89
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #5/A:77-89 #6/A:77-89 #7/A:77-89 #8/A:77-89 #9/A:77-89
535 atoms, 535 bonds, 65 residues, 5 models selected
. [ID: 1] region 5 chains [77-89] RMSD: 18.532
> select #5/A:9-87 #6/A:9-87 #7/A:9-87 #8/A:9-87 #9/A:9-87
3215 atoms, 3285 bonds, 395 residues, 5 models selected
> select #5/A:9-89 #6/A:9-89 #7/A:9-89 #8/A:9-89 #9/A:9-89
3305 atoms, 3375 bonds, 405 residues, 5 models selected
. [ID: 1] region 5 chains [9-89] RMSD: 28.045
> select #5/A:71-72 #6/A:71-72 #7/A:71-72 #8/A:71-72 #9/A:71-72
70 atoms, 65 bonds, 10 residues, 5 models selected
> select #5/A:71-84 #6/A:71-84 #7/A:71-84 #8/A:71-84 #9/A:71-84
585 atoms, 595 bonds, 70 residues, 5 models selected
. [ID: 1] region 5 chains [71-84] RMSD: 11.550
> select add #5
32842 atoms, 33478 bonds, 4077 residues, 10 models selected
> select add #6
65099 atoms, 66361 bonds, 8084 residues, 17 models selected
> select subtract #5
32725 atoms, 33359 bonds, 4063 residues, 23 models selected
> hide #!5 models
> select subtract #6
351 atoms, 357 bonds, 42 residues, 14 models selected
> show #!6 models
> select add #7
32608 atoms, 33240 bonds, 4049 residues, 6 models selected
> hide #!6 models
> show #!7 models
> select subtract #7
234 atoms, 238 bonds, 28 residues, 12 models selected
> show #!8 models
> hide #!7 models
> sequence associate #5-9/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 5
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 5 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 5
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 5 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 5
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 5 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 5
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 5 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif chain A from 5
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif chain A to 5 chains
with 0 mismatches
> sequence header rmsd show
Chains used in RMSD evaluation for alignment 1:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif #9/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
> select #5-9/A
34295 atoms, 34910 bonds, 4295 residues, 5 models selected
> color byattribute r:seq_rmsd #!5-9 & sel target c palette
> 0,blue:3,white:6,red
4295 residues, atom seq_rmsd range 2.32 to 91
> show #!7 models
> show #!6 models
> show #!5 models
> select #5/A:74 #6/A:74 #7/A:74 #8/A:74 #9/A:74
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #5/A:74-79 #6/A:74-79 #7/A:74-79 #8/A:74-79 #9/A:74-79
275 atoms, 285 bonds, 30 residues, 5 models selected
. [ID: 1] region 5 chains [74-79] RMSD: 6.476
> select #5/A:73 #6/A:73 #7/A:73 #8/A:73 #9/A:73
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #5/A:73-86 #6/A:73-86 #7/A:73-86 #8/A:73-86 #9/A:73-86
595 atoms, 605 bonds, 70 residues, 5 models selected
. [ID: 1] region 5 chains [73-86] RMSD: 13.603
> show sel & #!5-8 cartoons
> select add #5
32850 atoms, 33486 bonds, 4077 residues, 10 models selected
> select add #6
65105 atoms, 66367 bonds, 8084 residues, 17 models selected
> select add #7
97360 atoms, 99248 bonds, 12091 residues, 24 models selected
> select add #8
129615 atoms, 132129 bonds, 16098 residues, 31 models selected
> select add #9
161870 atoms, 165010 bonds, 20105 residues, 38 models selected
> hide sel & #!5-8 cartoons
> select #5/A:70 #6/A:70 #7/A:70 #8/A:70 #9/A:70
30 atoms, 25 bonds, 5 residues, 5 models selected
> select #5/A:70-82 #6/A:70-82 #7/A:70-82 #8/A:70-82 #9/A:70-82
530 atoms, 540 bonds, 65 residues, 5 models selected
. [ID: 1] region 5 chains [70-82] RMSD: 10.010
> show sel & #!5-8 cartoons
> select clear
> show #!9 models
> hide #!9 models
> open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_0.cif
Chain information for fold_scpif1_cdc45_model_0.cif #10
---
Chain | Description
A | .
B | .
> open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_1.cif
Chain information for fold_scpif1_cdc45_model_1.cif #11
---
Chain | Description
A | .
B | .
> open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_2.cif
Chain information for fold_scpif1_cdc45_model_2.cif #12
---
Chain | Description
A | .
B | .
> open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_3.cif
Chain information for fold_scpif1_cdc45_model_3.cif #13
---
Chain | Description
A | .
B | .
> open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_4.cif
Chain information for fold_scpif1_cdc45_model_4.cif #14
---
Chain | Description
A | .
B | .
Computing secondary structure
> close #9
Chains used in RMSD evaluation for alignment 1:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> select add #10
12090 atoms, 12303 bonds, 1509 residues, 1 model selected
> select add #12
24180 atoms, 24606 bonds, 3018 residues, 2 models selected
> select add #11
36270 atoms, 36909 bonds, 4527 residues, 3 models selected
> select add #13
48360 atoms, 49212 bonds, 6036 residues, 4 models selected
> select add #14
60450 atoms, 61515 bonds, 7545 residues, 5 models selected
> ui tool show Matchmaker
> matchmaker #10-13 to #14
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 fold_scpif1_cdc45_model_4.cif, chain A (#14) with
fold_scpif1_cdc45_model_0.cif, chain A (#10), sequence alignment score =
4242.6
RMSD between 535 pruned atom pairs is 0.596 angstroms; (across all 859 pairs:
45.545)
Matchmaker fold_scpif1_cdc45_model_4.cif, chain A (#14) with
fold_scpif1_cdc45_model_1.cif, chain A (#11), sequence alignment score =
4315.2
RMSD between 526 pruned atom pairs is 0.842 angstroms; (across all 859 pairs:
51.531)
Matchmaker fold_scpif1_cdc45_model_4.cif, chain A (#14) with
fold_scpif1_cdc45_model_2.cif, chain A (#12), sequence alignment score =
4264.8
RMSD between 531 pruned atom pairs is 0.943 angstroms; (across all 859 pairs:
42.410)
Matchmaker fold_scpif1_cdc45_model_4.cif, chain A (#14) with
fold_scpif1_cdc45_model_3.cif, chain A (#13), sequence alignment score =
4174.8
RMSD between 544 pruned atom pairs is 0.589 angstroms; (across all 859 pairs:
43.841)
> matchmaker #10 to #1 bring #11-14
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 8p5e, chain E (#1) with fold_scpif1_cdc45_model_0.cif, chain B
(#10), sequence alignment score = 3044.1
RMSD between 518 pruned atom pairs is 1.024 angstroms; (across all 549 pairs:
1.242)
> select clear
> select add #10
12090 atoms, 12303 bonds, 1509 residues, 1 model selected
> select add #11
24180 atoms, 24606 bonds, 3018 residues, 2 models selected
> select add #12
36270 atoms, 36909 bonds, 4527 residues, 3 models selected
> select add #13
48360 atoms, 49212 bonds, 6036 residues, 4 models selected
> select add #14
60450 atoms, 61515 bonds, 7545 residues, 5 models selected
> hide sel cartoons
> select #10-14/A
34295 atoms, 34910 bonds, 4295 residues, 5 models selected
> show sel cartoons
> select sequence chain
Nothing selected
> sequence chain #10-15/A
Alignment identifier is 2
> sequence associate #10-15/A
Associated fold_scpif1_cdc45_model_0.cif chain A to 5 chains with 0 mismatches
Chains used in RMSD evaluation for alignment 1:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A
Associated fold_scpif1_cdc45_model_1.cif chain A to 5 chains with 0 mismatches
Chains used in RMSD evaluation for alignment 1:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A
Associated fold_scpif1_cdc45_model_2.cif chain A to 5 chains with 0 mismatches
Chains used in RMSD evaluation for alignment 1:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A
Associated fold_scpif1_cdc45_model_3.cif chain A to 5 chains with 0 mismatches
Chains used in RMSD evaluation for alignment 1:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A
Associated fold_scpif1_cdc45_model_4.cif chain A to 5 chains with 0 mismatches
Chains used in RMSD evaluation for alignment 1:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Disassociated fold_scpif1_cdc45_model_0.cif chain A from 5 chains
Associated fold_scpif1_cdc45_model_0.cif chain A to 5 chains with 0 mismatches
Disassociated fold_scpif1_cdc45_model_1.cif chain A from 5 chains
Associated fold_scpif1_cdc45_model_1.cif chain A to 5 chains with 0 mismatches
Disassociated fold_scpif1_cdc45_model_2.cif chain A from 5 chains
Associated fold_scpif1_cdc45_model_2.cif chain A to 5 chains with 0 mismatches
Disassociated fold_scpif1_cdc45_model_3.cif chain A from 5 chains
Associated fold_scpif1_cdc45_model_3.cif chain A to 5 chains with 0 mismatches
Disassociated fold_scpif1_cdc45_model_4.cif chain A from 5 chains
Associated fold_scpif1_cdc45_model_4.cif chain A to 5 chains with 0 mismatches
> sequence header rmsd show
Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_model_0.cif
#10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif
#12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif
#14/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,blue:3,white:6,red
No atoms specified
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,blue:3,white:6,red
No atoms specified
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,blue:3,white:6,red
No atoms specified
> select #10/A:2 #11/A:2 #12/A:2 #13/A:2 #14/A:2
35 atoms, 35 bonds, 5 residues, 5 models selected
> select #10/A:2-71 #11/A:2-71 #12/A:2-71 #13/A:2-71 #14/A:2-71
2855 atoms, 2925 bonds, 350 residues, 5 models selected
. [ID: 2] region 5 chains [2-71] RMSD: 91.536
> select #10/A:2 #11/A:2 #12/A:2 #13/A:2 #14/A:2
35 atoms, 35 bonds, 5 residues, 5 models selected
> select #10/A:2-78 #11/A:2-78 #12/A:2-78 #13/A:2-78 #14/A:2-78
3160 atoms, 3245 bonds, 385 residues, 5 models selected
. [ID: 2] region 5 chains [2-78] RMSD: 91.003
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,blue:3,white:6,red
385 residues, atom seq_rmsd range 77.7 to 99.6
> select add #14
14618 atoms, 14899 bonds, 1817 residues, 5 models selected
> select add #13
26076 atoms, 26553 bonds, 3249 residues, 5 models selected
> select add #12
37534 atoms, 38207 bonds, 4681 residues, 5 models selected
> select add #11
48992 atoms, 49861 bonds, 6113 residues, 5 models selected
> select subtract #11
36902 atoms, 37558 bonds, 4604 residues, 4 models selected
> select add #11
48992 atoms, 49861 bonds, 6113 residues, 5 models selected
> select add #10
60450 atoms, 61515 bonds, 7545 residues, 5 models selected
> select subtract #11
48360 atoms, 49212 bonds, 6036 residues, 4 models selected
> select subtract #12
36270 atoms, 36909 bonds, 4527 residues, 3 models selected
> select subtract #10
24180 atoms, 24606 bonds, 3018 residues, 2 models selected
> select subtract #13
12090 atoms, 12303 bonds, 1509 residues, 1 model selected
> select subtract #14
Nothing selected
> select #10/A
6859 atoms, 6982 bonds, 859 residues, 1 model selected
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,blue:3,white:6,red
859 residues, atom seq_rmsd range 0.121 to 123
> select #10-14/A
34295 atoms, 34910 bonds, 4295 residues, 5 models selected
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,blue:3,white:6,red
4295 residues, atom seq_rmsd range 0.121 to 123
> select clear
> select #10/A:235-236 #11/A:235-236 #12/A:235-236 #13/A:235-236 #14/A:235-236
70 atoms, 65 bonds, 10 residues, 5 models selected
> select #10/A:234-236 #11/A:234-236 #12/A:234-236 #13/A:234-236 #14/A:234-236
105 atoms, 105 bonds, 15 residues, 5 models selected
. [ID: 2] region 5 chains [234-236] RMSD: 0.861
> select #10/A:195-202 #11/A:195-202 #12/A:195-202 #13/A:195-202 #14/A:195-202
335 atoms, 335 bonds, 40 residues, 5 models selected
> select #10/A:195-209 #11/A:195-209 #12/A:195-209 #13/A:195-209 #14/A:195-209
605 atoms, 610 bonds, 75 residues, 5 models selected
. [ID: 2] region 5 chains [195-209] RMSD: 14.324
> hide #!1 models
> hide #2 models
> select add #10
12574 atoms, 12791 bonds, 1569 residues, 5 models selected
> select add #11
24543 atoms, 24972 bonds, 3063 residues, 5 models selected
> select add #13
36512 atoms, 37153 bonds, 4557 residues, 5 models selected
> select add #14
48481 atoms, 49334 bonds, 6051 residues, 5 models selected
> select add #12
60450 atoms, 61515 bonds, 7545 residues, 5 models selected
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #10-13 to #14/B pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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_scpif1_cdc45_model_4.cif, chain B (#14) with
fold_scpif1_cdc45_model_0.cif, chain B (#10), sequence alignment score =
3321.3
RMSD between 576 pruned atom pairs is 0.462 angstroms; (across all 650 pairs:
3.529)
Matchmaker fold_scpif1_cdc45_model_4.cif, chain B (#14) with
fold_scpif1_cdc45_model_1.cif, chain B (#11), sequence alignment score =
3323.1
RMSD between 579 pruned atom pairs is 0.358 angstroms; (across all 650 pairs:
4.221)
Matchmaker fold_scpif1_cdc45_model_4.cif, chain B (#14) with
fold_scpif1_cdc45_model_2.cif, chain B (#12), sequence alignment score =
3296.7
RMSD between 595 pruned atom pairs is 0.450 angstroms; (across all 650 pairs:
2.009)
Matchmaker fold_scpif1_cdc45_model_4.cif, chain B (#14) with
fold_scpif1_cdc45_model_3.cif, chain B (#13), sequence alignment score =
3331.5
RMSD between 566 pruned atom pairs is 0.469 angstroms; (across all 650 pairs:
3.329)
> select #10-14/A
34295 atoms, 34910 bonds, 4295 residues, 5 models selected
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,blue:3,white:6,red
4295 residues, atom seq_rmsd range 0.405 to 120
> select #10-14/B
26155 atoms, 26605 bonds, 3250 residues, 5 models selected
> select color teal
Expected an objects specifier or a keyword
> color sel teal
> show #4 models
> hide #4 models
> select #10/A:195 #11/A:195 #12/A:195 #13/A:195 #14/A:195
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #10/A:195-210 #11/A:195-210 #12/A:195-210 #13/A:195-210 #14/A:195-210
635 atoms, 640 bonds, 80 residues, 5 models selected
. [ID: 2] region 5 chains [195-210] RMSD: 2.329
> select add #5
33009 atoms, 33642 bonds, 4101 residues, 6 models selected
> select add #6
65383 atoms, 66644 bonds, 8122 residues, 15 models selected
> select add #14
77346 atoms, 78819 bonds, 9615 residues, 23 models selected
> select clear
> select add #14
12090 atoms, 12303 bonds, 1509 residues, 1 model selected
> select add #13
24180 atoms, 24606 bonds, 3018 residues, 2 models selected
> select add #12
36270 atoms, 36909 bonds, 4527 residues, 3 models selected
> select add #11
48360 atoms, 49212 bonds, 6036 residues, 4 models selected
> select add #10
60450 atoms, 61515 bonds, 7545 residues, 5 models selected
> hide sel cartoons
> select #10/A:193 #11/A:193 #12/A:193 #13/A:193 #14/A:193
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #10/A:193-207 #11/A:193-207 #12/A:193-207 #13/A:193-207 #14/A:193-207
605 atoms, 605 bonds, 75 residues, 5 models selected
. [ID: 2] region 5 chains [193-207] RMSD: 3.410
> select #10/A:211 #11/A:211 #12/A:211 #13/A:211 #14/A:211
55 atoms, 55 bonds, 5 residues, 5 models selected
> select #10/A:195-211 #11/A:195-211 #12/A:195-211 #13/A:195-211 #14/A:195-211
690 atoms, 700 bonds, 85 residues, 5 models selected
. [ID: 2] region 5 chains [195-211] RMSD: 2.678
> show sel cartoons
> show #!1 models
> matchmaker #10/B to #1 bring #11-14
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 8p5e, chain E (#1) with fold_scpif1_cdc45_model_0.cif, chain B
(#10), sequence alignment score = 3044.1
RMSD between 518 pruned atom pairs is 1.024 angstroms; (across all 549 pairs:
1.242)
> select clear
> select #10/A:193-194 #11/A:193-194 #12/A:193-194 #13/A:193-194 #14/A:193-194
90 atoms, 85 bonds, 10 residues, 5 models selected
> select #10/A:193-211 #11/A:193-211 #12/A:193-211 #13/A:193-211 #14/A:193-211
780 atoms, 790 bonds, 95 residues, 5 models selected
. [ID: 2] region 5 chains [193-211] RMSD: 3.540
> view sel
> select clear
> view front
> select #5-15/A
61731 atoms, 62838 bonds, 7731 residues, 9 models selected
Fetching compressed palette 0,orange from
https://www.colourlovers.com/api/palettes?keywords=0%2Corange&format=json&numResults=100
Could not find palette 0,orange at COLOURlovers.com using keyword search
> color byattribute r:seq_rmsd #!5-9 & sel target c palette
> 0,red:3,orange:6,purple
3436 residues, atom seq_rmsd range 58.2 to 141
> color byattribute r:seq_rmsd #!5-14 & sel target c palette
> 0,red:3,orange:6,purple
7731 residues, atom seq_rmsd range 0.405 to 141
> color byattribute r:seq_rmsd #!5-14 & sel target c palette
> 0,yellow:3,orange:6,purple
7731 residues, atom seq_rmsd range 0.405 to 141
> select clear
> color byattribute r:seq_rmsd #!5-8 & sel target c palette
> 0,yellow:3,orange:6,purple
No atoms specified
> select clear
Fetching compressed palette 0,red from
https://www.colourlovers.com/api/palettes?keywords=0%2Cred&format=json&numResults=100
Could not find palette 0,red at COLOURlovers.com using keyword search
> color byattribute r:seq_rmsd #!5-8 & sel target c palette
> Red:0,white:3,blue:6,
Invalid "palette" argument: Invalid color name or specifier
> color byattribute r:seq_rmsd #!5-8 & sel target c palette
> red:0,white:3,blue:6,
Invalid "palette" argument: Missing color name or specifier
> color byattribute r:seq_rmsd #!5-8 & sel target c palette
> 0,red:3,white:6,blue
No atoms specified
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,red:3,white:6,blue
No atoms specified
> select add #5
32374 atoms, 33002 bonds, 4021 residues, 1 model selected
> select add #6
64748 atoms, 66004 bonds, 8042 residues, 10 models selected
> select add #10
76838 atoms, 78307 bonds, 9551 residues, 19 models selected
> select add #11
88928 atoms, 90610 bonds, 11060 residues, 20 models selected
> select add #12
101018 atoms, 102913 bonds, 12569 residues, 21 models selected
> select add #13
113108 atoms, 115216 bonds, 14078 residues, 22 models selected
> select add #14
125198 atoms, 127519 bonds, 15587 residues, 23 models selected
> color byattribute r:seq_rmsd #!10-14 & sel target c palette
> 0,red:3,white:6,blue
7545 residues, atom seq_rmsd range 0.405 to 120
> select clear
> select #10/A:133 #11/A:133 #12/A:133 #13/A:133 #14/A:133
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #10/A:133-151 #11/A:133-151 #12/A:133-151 #13/A:133-151 #14/A:133-151
760 atoms, 770 bonds, 95 residues, 5 models selected
. [ID: 2] region 5 chains [133-151] RMSD: 116.226
> select
> #10/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844
> #11/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844
> #12/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844
> #13/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844
> #14/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844
14035 atoms, 14095 bonds, 1690 residues, 5 models selected
> select #10/A:212 #11/A:212 #12/A:212 #13/A:212 #14/A:212
35 atoms, 30 bonds, 5 residues, 5 models selected
> select #10/A:196-212 #11/A:196-212 #12/A:196-212 #13/A:196-212 #14/A:196-212
680 atoms, 690 bonds, 85 residues, 5 models selected
. [ID: 2] region 5 chains [196-212] RMSD: 3.199
> select #10/A:194 #11/A:194 #12/A:194 #13/A:194 #14/A:194
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #10/A:194-213 #11/A:194-213 #12/A:194-213 #13/A:194-213 #14/A:194-213
815 atoms, 825 bonds, 100 residues, 5 models selected
. [ID: 2] region 5 chains [194-213] RMSD: 3.639
> select #5-8/A
27436 atoms, 27928 bonds, 3436 residues, 4 models selected
> sequence chain #5-8/A
Alignment identifier is 1
> sequence associate #5-8/A
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 5 chains
with 0 mismatches
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 5 chains
with 0 mismatches
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 5 chains
with 0 mismatches
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 5 chains
with 0 mismatches
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains
with 0 mismatches
> sequence header rmsd
> select #5-8/A
27436 atoms, 27928 bonds, 3436 residues, 4 models selected
Could not find palette 0,orange at COLOURlovers.com using keyword search
Could not find palette 0,orange at COLOURlovers.com using keyword search
> select add #8
52951 atoms, 53948 bonds, 6598 residues, 8 models selected
> select add #7
78466 atoms, 79968 bonds, 9760 residues, 15 models selected
> select add #5
103981 atoms, 105988 bonds, 12922 residues, 22 models selected
> select add #6
129496 atoms, 132008 bonds, 16084 residues, 29 models selected
> select clear
Could not find palette 0,orange at COLOURlovers.com using keyword search
> color byattribute r:seq_rmsd #!5-8 & sel target c palette
> 0,red:3,white:6,blue
No atoms specified
> select #5-8/A
27436 atoms, 27928 bonds, 3436 residues, 4 models selected
> color byattribute r:seq_rmsd #!5-8 & sel target c palette
> 0,red:3,white:6,blue
3436 residues, atom seq_rmsd range 63.2 to 143
> select add #5
52951 atoms, 53948 bonds, 6598 residues, 8 models selected
> select add #6
78466 atoms, 79968 bonds, 9760 residues, 15 models selected
> select add #7
103981 atoms, 105988 bonds, 12922 residues, 22 models selected
> select subtract #7
71607 atoms, 72986 bonds, 8901 residues, 28 models selected
> select add #7
103981 atoms, 105988 bonds, 12922 residues, 21 models selected
> select add #8
129496 atoms, 132008 bonds, 16084 residues, 29 models selected
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #!5-8 to #1/F pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 8p5e, chain F (#1) with
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain H (#5), sequence alignment
score = 3118
RMSD between 402 pruned atom pairs is 1.014 angstroms; (across all 548 pairs:
3.618)
Matchmaker 8p5e, chain F (#1) with
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif, chain H (#6), sequence alignment
score = 3112
RMSD between 403 pruned atom pairs is 1.008 angstroms; (across all 548 pairs:
3.962)
Matchmaker 8p5e, chain F (#1) with
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif, chain H (#7), sequence alignment
score = 3145
RMSD between 403 pruned atom pairs is 1.004 angstroms; (across all 548 pairs:
5.556)
Matchmaker 8p5e, chain F (#1) with
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif, chain H (#8), sequence alignment
score = 3131.8
RMSD between 395 pruned atom pairs is 1.036 angstroms; (across all 548 pairs:
5.353)
> select subtract #8
97122 atoms, 99006 bonds, 12063 residues, 35 models selected
> select subtract #7
64748 atoms, 66004 bonds, 8042 residues, 26 models selected
> select subtract #5
32374 atoms, 33002 bonds, 4021 residues, 17 models selected
> select subtract #6
8 models selected
> select add #5
32374 atoms, 33002 bonds, 4021 residues, 1 model selected
> select subtract #5
8 models selected
> hide #!5 models
> show #!5 models
> select add #5
32374 atoms, 33002 bonds, 4021 residues, 1 model selected
> select add #6
64748 atoms, 66004 bonds, 8042 residues, 10 models selected
> select add #7
97122 atoms, 99006 bonds, 12063 residues, 19 models selected
> select add #8
129496 atoms, 132008 bonds, 16084 residues, 28 models selected
> hide sel cartoons
> select subtract #5
97122 atoms, 99006 bonds, 12063 residues, 35 models selected
> select add #5
129496 atoms, 132008 bonds, 16084 residues, 28 models selected
> show sel cartoons
> sequence chain #5-8/A
Alignment identifier is 3
> sequence associate #5-8/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 5
chains
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 5 chains
with 0 mismatches
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 5
chains
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 5 chains
with 0 mismatches
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 5
chains
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 5 chains
with 0 mismatches
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 5
chains
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 5 chains
with 0 mismatches
Chains used in RMSD evaluation for alignment 2:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A,
fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A,
fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A,
fold_scpif1_cdc45_model_4.cif #14/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains
with 0 mismatches
> sequence header rmsd
> select #5-8/A
27436 atoms, 27928 bonds, 3436 residues, 4 models selected
> color byattribute r:seq_rmsd #!5-8 & sel target c palette
> 0,red:3,white:6,blue
3436 residues, atom seq_rmsd range 63.7 to 143
> sequence header rmsd
> show sel & #!5-8 cartoons
> sequence chain #5-8/A
Alignment identifier is 1
> sequence associate #5-8/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains
with 0 mismatches
> sequence header rmsd
> sequence header rmsd
> select #5/A:1-2 #6/A:1-2 #7/A:1-2 #8/A:1-2
60 atoms, 60 bonds, 8 residues, 4 models selected
> select #5/A:1-312 #6/A:1-312 #7/A:1-312 #8/A:1-312
9884 atoms, 10064 bonds, 1248 residues, 4 models selected
. [ID: 1] region 4 chains [1-312] RMSD: 47.118
> select #5/A:248-312 #6/A:248-312 #7/A:248-312 #8/A:248-312
1856 atoms, 1876 bonds, 260 residues, 4 models selected
> select #5/A:181-312 #6/A:181-312 #7/A:181-312 #8/A:181-312
4020 atoms, 4064 bonds, 528 residues, 4 models selected
. [ID: 1] region 4 chains [181-312] RMSD: 39.346
> sequence associate #5-8/A sequence header rmsd
Expected alignment-id or [alignment-id:]sequence-name-or-number or a keyword
> sequence associate #5-8/A
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains
with 0 mismatches
Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4
chains
Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains
with 0 mismatches
> sequence header rmsd
> select #5-8/A
27436 atoms, 27928 bonds, 3436 residues, 4 models selected
> sequence header rmsd
> sequence header rmsd show
Chains used in RMSD evaluation for alignment 1:
fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A,
fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
> select #5/A:70 #6/A:70 #7/A:70 #8/A:70
24 atoms, 20 bonds, 4 residues, 4 models selected
> select #5/A:70-86 #6/A:70-86 #7/A:70-86 #8/A:70-86
556 atoms, 564 bonds, 68 residues, 4 models selected
. [ID: 1] region 4 chains [70-86] RMSD: 6.706
> select #5/A:87-88 #6/A:87-88 #7/A:87-88 #8/A:87-88
72 atoms, 68 bonds, 8 residues, 4 models selected
> select #5/A:70-88 #6/A:70-88 #7/A:70-88 #8/A:70-88
628 atoms, 636 bonds, 76 residues, 4 models selected
. [ID: 1] region 4 chains [70-88] RMSD: 6.894
> select #5-8/A
27436 atoms, 27928 bonds, 3436 residues, 4 models selected
> color byattribute r:seq_rmsd #!5-8 & sel target c palette
> 0,red:3,white:6,blue
3436 residues, atom seq_rmsd range 1.28 to 98.1
> hide #5-8 cartoons
> select #5/A:70-71 #6/A:70-71 #7/A:70-71 #8/A:70-71
56 atoms, 52 bonds, 8 residues, 4 models selected
> select #5/A:70-88 #6/A:70-88 #7/A:70-88 #8/A:70-88
628 atoms, 636 bonds, 76 residues, 4 models selected
. [ID: 1] region 4 chains [70-88] RMSD: 6.894
> show sel cartoons
> select #5/A:86 #6/A:86 #7/A:86 #8/A:86
36 atoms, 32 bonds, 4 residues, 4 models selected
> select #5/A:86-89 #6/A:86-89 #7/A:86-89 #8/A:86-89
144 atoms, 140 bonds, 16 residues, 4 models selected
. [ID: 1] region 4 chains [86-89] RMSD: 9.807
> hide sel cartoons
> view side
> select #5/A:71-72 #6/A:71-72 #7/A:71-72 #8/A:71-72
56 atoms, 52 bonds, 8 residues, 4 models selected
> select #5/A:71-87 #6/A:71-87 #7/A:71-87 #8/A:71-87
568 atoms, 576 bonds, 68 residues, 4 models selected
. [ID: 1] region 4 chains [71-87] RMSD: 5.778
> view sel
> select clear
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1rmds-
> CMGE_side-zoom.png width 874 height 681 supersample 3 transparentBackground
> true
> view front
> turn x90
Expected an axis vector or a keyword
> turn x 90
> turn y 90
> turn y -180
> select add #10
12090 atoms, 12303 bonds, 1509 residues, 1 model selected
> select add #11
24180 atoms, 24606 bonds, 3018 residues, 2 models selected
> select add #12
36270 atoms, 36909 bonds, 4527 residues, 3 models selected
> select add #13
48360 atoms, 49212 bonds, 6036 residues, 4 models selected
> select add #14
60450 atoms, 61515 bonds, 7545 residues, 5 models selected
> view sel
> view bottom
> view sel
> select clear
> save
> /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1rmds-
> CMGE_cdc45side-zoom.png width 874 height 681 supersample 3
> transparentBackground true
> select #5/A:86-87 #6/A:86-87 #7/A:86-87 #8/A:86-87
72 atoms, 68 bonds, 8 residues, 4 models selected
> select #5/A:82-87 #6/A:82-87 #7/A:82-87 #8/A:82-87
204 atoms, 200 bonds, 24 residues, 4 models selected
. [ID: 1] region 4 chains [82-87] RMSD: 6.717
> select #5/A:71-72 #6/A:71-72 #7/A:71-72 #8/A:71-72
56 atoms, 52 bonds, 8 residues, 4 models selected
> select #5/A:71-86 #6/A:71-86 #7/A:71-86 #8/A:71-86
532 atoms, 540 bonds, 64 residues, 4 models selected
. [ID: 1] region 4 chains [71-86] RMSD: 5.757
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15G0007QDK/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 5 days, 21 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LS24A40xU:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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
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httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
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importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
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ipywidgets: 8.1.5
jaraco.context: 5.3.0
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jedi: 0.19.1
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matplotlib: 3.9.2
matplotlib-inline: 0.1.7
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
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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
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PyQt6-commercial: 6.7.1
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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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