﻿id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17963	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
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)


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{
  ""uptime"" : 210000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro18,3"",
  ""coalitionID"" : 1197,
  ""osVersion"" : {
    ""train"" : ""macOS 15.5"",
    ""build"" : ""24F74"",
    ""releaseType"" : ""User""
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  ""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""},
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  ""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"",
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  ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":6531},
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  ""faultingThread"" : 0,
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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
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2
}}}
"	defect	assigned	normal		Window Toolkit								all	ChimeraX
