The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000031ddac000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031cda9000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031bda6000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031ada3000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000319da0000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000318d9d000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000317d9a000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000316d97000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000315d94000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000314d91000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000313d8e000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000312d8b000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000311d88000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000200d4e280 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-08-24 18:41:56.00 -0700","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.4.1 (22F770820d)","roots_installed":0,"name":"ChimeraX","incident_id":"EFF39D7A-66B2-4C7C-A2A4-5B730D8B81F9"}
{
"uptime" : 760000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,4",
"coalitionID" : 10679,
"osVersion" : {
"train" : "macOS 13.4.1",
"build" : "22F770820d",
"releaseType" : "User"
},
"captureTime" : "2023-08-24 18:40:17.3375 -0700",
"incident" : "EFF39D7A-66B2-4C7C-A2A4-5B730D8B81F9",
"pid" : 76500,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-08-09 15:13:54.0609 -0700",
"procStartAbsTime" : 11776405956016,
"procExitAbsTime" : 18417242441822,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"EA6ABEBD-5E75-5084-9BE1-67221A78FB02","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "615851EF-D4A9-6607-87F2-9E91E8C5A723",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 2,
"sleepWakeUUID" : "F67FE9C7-DFAC-442C-AB93-FE65E1DDD289",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140722735431656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc90a84000-7ffc9fbb8000 [241.2M] r-x\/r-x SM=COW ...t_id=3e49f94f",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140722735431656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc90a84000-7ffc9fbb8000 [241.2M] r-x\/r-x SM=COW ...t_id=3e49f94f",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/luca/Downloads/cryosparc_P338_J28_class_00_00500_volume.mrc
Opened cryosparc_P338_J28_class_00_00500_volume.mrc as #1, grid size 64,64,64,
pixel 3.64, shown at level 0.793, step 1, values float32
> volume #1 level 1.09
> close session
> open /Users/luca/Downloads/cryosparc_P338_J28_class_00_00600_volume.mrc
Opened cryosparc_P338_J28_class_00_00600_volume.mrc as #1, grid size 64,64,64,
pixel 3.64, shown at level 0.756, step 1, values float32
> volume #1 level 1.282
> close session
> open /Users/luca/Downloads/cryosparc_P338_J28_class_00_00700_volume.mrc
Opened cryosparc_P338_J28_class_00_00700_volume.mrc as #1, grid size 64,64,64,
pixel 3.64, shown at level 0.744, step 1, values float32
> volume #1 level 1.432
> close session
> open /Users/luca/Downloads/cryosparc_P338_J28_class_00_final_volume.mrc
Opened cryosparc_P338_J28_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 1.82, shown at level 0.267, step 1, values float32
> volume #1 level 0.3339
> volume #1 level 0.3743
> open /Users/luca/Downloads/cryosparc_P338_J29_002_volume_map_sharp.mrc
Opened cryosparc_P338_J29_002_volume_map_sharp.mrc as #2, grid size
128,128,128, pixel 1.82, shown at level 0.908, step 1, values float32
> volume #2 level 1.124
> open /Users/luca/Downloads/cryosparc_P338_J26_003_volume_map_sharp.mrc
Opened cryosparc_P338_J26_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.91, shown at level 0.081, step 1, values float32
> volume #3 level 0.08355
> open /Users/luca/Downloads/cryosparc_P338_J25_class_00_final_volume.mrc
Opened cryosparc_P338_J25_class_00_final_volume.mrc as #4, grid size
128,128,128, pixel 1.82, shown at level 0.186, step 1, values float32
> hide #!3 models
> volume #4 level 0.3723
> open /Users/luca/Downloads/cryosparc_P338_J33_class_00_00000_volume.mrc
Opened cryosparc_P338_J33_class_00_00000_volume.mrc as #5, grid size 64,64,64,
pixel 3.64, shown at level 0.673, step 1, values float32
> volume #5 level 0.4716
> close session
> open "/Users/luca/Downloads/cryosparc_P338_J33_class_00_00000_volume
> (1).mrc"
Opened cryosparc_P338_J33_class_00_00000_volume (1).mrc as #1, grid size
64,64,64, pixel 3.64, shown at level 0.673, step 1, values float32
> volume #1 level 0.3924
> close session
> open "/Users/luca/Downloads/cryosparc_P338_J33_class_00_00000_volume
> (2).mrc"
Opened cryosparc_P338_J33_class_00_00000_volume (2).mrc as #1, grid size
64,64,64, pixel 3.64, shown at level 0.673, step 1, values float32
> volume #1 level 0.3776
> volume #1 level 0.7543
> close session
> open /Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume.mrc
Opened cryosparc_P338_J33_class_00_00400_volume.mrc as #1, grid size 64,64,64,
pixel 3.64, shown at level 0.821, step 1, values float32
> volume #1 level 0.5567
> volume #1 level 0.5658
> volume #1 level 0.7706
> volume #1 level 1.13
> open "/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume
> (1).mrc"
Opened cryosparc_P338_J33_class_00_00400_volume (1).mrc as #2, grid size
64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32
> volume #2 level 0.9799
> volume #2 level 1.044
> volume #2 level 0.7524
> volume #2 level 1.253
> volume #2 level 0.4793
> open "/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume
> (2).mrc"
Opened cryosparc_P338_J33_class_00_00400_volume (2).mrc as #3, grid size
64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32
> volume #3 level 0.7363
> close #3
> open "/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume
> (3).mrc"
Opened cryosparc_P338_J33_class_00_00400_volume (3).mrc as #3, grid size
64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32
> volume #3 level 0.502
> volume #2 level 0.3669
> close #3
> close #2
> close #1
> open "/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume
> (3).mrc"
Opened cryosparc_P338_J33_class_00_00400_volume (3).mrc as #1, grid size
64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32
> volume #1 level 0.4975
> volume #1 level 0.9753
> open "/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume
> (4).mrc"
Opened cryosparc_P338_J33_class_00_00400_volume (4).mrc as #2, grid size
64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32
> volume #2 level 0.9298
> open /Users/luca/Downloads/cryosparc_P338_J33_class_00_final_volume.mrc
Opened cryosparc_P338_J33_class_00_final_volume.mrc as #3, grid size
128,128,128, pixel 1.82, shown at level 0.274, step 1, values float32
> close #1
> close #2
> volume #3 level 0.3548
> oepn 4w5r
Unknown command: oepn 4w5r
> open 4w5r
4w5r title:
The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA
Containing Seed Pairing from 2-8 (Long Target) [more info...]
Chain information for 4w5r #1
---
Chain | Description | UniProt
A | Protein argonaute-2 | AGO2_HUMAN 1-859
B | RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*UP*U)-3') |
D | RNA (5'-R(P*AP*AP*UP*GP*UP*GP*AP*AP*A)-3') |
Non-standard residues in 4w5r #1
---
IPA — isopropyl alcohol (2-propanol)
IPH — phenol
MG — magnesium ion
> select add #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-3.071,0,1,0,7.3938,0,0,1,4.26
> select add #1
7005 atoms, 7070 bonds, 32 pseudobonds, 956 residues, 6 models selected
> view matrix models
> #3,1,0,0,-9.0761,0,1,0,17.328,0,0,1,19.342,#1,1,0,0,-6.0051,0,1,0,9.9338,0,0,1,15.082
> select subtract #3
7005 atoms, 7070 bonds, 32 pseudobonds, 956 residues, 4 models selected
> view matrix models #1,1,0,0,-47.563,0,1,0,101.28,0,0,1,85.733
> view matrix models #1,1,0,0,31.974,0,1,0,134.67,0,0,1,130.29
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.18479,-0.03013,0.98232,66.496,-0.86517,-0.47913,0.14806,171.07,0.46619,-0.87723,-0.11461,110.4
> view matrix models
> #1,-0.12749,0.92727,0.35201,101.81,-0.82843,0.095606,-0.55188,183.41,-0.5454,-0.36197,0.75599,162.76
> view matrix models
> #1,-0.28882,0.89363,0.34353,111.18,-0.70482,0.044373,-0.708,177.79,-0.64793,-0.44661,0.61703,169.99
> fitmap #1 inMap #3
Fit molecule 4w5r (#1) to map cryosparc_P338_J33_class_00_final_volume.mrc
(#3) using 7005 atoms
average map value = 0.4065, steps = 104
shifted from previous position = 23.7
rotated from previous position = 27.8 degrees
atoms outside contour = 2578, contour level = 0.35475
Position of 4w5r (#1) relative to cryosparc_P338_J33_class_00_final_volume.mrc
(#3) coordinates:
Matrix rotation and translation
-0.52514277 0.65064588 0.54852986 145.60182305
-0.80600685 -0.17342691 -0.56592938 175.56091051
-0.27308978 -0.73931255 0.61549892 114.73456628
Axis -0.10312104 0.48866491 -0.86635596
Axis point 125.63093130 75.24083125 0.00000000
Rotation angle (degrees) 122.78822009
Shift along axis -28.62512920
> volume #3 color #b2ffff80
> ui mousemode right translate
> select subtract #1
Nothing selected
> volume #3 level 0.3369
> volume #3 level 0.2458
> volume #3 level 0.2423
> open /Users/luca/Downloads/cryosparc_P338_J36_002_volume_map_sharp.mrc
Opened cryosparc_P338_J36_002_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.91, shown at level 0.118, step 1, values float32
> select add #1
7005 atoms, 7070 bonds, 32 pseudobonds, 956 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.52514,0.65065,0.54853,148.78,-0.80601,-0.17343,-0.56593,191.85,-0.27309,-0.73931,0.6155,112.75
> select subtract #1
Nothing selected
> fitmap #1 inMap #2
Fit molecule 4w5r (#1) to map cryosparc_P338_J36_002_volume_map_sharp.mrc (#2)
using 7005 atoms
average map value = 0.1592, steps = 124
shifted from previous position = 16.9
rotated from previous position = 2.43 degrees
atoms outside contour = 1324, contour level = 0.11795
Position of 4w5r (#1) relative to cryosparc_P338_J36_002_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.49299766 0.65561043 0.57195128 143.24545670
-0.82256967 -0.13707364 -0.55189668 176.50503678
-0.28342978 -0.74255355 0.60686224 115.38981914
Axis -0.11094751 0.49776542 -0.86018616
Axis point 126.98745031 75.31060187 0.00000000
Rotation angle (degrees) 120.77076574
Shift along axis -27.29134749
> volume #2 color #b2b2ff80
> volume #2 level 0.01723
> volume #2 level 0.1324
> open 7ki3
7ki3 title:
Human Argonaute2:miR-122 bound to the HCV genotype 1a site-1 RNA [more
info...]
Chain information for 7ki3 #4
---
Chain | Description | UniProt
A D | Protein argonaute-2 | AGO2_HUMAN 1-859
B E | miR-122 |
C F | HCV genotype 1a miR-122 site-1 |
Non-standard residues in 7ki3 #4
---
BA — barium ion
7ki3 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> split #4
Split 7ki3 (#4) into 6 models
Chain information for 7ki3 A #4.1
---
Chain | Description
A | No description available
Chain information for 7ki3 B #4.2
---
Chain | Description
B | No description available
Chain information for 7ki3 C #4.3
---
Chain | Description
C | No description available
Chain information for 7ki3 D #4.4
---
Chain | Description
D | No description available
Chain information for 7ki3 E #4.5
---
Chain | Description
E | No description available
Chain information for 7ki3 F #4.6
---
Chain | Description
F | No description available
> hide #!4.2 models
> hide #!4.3 models
> hide #!4.5 models
> hide #!4.4 models
> hide #!4.6 models
> select add #4.1
6434 atoms, 6585 bonds, 5 pseudobonds, 805 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> view matrix models #4.1,1,0,0,2.6709,0,1,0,104.26,0,0,1,70.271
> view matrix models #4.1,1,0,0,82.075,0,1,0,110.05,0,0,1,77.832
> ui mousemode right "rotate selected models"
> view matrix models
> #4.1,-0.22254,-0.95733,0.1844,111.5,0.65048,-0.28669,-0.70334,128.1,0.72619,-0.036575,0.68653,71.712
> view matrix models
> #4.1,-0.69944,0.61905,-0.35715,127.96,-0.077958,-0.56284,-0.82288,150.86,-0.71042,-0.54772,0.44193,116.63
> fitmap #4.1 inMap #3
Fit molecule 7ki3 A (#4.1) to map cryosparc_P338_J33_class_00_final_volume.mrc
(#3) using 6434 atoms
average map value = 0.4019, steps = 168
shifted from previous position = 32.9
rotated from previous position = 33.3 degrees
atoms outside contour = 1133, contour level = 0.24226
Position of 7ki3 A (#4.1) relative to
cryosparc_P338_J33_class_00_final_volume.mrc (#3) coordinates:
Matrix rotation and translation
-0.63240895 0.74930610 0.19646703 120.50726057
-0.48292867 -0.18306497 -0.85631018 166.49236275
-0.60567220 -0.63641778 0.47763332 115.53081255
Axis 0.14790952 0.53955496 -0.82885657
Axis point 113.57066268 88.94396613 -0.00000000
Rotation angle (degrees) 131.98378749
Shift along axis 11.89747755
> fitmap #4.1 inMap #2
Fit molecule 7ki3 A (#4.1) to map cryosparc_P338_J36_002_volume_map_sharp.mrc
(#2) using 6434 atoms
average map value = 0.1587, steps = 172
shifted from previous position = 27.7
rotated from previous position = 0.742 degrees
atoms outside contour = 1691, contour level = 0.13245
Position of 7ki3 A (#4.1) relative to
cryosparc_P338_J36_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.63650877 0.74738436 0.19045526 120.86109405
-0.47178353 -0.18194298 -0.86273811 166.44771829
-0.61014497 -0.63899403 0.46841194 115.83778862
Axis 0.15162932 0.54255947 -0.82621896
Axis point 113.55858005 89.56375972 0.00000000
Rotation angle (degrees) 132.45569595
Shift along axis 12.92649548
> select subtract #4.1
Nothing selected
> ui mousemode right translate
> hide #!1 models
> open /Users/luca/Downloads/cryosparc_P338_J38_002_volume_map_sharp.mrc
Opened cryosparc_P338_J38_002_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 0.91, shown at level 0.14, step 1, values float32
> volume #5 level 0.1773
> show #!1 models
> volume #5 color #ffb2ff80
> fitmap #1 inMap #5
Fit molecule 4w5r (#1) to map cryosparc_P338_J38_002_volume_map_sharp.mrc (#5)
using 7005 atoms
average map value = 0.2189, steps = 56
shifted from previous position = 0.736
rotated from previous position = 2.67 degrees
atoms outside contour = 2815, contour level = 0.17731
Position of 4w5r (#1) relative to cryosparc_P338_J38_002_volume_map_sharp.mrc
(#5) coordinates:
Matrix rotation and translation
-0.51150010 0.65824658 0.55233964 144.10619490
-0.81999133 -0.18176091 -0.54274965 175.51076010
-0.25686935 -0.73053022 0.63272722 113.62226947
Axis -0.11074177 0.47722318 -0.87177652
Axis point 125.34716977 74.16246341 0.00000000
Rotation angle (degrees) 122.02348987
Shift along axis -31.25399912
> hide #!4 models
> volume #5 level 0.3491
> volume #5 level 0.2406
> open "/Users/luca/Downloads/cryosparc_P338_J38_002_volume_map_sharp (1).mrc"
Opened cryosparc_P338_J38_002_volume_map_sharp (1).mrc as #6, grid size
256,256,256, pixel 0.91, shown at level 0.119, step 1, values float32
> volume #6 level 0.1603
> close #5
> volume #6 level 0.1467
> volume #6 level 0.1535
Must specify one map, got 0
Must specify one map, got 0
> volume #6 level 0.1239
> volume #6 color #ffb2b280
> close #2
> close #3
> close #4
> volume #6 level 0.2367
> volume #6 level 0.1681
> open
> /Users/luca/Downloads/cryosparc_P338_J81_class_00_00142_volume_sharp.mrc
Opened cryosparc_P338_J81_class_00_00142_volume_sharp.mrc as #2, grid size
128,128,128, pixel 1.82, shown at level 0.288, step 1, values float32
> open
> /Users/luca/Downloads/cryosparc_P338_J81_class_01_00142_volume_sharp.mrc
Opened cryosparc_P338_J81_class_01_00142_volume_sharp.mrc as #3, grid size
128,128,128, pixel 1.82, shown at level 0.37, step 1, values float32
> open
> /Users/luca/Downloads/cryosparc_P338_J81_class_02_00142_volume_sharp.mrc
Opened cryosparc_P338_J81_class_02_00142_volume_sharp.mrc as #4, grid size
128,128,128, pixel 1.82, shown at level 0.18, step 1, values float32
> open
> /Users/luca/Downloads/cryosparc_P338_J81_class_03_00142_volume_sharp.mrc
Opened cryosparc_P338_J81_class_03_00142_volume_sharp.mrc as #5, grid size
128,128,128, pixel 1.82, shown at level 0.224, step 1, values float32
> hide #!1 models
> hide #!6 models
> tile #2-5
4 models tiled
> ui hideFloating toggle
> ~tile #2-5
> hide #!2 models
> hide #!4 models
> hide #!5 models
> volume #3 level 0.3259
> show #!1 models
> open 6n4o
6n4o title:
Human Argonaute2-miR-122 bound to a seed and supplementary paired target [more
info...]
Chain information for 6n4o #7
---
Chain | Description | UniProt
A | Protein argonaute-2 | AGO2_HUMAN 1-859
C | RNA
(5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3') |
D | RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3') |
> hide #!1 models
> view
> select add #7
7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected
> color #7 silver
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,134.41,0,1,0,86.47,0,0,1,145.57
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.92303,-0.3844,-0.015891,137.82,-0.33201,-0.775,-0.53772,87.264,0.19438,0.50161,-0.84297,81.09
> view matrix models
> #7,0.8078,-0.33082,-0.48786,120.04,-0.27178,-0.94347,0.18975,114.19,-0.52306,-0.02069,-0.85205,77.825
> select subtract #7
Nothing selected
> view
> fitmap #7 inMap #3
Fit molecule 6n4o (#7) to map
cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) using 7064 atoms
average map value = 0.5235, steps = 76
shifted from previous position = 12.1
rotated from previous position = 6.89 degrees
atoms outside contour = 1179, contour level = 0.32585
Position of 6n4o (#7) relative to
cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.64862780 0.66298115 -0.37381541 105.48492075
-0.24663666 0.64773526 0.72083938 126.01241295
0.72003634 -0.37535987 0.58365455 152.38074407
Axis -0.61036037 -0.60905330 -0.50647240
Axis point 0.00000000 65.30435132 41.55386414
Rotation angle (degrees) 63.89555715
Shift along axis -218.30873293
> volume #3 color #e5bf9980
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!3 models
> select add #2
2 models selected
> view matrix models
> #2,-0.57006,0.78117,-0.25456,129.4,0.63265,0.61504,0.47062,-87.102,0.5242,0.10724,-0.84482,140.11
> view matrix models
> #2,0.22379,-0.50724,-0.83224,244.28,0.77159,-0.42949,0.46924,11.616,-0.59546,-0.74716,0.29526,234.51
> view matrix models
> #2,-0.63442,0.71251,0.29972,80.286,0.71648,0.39651,0.57396,-84.953,0.29011,0.57888,-0.76206,106.3
> view matrix models
> #2,-0.59942,0.60826,0.52031,62.035,0.80007,0.4356,0.41249,-80.423,0.024257,0.66353,-0.74775,126.79
> hide #!3 models
> hide #!7 models
> view matrix models
> #2,-0.27642,-0.95564,0.10168,244.54,-0.71411,0.27505,0.64373,89.698,-0.64314,0.10533,-0.75847,268.51
> view matrix models
> #2,-0.41526,-0.87606,-0.24509,292.44,0.84008,-0.26594,-0.47281,94.768,0.34903,-0.40223,0.8464,20.781
> view matrix models
> #2,-0.26903,-0.90879,-0.31894,287.3,0.93496,-0.16692,-0.31303,54.101,0.23124,-0.38241,0.89459,26.955
> show #!3 models
> view matrix models
> #2,0.065034,0.94046,0.33363,-31.554,-0.74388,0.26854,-0.61198,239.59,-0.66514,-0.20838,0.71706,134.51
> view matrix models
> #2,-0.93809,0.08739,-0.3352,258.71,0.28792,-0.34132,-0.89476,217.38,-0.1926,-0.93588,0.29503,207.62
> volume #2 flipNormals
Missing "flipNormals" keyword's argument
> volume #2 flipNormals z
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> volume #2 flipz
Expected a keyword
> volume flip #2
Opened cryosparc_P338_J81_class_00_00142_volume_sharp.mrc z flip as #8, grid
size 128,128,128, pixel 1.82, shown at step 1, values float32
> select subtract #2
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.26322,0.94827,0.1775,24.99,-0.6288,-0.029099,-0.77702,277.98,-0.73166,-0.31614,0.60393,167.63
> view matrix models
> #8,-0.44751,0.89256,0.055398,67.001,0.52616,0.2127,0.82335,-69.664,0.72311,0.3976,-0.56482,51.394
> view matrix models
> #8,-0.43927,0.64907,0.62109,27.696,0.84768,0.070549,0.5258,-57.813,0.29746,0.75745,-0.5812,64.052
> view matrix models
> #8,-0.27642,0.71873,0.63799,-1.1989,0.92354,0.015032,0.3832,-44.263,0.26583,0.69513,-0.66793,84.646
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.27642,0.71873,0.63799,-9.0153,0.92354,0.015032,0.3832,-43.882,0.26583,0.69513,-0.66793,76.115
> select subtract #8
Nothing selected
> ui mousemode right translate
> fitmap #8 inMap #3
Fit map cryosparc_P338_J81_class_00_00142_volume_sharp.mrc z flip in map
cryosparc_P338_J81_class_01_00142_volume_sharp.mrc using 20966 points
correlation = 0.9155, correlation about mean = 0.3598, overlap = 5706
steps = 108, shift = 2.95, angle = 13.2 degrees
Position of cryosparc_P338_J81_class_00_00142_volume_sharp.mrc z flip (#8)
relative to cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3)
coordinates:
Matrix rotation and translation
-0.99567086 0.06298972 0.06835091 217.19583721
-0.07382409 -0.98271577 -0.16976376 259.76578932
0.05647615 -0.17407477 0.98311161 19.46765305
Axis -0.03137660 0.08642742 -0.99576393
Axis point 112.78241990 126.97925006 0.00000000
Rotation angle (degrees) 176.06079682
Shift along axis -3.74916630
> hide #!3 models
> volume #8 level 0.4246
> show #!2 models
> hide #!8 models
> volume #8 level 0.4524
> hide #!8 models
> volume #2 level 0.4942
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!3 models
> select add #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.50566,-0.47369,-0.72105,305.97,0.69708,0.26811,-0.66498,67.807,0.50832,-0.83889,0.19462,132.82
> view matrix models
> #5,-0.1187,-0.29358,-0.94854,264.66,0.77891,0.56492,-0.27232,-19.749,0.61579,-0.77115,0.16162,115.96
> fitmap #5 inMap #3
Fit map cryosparc_P338_J81_class_03_00142_volume_sharp.mrc in map
cryosparc_P338_J81_class_01_00142_volume_sharp.mrc using 20953 points
correlation = 0.8656, correlation about mean = 0.3181, overlap = 4732
steps = 120, shift = 6.76, angle = 22.4 degrees
Position of cryosparc_P338_J81_class_03_00142_volume_sharp.mrc (#5) relative
to cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.65589195 -0.72842587 0.19799370 255.15172882
-0.40663589 0.56193744 0.72032880 12.64178605
-0.63596621 0.39194651 -0.66477434 216.39418224
Axis -0.34483118 0.87573352 0.33790866
Axis point 161.55241525 0.00000000 69.03857300
Rotation angle (degrees) 151.56578913
Shift along axis -3.79196762
> select subtract #5
Nothing selected
> volume #5 level 0.1967
> open 7KX9
Summary of feedback from opening 7KX9 fetched from pdb
---
notes | Fetching compressed mmCIF 7kx9 from
http://files.rcsb.org/download/7kx9.cif
Fetching CCD OMG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif
7kx9 title:
Cryo-EM structure of Ephydatia fluviatilis PiwiA-piRNA-target complex [more
info...]
Chain information for 7kx9 #9
---
Chain | Description | UniProt
A | Piwi-A | D5MRY8_9METZ 220-987
B | RNA
(5'-R(P*UP*CP*UP*CP*UP*UP*GP*AP*GP*UP*UP*GP*GP*AP*CP*AP*AP*AP*UP*GP*GP*CP*AP*(OMG))-3')
|
C | RNA (5'-R(P*UP*GP*UP*CP*CP*AP*AP*CP*UP*CP*AP*AP*GP*AP*GP*A)-3') |
Non-standard residues in 7kx9 #9
---
MG — magnesium ion
> select add #9
12424 atoms, 12646 bonds, 43 pseudobonds, 776 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,37.459,0,1,0,79.187,0,0,1,49.245
> view matrix models #9,1,0,0,72.428,0,1,0,63.017,0,0,1,45.299
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.071579,-0.47086,-0.8793,198.84,0.37597,0.8038,-0.46103,78.537,0.92386,-0.36359,0.11949,63.578
> view matrix models
> #9,-0.95277,-0.14204,0.26845,165.79,-0.25182,0.86358,-0.43682,106.54,-0.16978,-0.48379,-0.85856,178.64
> view matrix models
> #9,-0.95632,0.28493,0.065261,154.99,0.12818,0.60943,-0.78241,118.53,-0.2627,-0.73987,-0.61934,183.72
> fitmap #9 inMap #3
Fit molecule 7kx9 (#9) to map
cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) using 12424 atoms
average map value = 0.4928, steps = 116
shifted from previous position = 13.7
rotated from previous position = 24 degrees
atoms outside contour = 2529, contour level = 0.32585
Position of 7kx9 (#9) relative to
cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.64716431 -0.08501905 0.75759495 115.36697829
0.74746078 -0.26621230 0.60863239 59.60477086
0.14993574 0.96015768 0.23583151 50.79616015
Axis 0.32280710 0.55801592 0.76446962
Axis point 47.23097824 26.77123450 0.00000000
Rotation angle (degrees) 147.01073029
Shift along axis 109.33381277
> select subtract #9
Nothing selected
> hide #!5 models
> close #9
> volume #3 level 0.3148
> volume #3 level 0.3617
> show #!1 models
> hide #!1 models
> volume #3 level 0.414
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!3 models
> open "/Users/luca/Dropbox (Scripps Research)/Modified_Guides/structures and
> maps/221027_Ago2-ON1_modified_guide_modelled_WIP.pdb"
Chain information for 221027_Ago2-ON1_modified_guide_modelled_WIP.pdb #9
---
Chain | Description
A | No description available
B | No description available
> view #9 clip false
> open /Users/luca/Downloads/cryosparc_P338_J137_004_volume_map_sharp.mrc
Opened cryosparc_P338_J137_004_volume_map_sharp.mrc as #10, grid size
128,128,128, pixel 1.82, shown at level 0.372, step 1, values float32
> close session
> open /Users/luca/Downloads/cryosparc_P338_J137_004_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P338_J137_004_volume_map_sharp.mrc as #1, grid size
128,128,128, pixel 1.82, shown at level 0.372, step 1, values float32
> volume #1 level 0.9025
> volume #1 color #b2b2b280
> open 6n4o
6n4o title:
Human Argonaute2-miR-122 bound to a seed and supplementary paired target [more
info...]
Chain information for 6n4o #2
---
Chain | Description | UniProt
A | Protein argonaute-2 | AGO2_HUMAN 1-859
C | RNA
(5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3') |
D | RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3') |
> select add #2
7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,149.19,0,1,0,80.787,0,0,1,143.45
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.10865,-0.99388,0.020007,147.68,-0.7006,0.090839,0.70775,106.34,-0.70523,0.062882,-0.70618,76.954
> fitmap #2 inMap #1
Fit molecule 6n4o (#2) to map cryosparc_P338_J137_004_volume_map_sharp.mrc
(#1) using 7064 atoms
average map value = 0.6122, steps = 228
shifted from previous position = 27
rotated from previous position = 54.8 degrees
atoms outside contour = 5152, contour level = 0.90246
Position of 6n4o (#2) relative to cryosparc_P338_J137_004_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.67901032 -0.52854607 0.50949390 129.14480096
-0.11621978 0.76265161 0.63628256 123.56513617
-0.72487099 0.37282915 -0.57927582 80.16845187
Axis -0.19841209 0.92962518 0.31053127
Axis point 86.89605717 0.00000000 -11.56484224
Rotation angle (degrees) 138.40165473
Shift along axis 114.14018341
> ui mousemode right translate
> select subtract #2
Nothing selected
> volume #1 level 0.8371
> open /Users/luca/Downloads/cryosparc_P318_J65_005_volume_map_sharp.mrc
Opened cryosparc_P318_J65_005_volume_map_sharp.mrc as #3, grid size
128,128,128, pixel 1.82, shown at level 0.352, step 1, values float32
> hide #!2 models
> volume #3 level 0.9178
> close #3
> open /Users/luca/Downloads/cryosparc_P338_J142_003_volume_map_sharp.mrc
Opened cryosparc_P338_J142_003_volume_map_sharp.mrc as #3, grid size
128,128,128, pixel 1.82, shown at level 0.356, step 1, values float32
> hide #!1 models
> volume #3 level 0.5851
> volume #3 level 0.6044
> show #!1 models
> volume #1 level 0.6772
> open /Users/luca/Downloads/cryosparc_P338_J150_003_volume_map_sharp.mrc
Opened cryosparc_P338_J150_003_volume_map_sharp.mrc as #4, grid size
128,128,128, pixel 1.82, shown at level 0.301, step 1, values float32
> volume #4 level 0.5582
> open /Users/luca/Downloads/cryosparc_P338_J149_004_volume_map_sharp.mrc
Opened cryosparc_P338_J149_004_volume_map_sharp.mrc as #5, grid size
128,128,128, pixel 1.82, shown at level 0.314, step 1, values float32
> hide #!4 models
> volume #5 level 0.8024
> show #!2 models
> fitmap #2 inMap #5
Fit molecule 6n4o (#2) to map cryosparc_P338_J149_004_volume_map_sharp.mrc
(#5) using 7064 atoms
average map value = 0.5297, steps = 80
shifted from previous position = 2.7
rotated from previous position = 7.28 degrees
atoms outside contour = 5392, contour level = 0.80242
Position of 6n4o (#2) relative to cryosparc_P338_J149_004_volume_map_sharp.mrc
(#5) coordinates:
Matrix rotation and translation
-0.74089486 -0.42110233 0.52320898 125.49275417
-0.03059541 0.79937714 0.60005009 124.93352663
-0.67092379 0.42856623 -0.60513821 80.77151964
Axis -0.13523831 0.94173588 0.30796775
Axis point 79.70912723 0.00000000 -7.08664080
Rotation angle (degrees) 140.65368478
Shift along axis 125.55797880
> volume #5 level 0.4616
> volume #5 level 0.6182
> open /Users/luca/Downloads/cryosparc_P338_J146_005_volume_map_sharp.mrc
Opened cryosparc_P338_J146_005_volume_map_sharp.mrc as #6, grid size
128,128,128, pixel 1.82, shown at level 0.363, step 1, values float32
> hide #!5 models
> volume #6 level 0.4134
> open /Users/luca/Documents/my_alphafold/230811_VEE-nsP1234_XtoG/ranked_0.pdb
Chain information for ranked_0.pdb #7
---
Chain | Description
A | No description available
> close session
> open /Users/luca/Documents/my_alphafold/230811_VEE-nsP1234_XtoG/ranked_0.pdb
> format pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
> ui tool show "AlphaFold Error Plot"
Must choose path to predicted aligned file
> alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE-
> nsP1234_XtoG/confidence_model_1_multimer_v3_pred_0.json
JSON file "/Users/luca/Documents/my_alphafold/230811_VEE-
nsP1234_XtoG/confidence_model_1_multimer_v3_pred_0.json" is not AlphaFold
predicted aligned error data, expected a top level list
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE-
> nsP1234_XtoG/pae_model_1_multimer_v3_pred_0.json
> color #1:511-1675 lime
> color #1:1022-1022 lime
> color #1:1978-1978 magenta
> color #1:734-734 lime
> color #1:1164-1164 magenta
> color #1:557-557 lime
> color #1:820-820 magenta
> color #1:537-537 lime
> color #1:754-754 magenta
> color #1:511-992 lime
> color #1:491-491 lime
> color #1:506-506 magenta
> color #1:56-289 lime
> color #1:385-385 lime
> color #1:486-486 magenta
> color #1:1-501 lime
> color #1:1270-1270 lime
> color #1:537-537 magenta
> color #1:466-466 lime
> color #1:785-785 magenta
> color #1:527-1675 lime
> color #1:1073-1073 lime
> color #1:1316-1316 magenta
> color #1:1326-1508 lime
> color #1:525-1674 lime
> color #1:532-532 lime
> color #1:1543-1543 magenta
> color #1:1853-2491 lime
> color #1:1853-1853 lime
> color #1:2041-2041 magenta
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE-
> nsP1234_XtoG/features.pkl
File /Users/luca/Documents/my_alphafold/230811_VEE-nsP1234_XtoG/features.pkl
does not contain AlphaFold predicted aligned error (PAE) data. The AlphaFold
"monomer" preset does not compute PAE. Run AlphaFold with the "monomer_ptm" or
"multimer" presets to get PAE values.
> hide #1 models
> show #1 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE-
> nsP1234_XtoG/pae_model_3_multimer_v3_pred_0.json
> color #1:129-566 lime
> color #1:896-896 lime
> color #1:384-384 magenta
> color #1:5-519 lime
> color #1:634-634 lime
> color #1:394-394 magenta
> color #1:510-1689 lime
> color #1:488-488 lime
> color #1:677-677 magenta
> color #1:492-1682 lime
> color #1:1104-1104 lime
> color #1:1974-1974 magenta
> color #1:519-1671 lime
> color #1:1863-2499 magenta
> color #1:1148-1148 lime
> color #1:2010-2010 magenta
> color #1:532-1006 lime
> color #1:1838-2494 magenta
> color #1:1884-1884 lime
> color #1:1808-1808 magenta
> color #1:1818-2474 lime
> color #1:1374-1374 lime
> color #1:1641-1641 magenta
> color #1:488-990 lime
> color #1:116-116 lime
> color #1:970-970 magenta
> color #1:490-997 lime
> color #1:390-390 lime
> color #1:1788-1788 magenta
> color #1:510-1689 lime
> color #1:351-351 lime
> color #1:854-854 magenta
> color #1:1838-2499 lime
> color #1:500-995 lime
> color #1:448-448 lime
> color #1:1863-1863 magenta
> open /Users/luca/Downloads/cryosparc_P338_J141_003_volume_map_sharp.mrc
Opened cryosparc_P338_J141_003_volume_map_sharp.mrc as #2, grid size
128,128,128, pixel 1.82, shown at level 0.35, step 1, values float32
> open /Users/luca/Downloads/cryosparc_P338_J141_003_volume_mask_refine.mrc
Opened cryosparc_P338_J141_003_volume_mask_refine.mrc as #3, grid size
128,128,128, pixel 1.82, shown at level 1, step 1, values float32
> hide #1 models
> volume #3 level 1
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 1
> volume #2 level 0.1019
> volume #2 level 0.08281
> open /Users/luca/Downloads/cryosparc_P338_J143_003_volume_map_sharp.mrc
Opened cryosparc_P338_J143_003_volume_map_sharp.mrc as #4, grid size
128,128,128, pixel 1.82, shown at level 0.368, step 1, values float32
> hide #!2 models
> volume #4 level 0.219
> volume #4 level 0.4265
> open 6n4o
6n4o title:
Human Argonaute2-miR-122 bound to a seed and supplementary paired target [more
info...]
Chain information for 6n4o #5
---
Chain | Description | UniProt
A | Protein argonaute-2 | AGO2_HUMAN 1-859
C | RNA
(5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3') |
D | RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3') |
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select add #5
7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected
> view matrix models #5,1,0,0,91.347,0,1,0,108,0,0,1,173.46
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.8277,-0.36026,0.43027,85.377,-0.092838,0.84407,0.52813,126.13,-0.55344,0.39719,-0.73208,103.84
> fitmap #5 inMap #4
Fit molecule 6n4o (#5) to map cryosparc_P338_J143_003_volume_map_sharp.mrc
(#4) using 7064 atoms
average map value = 0.643, steps = 204
shifted from previous position = 45.4
rotated from previous position = 13.9 degrees
atoms outside contour = 2486, contour level = 0.4265
Position of 6n4o (#5) relative to cryosparc_P338_J143_003_volume_map_sharp.mrc
(#4) coordinates:
Matrix rotation and translation
-0.68599554 -0.51093406 0.51803139 128.74194912
-0.10048106 0.77166942 0.62803652 123.52402063
-0.72063422 0.37877790 -0.58070098 79.94218834
Axis -0.18762507 0.93238390 0.30896132
Axis point 85.80712635 0.00000000 -11.16278108
Rotation angle (degrees) 138.37545014
Shift along axis 115.71563536
> select subtract #5
Nothing selected
> ui mousemode right zoom
> volume #4 color silver
> volume #4 color #c0c0c080
> volume #4 level 0.5261
> open /Users/luca/Documents/my_xray/hago2_af2_adjusted-and-aligned.pdb
Chain information for hago2_af2_adjusted-and-aligned.pdb #6
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!6 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6n4o, chain A (#5) with hago2_af2_adjusted-and-aligned.pdb, chain A
(#6), sequence alignment score = 4072.6
RMSD between 517 pruned atom pairs is 0.608 angstroms; (across all 796 pairs:
6.100)
> matchmaker #!6 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6n4o, chain A (#5) with hago2_af2_adjusted-and-aligned.pdb, chain A
(#6), sequence alignment score = 4072.6
RMSD between 517 pruned atom pairs is 0.608 angstroms; (across all 796 pairs:
6.100)
> hide #!5 models
> hide #!6 models
> show #!5 models
> select add #5
7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected
> show sel atoms
> select subtract #5
Nothing selected
> select add #5
7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected
> hide sel atoms
> select subtract #5
Nothing selected
> molmap #6 4
Opened hago2_af2_adjusted-and-aligned.pdb map 4 as #7, grid size 70,88,79,
pixel 1.33, shown at level 0.0977, step 1, values float32
> hide #!5 models
> volume #7 level 0.5598
> volume #7 level 0.5872
> volume #4 level 0.6257
> volume #4 level 0.8083
> hide #!7 models
> hide #!4 models
> show #1 models
> view
> color #1:244-244 lime
> color #1:1387-1387 magenta
> color #1:67-67 lime
> color #1:2143-2143 magenta
> color #1:191-191 lime
> color #1:862-862 magenta
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
39157 atoms, 2499 residues, atom bfactor range 12.7 to 97
> color #1:505-1684 lime
> color #1:510-1675 lime
> color #1:1888-2499 magenta
> color #1:435-435 lime
> color #1:1905-1905 magenta
> color #1:501-1020 lime
> color #1:1894-2499 magenta
> color #1:541-541 lime
> color #1:501-501 magenta
> color #1:1-537 lime
> color #1:531-1006 lime
> color #1:1028-1028 lime
> color #1:1055-1055 magenta
> color #1:997-1671 lime
> color #1:1228-1228 lime
> color #1:1410-1410 magenta
> color #1:1317-1498 lime
> color #1:1507-1667 lime
> color #1:1835-2499 lime
> open "/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final
> structures and maps/ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo-
> DFc_no_fill_no_fill.ccp4"
Opened ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo-
DFc_no_fill_no_fill.ccp4 as #8, grid size 154,171,167, pixel
0.585,0.595,0.571, shown at level 3.14, step 1, values float32
> close #8
> color #1:488-1690 lime
> color #1:510-1667 lime
> color #1:1873-2499 magenta
> color #1:466-466 lime
> color #1:1881-1881 magenta
> color #1:497-993 lime
> color #1:1873-2499 magenta
> open /Users/luca/Downloads/AF-Q9VUQ5-F1-model_v4.pdb
AF-Q9VUQ5-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for protein argonaute-2 (Q9VUQ5) [more
info...]
Chain information for AF-Q9VUQ5-F1-model_v4.pdb #8
---
Chain | Description | UniProt
A | protein argonaute-2 | AGO2_DROME 1-1214
> hide #8 models
> show #!5 models
> hide #1 models
> show #8 models
> ui tool show Matchmaker
> matchmaker #8 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6n4o, chain A (#5) with AF-Q9VUQ5-F1-model_v4.pdb, chain A (#8),
sequence alignment score = 1533.4
RMSD between 493 pruned atom pairs is 1.010 angstroms; (across all 756 pairs:
4.353)
> matchmaker #8 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6n4o, chain A (#5) with AF-Q9VUQ5-F1-model_v4.pdb, chain A (#8),
sequence alignment score = 1533.4
RMSD between 493 pruned atom pairs is 1.010 angstroms; (across all 756 pairs:
4.353)
> view
> hide #8 models
Drag select of 116 residues, 5 pseudobonds
> show #8 models
> ui tool show Matchmaker
> matchmaker #8 to #5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6n4o, chain A (#5) with AF-Q9VUQ5-F1-model_v4.pdb, chain A (#8),
sequence alignment score = 196.2
RMSD between 76 pruned atom pairs is 0.839 angstroms; (across all 100 pairs:
2.505)
> matchmaker #8 to #5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6n4o, chain A (#5) with AF-Q9VUQ5-F1-model_v4.pdb, chain A (#8),
sequence alignment score = 196.2
RMSD between 76 pruned atom pairs is 0.839 angstroms; (across all 100 pairs:
2.505)
> select clear
> hide #!5 models
> hide #8 models
> show #!5 models
Drag select of 120 residues, 5 pseudobonds
> show sel atoms
> select clear
> select add #5
7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected
> hide sel cartoons
> show #8 models
> select add #8
16696 atoms, 17127 bonds, 38 pseudobonds, 2043 residues, 4 models selected
> select subtract #5
9632 atoms, 9840 bonds, 1214 residues, 1 model selected
> select subtract #8
Nothing selected
Drag select of 406 atoms, 1 pseudobonds, 411 bonds, 77 residues
> select clear
Drag select of 953 atoms, 5 pseudobonds, 972 bonds, 12 shapes, 196 residues
> show sel atoms
> select add #5
8626 atoms, 7287 bonds, 38 pseudobonds, 1025 residues, 4 models selected
> select subtract #5
1562 atoms, 196 residues, 1 model selected
> select add #8
9632 atoms, 9840 bonds, 1214 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
9632 atoms, 9840 bonds, 1214 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 130 atoms, 130 bonds
Drag select of 9 atoms, 11 bonds
> select clear
Drag select of 135 atoms, 136 bonds
> hide sel atoms
Drag select of 247 atoms, 253 bonds
> select clear
Drag select of 249 atoms, 255 bonds
> hide sel atoms
Drag select of 2 atoms
> hide sel atoms
Drag select of 1853 atoms, 5 pseudobonds, 1899 bonds, 12 shapes
> nucleotides sel atoms
> style nucleic & sel stick
Changed 75 atom styles
> select clear
> hide #8 models
> select clear
> select #5/C:18@C1'
1 atom, 1 residue, 1 model selected
> select clear
> select #5/B:17-18
Nothing selected
> select #5/C:17-18
43 atoms, 47 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select #5/C
411 atoms, 457 bonds, 2 pseudobonds, 19 residues, 2 models selected
> color #5/C cornflower blue
> select clear
> open /Users/luca/Documents/my_alphafold/230816_VEE-nsP123/230816_VEE-
> nsP123_ranked_0.pdb
Chain information for 230816_VEE-nsP123_ranked_0.pdb #9
---
Chain | Description
A | No description available
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/luca/Documents/my_alphafold/230816_VEE-
> nsP123/pae_model_4_multimer_v3_pred_0.json
Number of residues in structure "ranked_0.pdb #1" is 2499 which does not match
PAE matrix size 1885.
This can happen if chains were deleted from the AlphaFold model or if the PAE
data was applied to a structure that was not the one predicted by AlphaFold.
Use the full-length AlphaFold model to show predicted aligned error.
> close #9
> close #1
> open /Users/luca/Documents/my_alphafold/230816_VEE-nsP123/ranked_0.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
> ui tool show "AlphaFold Error Plot"
Must choose structure to associate with predicted aligned error
> alphafold pae #1 file /Users/luca/Documents/my_alphafold/230816_VEE-
> nsP123/pae_model_4_multimer_v3_pred_0.json
> hide #1 models
> hide #!5 models
> show #1 models
> view
> color #1:525-993 lime
> color #1:515-986 lime
> color #1:1320-1668 magenta
> color #1:525-986 lime
> color #1:1019-1293 magenta
> color #1:993-1624 lime
> color #1:1170-1170 lime
> color #1:1494-1498 magenta
> color #1:983-1642 lime
> color #1:1180-1180 lime
> color #1:1511-1511 magenta
> color #1:542-970 lime
> color #1:976-1280 magenta
> color #1:970-970 lime
> color #1:1280-1280 magenta
> color #1:455-719 lime
> color #1:836-1080 magenta
> color #1:425-425 lime
> color #1:1150-1150 magenta
> color #1:540-990 lime
> color #1:996-1314 lime
> color #1:539-1314 lime
> color #1:989-1658 lime
> close #1
> open /Users/luca/Documents/my_alphafold/230811_VEE-nsP1234_XtoG/ranked_0.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
> open /Users/luca/Documents/my_alphafold/230811_VEE-
> nsP1234_XtoG/confidence_model_3_multimer_v3_pred_0.json
confidence_model_3_multimer_v3_pred_0.json does not look like Mole Online json
file, does not contain Channels.
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE-
> nsP1234_XtoG/confidence_model_3_multimer_v3_pred_0.json
JSON file "/Users/luca/Documents/my_alphafold/230811_VEE-
nsP1234_XtoG/confidence_model_3_multimer_v3_pred_0.json" is not AlphaFold
predicted aligned error data, expected a top level list
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE-
> nsP1234_XtoG/pae_model_3_multimer_v3_pred_0.json
> color #1:510-984 lime
> color #1:1884-2484 magenta
> hide #1 models
> show #8 models
> show #!5 models
> view
> zone #5/C:21
> view
> hide #5
> hide #5 cartoons
> zone #5/C:21
> hide #5 cartoons
> zone #5/C:21 residueDistance 10
> select add #5
7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 4 models selected
> hide sel cartoons
> select subtract #5
Nothing selected
> open /Users/luca/Downloads/AF-B4ESF5-F1-model_v4.pdb
AF-B4ESF5-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for papain-like cysteine proteinase (B4ESF5)
[more info...]
Chain information for AF-B4ESF5-F1-model_v4.pdb #9
---
Chain | Description | UniProt
A | papain-like cysteine proteinase | B4ESF5_HORVV 1-355
> hide #!5 models
> hide #8 models
> show #1 models
> view
> ui tool show Matchmaker
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with AF-B4ESF5-F1-model_v4.pdb, chain A
(#9), sequence alignment score = 88.1
RMSD between 12 pruned atom pairs is 1.304 angstroms; (across all 297 pairs:
63.656)
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with AF-B4ESF5-F1-model_v4.pdb, chain A
(#9), sequence alignment score = 88.1
RMSD between 12 pruned atom pairs is 1.304 angstroms; (across all 297 pairs:
63.656)
> color #1:503-1254 lime
> color #1:510-989 lime
> select #1:500-990
7694 atoms, 7772 bonds, 491 residues, 1 model selected
> select #1:500-900
6269 atoms, 6329 bonds, 401 residues, 1 model selected
> select #1:600-900
4764 atoms, 4812 bonds, 301 residues, 1 model selected
> select #1:550-900
5537 atoms, 5593 bonds, 351 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #9 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with AF-B4ESF5-F1-model_v4.pdb, chain A
(#9), sequence alignment score = 13.4
RMSD between 8 pruned atom pairs is 1.211 angstroms; (across all 225 pairs:
30.953)
> matchmaker #9 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with AF-B4ESF5-F1-model_v4.pdb, chain A
(#9), sequence alignment score = 13.4
RMSD between 8 pruned atom pairs is 1.211 angstroms; (across all 225 pairs:
30.953)
> hide #9 models
> show #9 models
> hide #9 models
> select #1:510,511,546,706
69 atoms, 67 bonds, 4 residues, 1 model selected
> color #1:510,511,546,706 firebrick
> color #1:204-204 lime
> color #1:1310-1310 magenta
> select #1:510,511,546,706 firebrick
Expected a keyword
> select #1:510,511,546,706
69 atoms, 67 bonds, 4 residues, 1 model selected
> select clear
> select #1:510,511,546,706
69 atoms, 67 bonds, 4 residues, 1 model selected
> view #1:536
> open /Users/luca/Documents/my_alphafold/230819_VEE-nsP2/ranked_0.pdb
Chain information for ranked_0.pdb #10
---
Chain | Description
A | No description available
> view
> hide #1 models
> hide #10 models
> show #10 models
> show #1 models
> ui tool show Matchmaker
> matchmaker #10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with ranked_0.pdb, chain A (#10),
sequence alignment score = 3912
RMSD between 529 pruned atom pairs is 0.841 angstroms; (across all 794 pairs:
2.898)
> matchmaker #10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with ranked_0.pdb, chain A (#10),
sequence alignment score = 3912
RMSD between 529 pruned atom pairs is 0.841 angstroms; (across all 794 pairs:
2.898)
> select clear
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> open /Users/luca/Documents/my_alphafold/230821_VEE-nsP1/230821_VEE-
> nsP1_ranked_0.pdb
Chain information for 230821_VEE-nsP1_ranked_0.pdb #11
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.pdb, chain A (#1) with 230821_VEE-nsP1_ranked_0.pdb, chain
A (#11), sequence alignment score = 2645.2
RMSD between 452 pruned atom pairs is 0.424 angstroms; (across all 535 pairs:
30.415)
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> close session
> open "/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final
> structures and maps/unmod YX_Ago2-122-21mer_refine_2.pdb"
Chain information for unmod YX_Ago2-122-21mer_refine_2.pdb #1
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
> set bgColor #ffffff00
> lighting soft
> select #1/B
219 atoms, 242 bonds, 1 pseudobond, 11 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 219 atom styles
> select clear
> hide pseudobonds
> open "/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final
> structures and maps/unmod YX_Ago2-122-21mer_refine_2_2mFo-
> DFc_no_fill_no_fill.ccp4"
Opened unmod YX_Ago2-122-21mer_refine_2_2mFo-DFc_no_fill_no_fill.ccp4 as #2,
grid size 194,236,212, pixel 0.468,0.449,0.459, shown at level 3.26, step 1,
values float32
> volume cover #2 atomBox #1
Extended map unmod YX_Ago2-122-21mer_refine_2_2mFo-DFc_no_fill_no_fill.ccp4 to
box of size (182, 223, 198),
cell size (135, 240, 150) grid points, 1 symmetry operations,
0 points not covered by any symmetry,
maximum value difference where symmetric map copies overlap = 0
Opened unmod YX_Ago2-122-21mer_refine_2_2mFo-DFc_no_fill_no_fill.ccp4 extended
as #3, grid size 182,223,198, pixel 0.468,0.449,0.459, shown at step 1, values
float32
> close #2
> volume zone #3 nearAtoms #1 range 5
> volume #3 level 1.5
> volume #3 style mesh
> volume #3 color #76d6ff
> volume zone #3 nearAtoms #1/B range 5
> volume zone #3 nearAtoms #1/B range 2
> volume zone #3 nearAtoms #1/B:21 range 5
> volume zone #3 nearAtoms #1/B:21 range 10
> color #1/A silver
> color #1/B firebrick
> view
> view name front
> volume zone #3 nearAtoms #1/B:21 range 5
> volume zone #3 nearAtoms #1/B:21 range 8
> volume zone #3 nearAtoms #1/B:21 range 7
> select (intersect) zone #1/B:21 8
Expected an objects specifier or a keyword
> select zone #1/B:21 8
Selected 203 atoms, 1 surfaces
> select zone #1/B:21 8 AND #1A
Expected an objects specifier or a keyword
> select zone #1/B:21 8,#1A
Missing or invalid "range" argument: Expected a number
> select zone #1/B:21 8 & #1/A
Expected an objects specifier or a keyword
> select intersect zone #1/B:21 8 & #1/A
Missing or invalid "objects" argument: invalid objects specifier
> select intersect (zone #1/B:21 8 & #1/A)
Missing or invalid "objects" argument: invalid objects specifier
> select zone #1/B:21 8 & #1/A
Expected an objects specifier or a keyword
> select #1/B & :21
20 atoms, 21 bonds, 1 residue, 1 model selected
> select (zone #1/B:21 5) & #1/A
Expected an objects specifier or a keyword
> select (zone #1/B:21 5)
Expected an objects specifier or a keyword
> select zone #1/B:21 5
Selected 76 atoms, 1 surfaces
> select zone #1/B:21 5 & #1/A
Expected an objects specifier or a keyword
> select #1/A & zone #1/B:21 5
Expected a keyword
> select zone #1/B:21 5
Selected 76 atoms, 1 surfaces
> select intersect #1/A
59 atoms, 14 residues, 1 model selected
> show sel atoms
> view name PAZ-view
> select zone #1/B:21 5 residues
Missing "residues" keyword's argument
> select zone #1/B:21 5 residues true
Selected 154 atoms, 1 surfaces
> select intersect #1/A
133 atoms, 14 residues, 1 model selected
> show sel atoms
> ~select
Nothing selected
> rename #3 id #2
> save "/Users/luca/Desktop/230822 modified siRNAs session.cxs" includeMaps
> true
> open "/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final
> structures and maps/ON1 apo-Ago_dials_220928_509_A9_r2_refine_34.pdb"
Chain information for ON1 apo-Ago_dials_220928_509_A9_r2_refine_34.pdb #3
---
Chain | Description
A | No description available
B | No description available
> open "/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final
> structures and maps/ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo-
> DFc_no_fill_no_fill.ccp4"
Opened ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo-
DFc_no_fill_no_fill.ccp4 as #4, grid size 154,171,167, pixel
0.585,0.595,0.571, shown at level 3.14, step 1, values float32
> volume cover #4 atomBox #3
Extended map ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo-
DFc_no_fill_no_fill.ccp4 to box of size (146, 165, 159),
cell size (108, 180, 120) grid points, 1 symmetry operations,
0 points not covered by any symmetry,
maximum value difference where symmetric map copies overlap = 0
Opened ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo-
DFc_no_fill_no_fill.ccp4 extended as #5, grid size 146,165,159, pixel
0.585,0.595,0.571, shown at step 1, values float32
> volume zone #5 nearAtoms #3/B:21 range 8
> close #4
> rename #5 id #4
> volume #4 level 1.5
> volume #4 style mesh
> color #3/A dim grey
> color #3/B sea green
> color #3/B dark orange
> hide #!1 models
> hide #!2 models
> select #3/A
6386 atoms, 6534 bonds, 7 pseudobonds, 795 residues, 2 models selected
> hide sel atoms
> select zone #3/B:21 5 residues true
Selected 327 atoms, 2 surfaces
> select intersect #3/A
147 atoms, 16 residues, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide pseudobonds
> view PAZ-view
> view name PAZ-view
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!4 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!2 models
> save "/Users/luca/Desktop/230822 WT-PAZ-view.jpg" width 1344 height 908
> supersample 3
> hide #!2 models
> show #!3 models
> show #!4 models
> hide #!1 models
> save "/Users/luca/Desktop/230822 ON1-PAZ-view.jpg" width 1344 height 908
> supersample 3
> hide #!3 models
> show #!2 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> view PAZ-view
> select #1/A
6497 atoms, 6650 bonds, 4 pseudobonds, 810 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> volume zone #2 nearAtoms #1/B:21 range 1
> volume zone #2 nearAtoms #1/B:21 range 2
> volume zone #2 nearAtoms #1/B:21 range 1.5
> select #1/B:22
Nothing selected
> select #1/B:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> view name nucleotide
> hide #!1 models
> hide #!2 models
> show #!3 models
> show #!4 models
> select up
219 atoms, 242 bonds, 11 residues, 1 model selected
> select #3/A
6386 atoms, 6534 bonds, 7 pseudobonds, 795 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> volume zone #4 nearAtoms #3/B:21 range 1.5
> show #!1 models
> show #!2 models
> hide #!4 models
> hide #!3 models
> save "/Users/luca/Desktop/230822 WT-nt21-view.jpg" width 1344 height 908
> supersample 3
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!4 models
> save "/Users/luca/Desktop/230822 ON1-nt21-view.jpg" width 1344 height 908
> supersample 3
> show #!1 models
> show #!2 models
> select #1/A
6497 atoms, 6650 bonds, 4 pseudobonds, 810 residues, 2 models selected
> show sel cartoons
> select #1/,3A
Expected an objects specifier or a keyword
> select #1,3/A
12883 atoms, 13184 bonds, 11 pseudobonds, 1605 residues, 4 models selected
> show sel cartoons
> select zone #3/B:21 5 residues true
Selected 327 atoms, 2 surfaces
> select intersect #3/A
147 atoms, 16 residues, 1 model selected
> show sel atoms
> select zone #1/B:21 5 residues true
Selected 298 atoms, 2 surfaces
> select intersect #1/A
133 atoms, 14 residues, 1 model selected
> show sel atoms
> select clear
> open 4w5n
Summary of feedback from opening 4w5n fetched from pdb
---
note | Fetching compressed mmCIF 4w5n from
http://files.rcsb.org/download/4w5n.cif
4w5n title:
The Crystal Structure of Human Argonaute2 Bound to a Defined Guide RNA [more
info...]
Chain information for 4w5n #5
---
Chain | Description | UniProt
A | Protein argonaute-2 | AGO2_HUMAN 1-859
B | RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*CP*AP*AP*GP*UP*CP*UP*CP*UP*U)-3') |
Non-standard residues in 4w5n #5
---
IPH — phenol
MG — magnesium ion
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
Drag select of 112 atoms, 104 residues, 107 bonds
> ui tool show Matchmaker
> matchmaker #!5 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker unmod YX_Ago2-122-21mer_refine_2.pdb, chain A (#1) with 4w5n, chain
A (#5), sequence alignment score = 523
RMSD between 100 pruned atom pairs is 0.414 angstroms; (across all 102 pairs:
0.544)
> show #!5 models
> select #5/B
360 atoms, 392 bonds, 1 pseudobond, 23 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 355 atom styles
> hide waters
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ligands
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select clear
> hide pseudobonds
> hide #!1 models
> select zone #5/B:21 5 residues true
Selected 480 atoms, 2 surfaces
> select intersect #5/A
124 atoms, 13 residues, 1 model selected
> show sel atoms
> select clear
> select zone #5/B:21 5 residues true
Selected 480 atoms, 2 surfaces
> select intersect #5:cys
Nothing selected
> select zone #5/B:21 20 residues true
Selected 2792 atoms, 2 surfaces
> select intersect #5:cys
30 atoms, 5 residues, 1 model selected
> show sel atoms
> color sel yellow
> select clear
> view #5/B:21
> ui tool show "Side View"
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,4
Model Number: MKH53LL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4.1 (c) (22F770820d)
Kernel Version: Darwin 22.5.0
Time since boot: 41 days, 13 hours, 42 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Luca,
--Eric