![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Last modified 2 years ago
#9245 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002ebd23000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000029408b000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000029307f000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000292073000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000291067000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000029005b000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028f04f000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028e043000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028d037000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028c02b000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028b01f000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028a013000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001fe6c9b40 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 197 in get_prop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/coulombic/cmd.py", line 43 in cmd_coulombic
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 512 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 569 in run_expanded_command
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 61 in func_plus_tip
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 327 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 408 in run_shortcut
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 390 in try_shortcut
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 1334 in run_provider
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/shortcuts/__init__.py", line 52 in run_provider
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1289 in run_provider
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.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":"2023-06-24 00:21:47.00 +0300","app_version":"1.5.0","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.3.1 (22E772610a)","roots_installed":0,"name":"ChimeraX","incident_id":"3FD0963F-637D-4ADD-9BF4-9CBAFE15133E"}
{
"uptime" : 210000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 26178,
"osVersion" : {
"train" : "macOS 13.3.1",
"build" : "22E772610a",
"releaseType" : "User"
},
"captureTime" : "2023-06-24 00:21:41.5649 +0300",
"incident" : "3FD0963F-637D-4ADD-9BF4-9CBAFE15133E",
"pid" : 72944,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-06-23 18:46:47.3741 +0300",
"procStartAbsTime" : 4975246105730,
"procExitAbsTime" : 5146322164842,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"EE7F4037-FBBD-5660-9106-8AF79EE4F2A1","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7C7118B4-D68D-E341-76AD-DC7A3EEE0086",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1942,
"sleepWakeUUID" : "99B36D44-43B1-4FC9-BFBA-55EED80C0320",
"sip" : "enabled",
"vmRegionInfo" : "0x805d8af5 is not in any region. Bytes before following region: 2186949899\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102b7c000-102b80000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000805d8af5","rawCodes":[1,2153614069],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000805d8af5"},
"vmregioninfo" : "0x805d8af5 is not in any region. Bytes before following region: 2186949899\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102b7c000-102b80000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"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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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "a388a2ff04fad7dd8ea5b60238710370dafd2902",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62c751b6bcb0435c2153fe92",
"factorPackIds" : {
"SIRI_UNDERSTANDING_ASR_ASSISTANT" : "648101bb696562099ca1b723",
"SIRI_UNDERSTANDING_MORPHUN" : "63f00b1c06644d312600c7bd"
},
"deploymentId" : 240000242
},
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "63508beab3714d3622fc7808"
},
"deploymentId" : 240000004
}
],
"experiments" : [
{
"treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
"experimentId" : "6317d2003d24842ff850182a",
"deploymentId" : 400000012
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Updating list of available bundles failed: Internal Server Error
> open "/Users/nitsanyehishalom/Library/CloudStorage/OneDrive-SharedLibraries-
> Technion/Marx Ailie - Densities/GFP/Structure25.pdb" format pdb
Chain information for Structure25.pdb #1
---
Chain | Description
A B | No description available
> select backbone
1816 atoms, 1812 bonds, 454 residues, 1 model selected
> hide ~sel
> select /A:145
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
158 atoms, 161 bonds, 19 residues, 1 model selected
> hide ~sel
> hide ~sel ribbons
> show
> show sel
> hide sel ribbons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
158 atoms, 161 bonds, 19 residues, 1 model selected
> select down
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 33 atoms, 32 bonds
> help
> select :144-145
30 atoms, 26 bonds, 6 residues, 1 model selected
> select :144-146
51 atoms, 48 bonds, 9 residues, 1 model selected
> select :142-143
40 atoms, 38 bonds, 6 residues, 1 model selected
> select :142-144
57 atoms, 54 bonds, 9 residues, 1 model selected
> select :142-145
70 atoms, 66 bonds, 12 residues, 1 model selected
> hide ~sel
> select clear
> dihedral true
Unknown command: dihedral true
> help
Downloading bundle ChimeraX_QScore-1.0-cp39-cp39-macosx_10_13_universal2.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip available: 22.2.2 -> 23.1.2
[notice] To update, run:
/Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
/Users/nitsanyehishalom/Downloads/ChimeraX_QScore-1.0-cp39-cp39-macosx_10_13_universal2.whl
Requirement already satisfied: ChimeraX-Core>=1.5 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-QScore==1.0) (1.5)
Installing collected packages: ChimeraX-QScore
Successfully installed ChimeraX-QScore-1.0
\---
Successfully installed ChimeraX-QScore-1.0
Installed ChimeraX-QScore (1.0)
> ui tool show "Model-map Q-Score"
> style #1 stick
Changed 3858 atom styles
> color #1 byhetero
Must select a model and map first!
> label #1 residues attribute phi
> undo
> angle
Missing or invalid "objects" argument: empty atom specifier
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> angle sel
Must specify exactly 3 atoms/centroids or two measurable objects (e.g.
axes/planes)
> select :143
23 atoms, 22 bonds, 3 residues, 1 model selected
> angels sel
Unknown command: angels sel
> angle sel
Must specify exactly 3 atoms/centroids or two measurable objects (e.g.
axes/planes)
> select clear
Drag select of 33 atoms, 33 bonds
> angle sel
Must specify exactly 3 atoms/centroids or two measurable objects (e.g.
axes/planes)
> select clear
> style ball
Changed 3858 atom styles
> cartoon style modeHelix tube sides 20
> ui tool show Axes/Planes/Centroids
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select /A:143@N
1 atom, 1 residue, 1 model selected
> select add /A:143@CA
2 atoms, 1 residue, 1 model selected
> select add /A:143@C
3 atoms, 1 bond, 1 residue, 1 model selected
> angle sel
Angle between /A PHE 143 N, /A PHE 143 CA, and /A PHE 143 C: 110.162
> define plane sel
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 1.3
> define centroid sel
Centroid 'centroid' placed at [-21.40533333 25.574 15.30566667]
value: None default: None
> define axis perHelix true name "helix axes"
Axis 'Structure25.pdb #!1/helix axes/chain A helix 1' centered at
[-17.27238126 -1.29708508 32.03992106] with direction [-0.74104052 0.63631348
0.21439241], radius 1.19661, and length 5.35751
Axis 'Structure25.pdb #!1/helix axes/chain A helix 2' centered at [-21.8315335
0.2968683 28.71759421] with direction [-0.80684425 0.44471499 -0.3888842 ],
radius 1.57558, and length 6.47536
Axis 'Structure25.pdb #!1/helix axes/chain A helix 3' centered at
[-24.34518934 28.46343548 23.7800401 ] with direction [ 0.64493057 -0.42416072
0.6357297 ], radius 1.53514, and length 6.54968
Axis 'Structure25.pdb #!1/helix axes/chain A helix 4' centered at
[-19.41641102 10.61622012 26.33971502] with direction [-0.36912945 -0.74637579
-0.55377488], radius 1.18606, and length 5.82732
Axis 'Structure25.pdb #!1/helix axes/chain A helix 5' centered at [-9.44334259
1.73930308 23.72302123] with direction [0.14072585 0.44156178 0.88612608],
radius 1.54016, and length 10.3001
Axis 'Structure25.pdb #!1/helix axes/chain A helix 6' centered at
[-14.67182631 6.50902984 31.34476511] with direction [-0.60790279 -0.70686576
0.3616559 ], radius 1.58684, and length 5.65226
Axis 'Structure25.pdb #!1/helix axes/chain B helix 1' centered at [-9.82953682
24.26426795 -1.730028 ] with direction [-0.84576161 0.33702053 0.41364775],
radius 1.53574, and length 9.46359
Axis 'Structure25.pdb #!1/helix axes/chain B helix 2' centered at [-29.9510665
3.57270637 0.6565128 ] with direction [ 0.90663197 -0.07806668 -0.41463727],
radius 1.54186, and length 6.44979
Axis 'Structure25.pdb #!1/helix axes/chain B helix 3' centered at
[-15.26266442 15.38447193 0.91175775] with direction [-0.02827089 0.83810341
0.54477832], radius 1.18643, and length 5.73177
Axis 'Structure25.pdb #!1/helix axes/chain B helix 4' centered at [-3.04470004
16.69078953 6.99650009] with direction [ 0.09342461 -0.47062789 -0.87737178],
radius 1.52068, and length 10.2336
Axis 'Structure25.pdb #!1/helix axes/chain B helix 5' centered at [-7.94273645
15.6876803 -2.61308687] with direction [-0.07253961 -0.86943687 0.48868961],
radius 1.5623, and length 6.20119
> select #1.2
1 model selected
> select #1.4.11
1 model selected
> close #1.2-3#1.4.1-11
Either three or four atoms must be selected!
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 1 residue, 1 model selected
> select add /A:143@C
3 atoms, 1 residue, 1 model selected
Choose exactly one axis or plane in table
> define plane sel color #909090
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 1.3
> select clear
> label hide
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> help
> label delete
> select #1.2
1 model selected
> select clear
> select /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090
Plane 'plane' placed at [-19.11866667 24.97966667 14.887 ] with normal [
0.05701853 -0.68657749 0.72481738] and radius 1.3
> select clear
value: None default: None
> define axis #1.2 name normal padding 2.5
Plane normal for plane #1.2 centered at [-21.40533333 25.574 15.30566667] with
direction [-0.48407451 -0.87205193 0.07209225], radius 0.0637005, and length
1.27401
> undo
> select #1.2.1
1 model selected
> close #1.2.1
Need to select at least 3 atoms to define a plane
> select /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 4 thickness 0.15
Plane 'plane' placed at [-19.11866667 24.97966667 14.887 ] with normal [
0.05701853 -0.68657749 0.72481738] and radius 5.3
> close #1.3
> select #1.2
1 model selected
> select clear
> view #1.2 zalign #1.2
> turn y 90 center #1.2
> ui tool show "Side View"
plane #1.1 to plane #1.2: distance: 0.000Å; angle: 51.4°
> close #1.1-2
> select add /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 1 residue, 1 model selected
> select add /A:143@C
3 atoms, 1 residue, 1 model selected
> define plane sel color #909090 padding 1 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.3
> close #1.1
> define plane sel color #909090 padding 1.5 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.8
> close #1.1
> define plane sel color #909090 padding 1.1 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.4
> close #1.1
> define plane sel color #909090 padding 0.5 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 1.8
> rename #1.1 "Ca plane"
> select subtract /A:143@C
2 atoms, 1 residue, 1 model selected
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select subtract /A:143@CA
Nothing selected
> select add /A:144@N
1 atom, 1 bond, 1 residue, 1 model selected
> select add /A:143@C
2 atoms, 1 bond, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 1 bond, 2 residues, 1 model selected
> select /A:144@N
1 atom, 1 residue, 1 model selected
> select /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.5 thickness 0.15
Plane 'plane' placed at [-19.11866667 24.97966667 14.887 ] with normal [
0.05701853 -0.68657749 0.72481738] and radius 1.8
> color #1.2 #9090909f
> color #1.2 #9090909e
> color #1.2 #9090909d
> color #1.2 #9090909b
> color #1.2 #90909096
> color #1.2 #9090908f
> color #1.2 #9090908b
> color #1.2 #90909086
> color #1.2 #90909081
> color #1.2 #9090907b
> color #1.2 #90909075
> color #1.2 #90909073
> color #1.2 #90909071
> color #1.2 #90909072
> color #1.2 #90909073
> color #1.2 #90909074
> color #1.2 #90909076
> color #1.2 #90909079
> color #1.2 #9090907b
> color #1.2 #9090907d
> color #1.2 #9090907e
> color #1.2 #90909080
> color #1.2 #a1a09680
> color #1.2 #a1a09780
> color #1.2 #a1a09880
> color #1.2 #a19d9c80
> color #1.2 #a19ba180
> color #1.2 #9d98a180
> color #1.2 #9a94a180
> color #1.2 #928ba180
> color #1.2 #8d85a180
> color #1.2 #877fa180
> color #1.2 #847ba180
> color #1.2 #7f75a180
> color #1.2 #796ea180
> color #1.2 #7064a180
> color #1.2 #6a5da180
> color #1.2 #685aa180
> color #1.2 #6254a180
> color #1.2 #5d4ea180
> color #1.2 #5b4ca180
> color #1.2 #5647a180
> color #1.2 #5344a180
> color #1.2 #5142a180
> color #1.2 #4d3ea180
> color #1.2 #4b3ca180
> color #1.2 #4839a180
> color #1.2 #4537a180
> color #1.2 #4335a180
> color #1.2 #4133a180
> color #1.2 #4032a180
> color #1.2 #3f31a180
> color #1.2 #3f32a180
> color #1.2 #3f33a180
> color #1.2 #3e33a180
> color #1.2 #3e34a180
> color #1.2 #3e35a180
> color #1.2 #3d35a180
> color #1.2 #3c36a180
> color #1.2 #3a38a180
> color #1.2 #3938a180
> color #1.2 #393ba180
> color #1.2 #3a3da180
> color #1.2 #3a3ea180
> color #1.2 #3b3fa180
> color #1.2 #3c3fa180
> color #1.2 #3c3ea180
> color #1.2 #3d3ea180
> color #1.2 #3d3da180
> color #1.2 #3e3da180
> color #1.2 #3f3ea180
> color #1.2 #423ea180
> color #1.2 #443fa180
> color #1.2 #4640a180
> color #1.2 #4740a180
> color #1.2 #4841a180
> color #1.2 #4a41a180
> color #1.2 #4c42a180
> color #1.2 #4d42a180
> color #1.2 #4e42a180
> color #1.2 #4e43a180
> color #1.2 #5649a180
> color #1.2 #6256a180
> color #1.2 #6c62a180
> color #1.2 #8781a180
> color #1.2 #9fa19e80
> color #1.2 #9aa18e80
> color #1.2 #98a18480
> color #1.2 #95a17e80
> color #1.2 #94a17d80
> color #1.2 #94a17c80
> color #1.2 #93a17a80
> color #1.2 #8fa17680
> color #1.2 #8ba17380
> color #1.2 #7aa16380
> color #1.2 #6aa15680
> color #1.2 #5aa14980
> color #1.2 #4fa14180
> color #1.2 #40a13580
> color #1.2 #39a13080
> color #1.2 #32a12b80
> color #1.2 #31a12b80
> color #1.2 #2fa12980
> color #1.2 #2ea12980
> color #1.2 #2ea12880
> color #1.2 #2da12880
> color #1.2 #2ea12880
> color #1.2 #2ea12980
> select add #1.1
3 atoms, 2 residues, 2 models selected
> color #1.1 #9ca19a
> color #1.1 #9ca19c
> color #1.1 #9ca0a1
> color #1.1 #999ca1
> color #1.1 #9498a1
> color #1.1 #8b90a1
> color #1.1 #838aa1
> color #1.1 #8088a1
> color #1.1 #7b84a1
> color #1.1 #737da1
> color #1.1 #6f79a1
> color #1.1 #6b76a1
> color #1.1 #6873a1
> color #1.1 #6671a1
> color #1.1 #6470a1
> color #1.1 #636fa1
> color #1.1 #636ea1
> color #1.1 #626da1
> color #1.1 #616da1
> color #1.1 #626da1
> color #1.1 #626ea1
> color #1.1 #636fa1
> color #1.1 #6471a1
> color #1.1 #6774a1
> color #1.1 #6876a1
> color #1.1 #6978a1
> color #1.1 #6a7aa1
> color #1.1 #6b7ca1
> color #1.1 #6f82a1
> color #1.1 #7187a1
> color #1.1 #7289a1
> color #1.1 #748da1
> color #1.1 #758ea1
> color #1.1 #7692a1
> color #1.1 #7597a1
> color #1.1 #739ba1
> color #1.1 #729da1
> color #1.1 #6fa1a0
> color #1.1 #6da19e
> color #1.1 #6da19d
> color #1.1 #6ca19b
> color #1.1 #6ba19b
> color #1.1 #6aa19b
> color #1.1 #68a19b
> color #1.1 #65a19b
> color #1.1 #5da19b
> color #1.1 #53a199
> color #1.1 #48a196
> color #1.1 #3fa194
> color #1.1 #34a192
> color #1.1 #31a192
> color #1.1 #2ba191
> color #1.1 #29a191
> color #1.1 #28a191
> color #1.1 #27a191
> color #1.1 #26a191
> color #1.1 #25a191
> color #1.1 #24a191
> color #1.1 #23a191
> color #1.1 #22a191
> color #1.1 #22a192
> color #1.1 #21a192
> color #1.1 #20a192
> color #1.1 #1fa192
> color #1.1 #1fa193
> color #1.1 #1fa193fe
> color #1.1 #1fa193f2
> color #1.1 #1fa193d7
> color #1.1 #1fa193be
> color #1.1 #1fa193b5
> color #1.1 #1fa193ac
> color #1.1 #1fa193aa
> color #1.1 #1fa193a7
> color #1.1 #1fa193a3
> color #1.1 #1fa1939f
> color #1.1 #1fa1939e
> color #1.1 #1fa1939b
> color #1.1 #1fa19399
> color #1.1 #1fa19398
> color #1.1 #1fa19397
> color #1.1 #1fa19398
> color #1.1 #1fa19399
> color #1.1 #1fa1939a
> color #1.1 #1fa1939b
> color #1.1 #1fa1939c
> select clear
> select add /A:142@C
1 atom, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 2 residues, 1 model selected
> select add /A:143@CA
3 atoms, 2 residues, 1 model selected
> select add /A:142@CA
4 atoms, 2 residues, 1 model selected
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select /A:142@C
1 atom, 1 residue, 1 model selected
> select add /A:142@CA
2 atoms, 1 residue, 1 model selected
> select add /A:143@N
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.5 thickness 0.15
Plane 'plane' placed at [-23.40666667 26.94866667 15.07466667] with normal
[-0.55887244 -0.64599619 0.51995243] and radius 1.8
> color #1.3 #909090fe
> color #1.3 #909090e2
> color #1.3 #909090d1
> color #1.3 #909090b5
> color #1.3 #909090a4
> color #1.3 #9090909b
> color #1.3 #90909093
> color #1.3 #9090908c
> color #1.3 #9090908a
> color #1.3 #90909089
> color #1.3 #90909088
> color #1.3 #90909085
> color #1.3 #90909082
> color #1.3 #9090907e
> color #1.3 #90909078
> color #1.3 #90909077
> color #1.3 #90909073
> color #1.3 #90909072
> color #1.3 #90909073
> color #1.3 #90909074
> color #1.3 #90909075
> color #1.3 #90909076
> color #1.3 #90909077
> color #1.3 #90909078
> color #1.3 #90909079
> color #1.3 #9090907a
> color #1.3 #9090907c
> color #1.3 #9090907e
> color #1.3 #90909081
> color #1.3 #90909082
> color #1.3 #90909083
> color #1.3 #93a19083
> color #1.3 #94a18e83
> color #1.3 #96a18983
> color #1.3 #98a17f83
> color #1.3 #9ca17483
> color #1.3 #9ea16b83
> color #1.3 #9fa16683
> color #1.3 #a0a16383
> color #1.3 #9fa16283
> color #1.3 #9fa16183
> color #1.3 #9fa15f83
> color #1.3 #a1a15783
> color #1.3 #a19e4683
> color #1.3 #a19c3f83
> color #1.3 #a19a3783
> color #1.3 #a1983183
> color #1.3 #a1982f83
> color #1.3 #a1972c83
> color #1.3 #a1972b83
> color #1.3 #a1962b83
> color #1.3 #a1962a83
> color #1.3 #a1952a83
> color #1.3 #a1952983
> color #1.3 #a1922483
> color #1.3 #a1912283
> color #1.3 #a1912083
> color #1.3 #a1901f83
> color #1.3 #a18f1e83
> color #1.3 #a1901f83
> color #1.3 #a18f1f83
> color #1.3 #a1902083
> color #1.3 #a1902183
> color #1.3 #a1922483
> color #1.3 #a1942883
> color #1.3 #a1962d83
> color #1.3 #a1983183
> color #1.3 #a19a3483
> color #1.3 #a19a3583
> color #1.3 #a19b3683
> color #1.3 #a19c3783
> color #1.3 #a19d3883
> color #1.3 #a1a03e83
> color #1.3 #a1a14283
> color #1.3 #9fa14483
> color #1.3 #9ea14683
> color #1.3 #9ea14783
> color #1.3 #9ca14483
> color #1.3 #9da14583
> color #1.3 #9ea14683
> color #1.3 #a1a04883
> color #1.3 #a19b4983
> color #1.3 #a18e4b83
> color #1.3 #a1844a83
> color #1.3 #a17e4983
> color #1.3 #a1754683
> color #1.3 #a1744683
> color #1.3 #a1734583
> color #1.3 #a1744583
> color #1.3 #a1764583
> color #1.3 #a1784583
> color #1.3 #a17e4683
> color #1.3 #a1854683
> color #1.3 #a1884683
> color #1.3 #a1924583
> color #1.3 #a1964583
> color #1.3 #a1994583
> color #1.3 #a19a4683
> color #1.3 #a19c4783
> color #1.3 #a19e4983
> color #1.3 #a1a15183
> color #1.3 #a1a15b83
> color #1.3 #a1a16183
> color #1.3 #a19f7783
> color #1.3 #a19c8683
> color #1.3 #a1959783
> color #1.3 #a18fa183
> color #1.3 #9d89a183
> color #1.3 #9379a183
> color #1.3 #8c6ba183
> color #1.3 #8a68a183
> color #1.3 #865fa183
> color #1.3 #865ca183
> color #1.3 #865aa183
> color #1.3 #8653a183
> color #1.3 #864ca183
> color #1.3 #8646a183
> color #1.3 #863fa183
> color #1.3 #873ca183
> color #1.3 #873aa183
> color #1.3 #8739a183
> color #1.3 #8738a183
> color #1.3 #8838a183
> color #1.3 #8938a183
> color #1.3 #8a37a183
> color #1.3 #8d36a183
> color #1.3 #9134a183
> color #1.3 #9432a183
> color #1.3 #9831a183
> color #1.3 #9930a183
> color #1.3 #9a30a183
> color #1.3 #9a2fa183
> color #1.3 #9b30a183
> color #1.3 #9c30a183
> color #1.3 #9d31a183
> color #1.3 #9e32a183
> color #1.3 #a034a183
> color #1.3 #a135a183
> color #1.3 #a135a185
> select clear
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:143@C
2 atoms, 1 residue, 1 model selected
> select add /A:143@N
3 atoms, 1 residue, 1 model selected
> ui tool show Angles/Torsions
> select clear
> set bgColor white
> help
> select add /A:144@CB
1 atom, 1 residue, 1 model selected
> select add /A:144@CG
2 atoms, 1 residue, 1 model selected
> select add /A:144@ND2
3 atoms, 1 residue, 1 model selected
Drag select of 4 atoms, 3 bonds
> select add /A:144@CB
2 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel
Drag select of 2 atoms, 1 bonds
> hide sel
Drag select of 4 atoms, 3 bonds
> hide sel
> undo
Drag select of Ca plane, plane, plane, 33 atoms, 33 bonds
> select /A:145@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
158 atoms, 161 bonds, 19 residues, 1 model selected
> select :142-145
70 atoms, 66 bonds, 12 residues, 1 model selected
> delete ~sel
> select clear
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> label sel
> label delete
> label atoms
> label :143 Ca
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label :143 CA
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label :143CA
> show label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show lable
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label /:143 residues text "{0.phi:.1f},{0.psi:.1f}"
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label :143 residues text {0.phi:.1f},{0.psi:.1f}
> label :143 residues text "Phi {0.phi:.1f},Psi {0.psi:.1f}"
> ui mousemode right label
> label delete residues
> label :143 residues text "Phi {0.phi:.1f},Psi {0.psi:.1f}"
> ui mousemode right "move label"
> label :143 residues text "Phi {0.phi:.1f}"
> label :143 residues text "Psi {0.psi:.1f}"
> select #1.2
1 model selected
> color #1.2 #2ea22980
> color #1.2 #2eab2980
> color #1.2 #2eb12980
> color #1.2 #2eb52980
> color #1.2 #2eb92980
> color #1.2 #2ebb2980
> color #1.2 #2ebc2980
> color #1.2 #2ebd2980
> color #1.2 #2ebe2980
> color #1.2 #2ebf2980
> color #1.2 #2ec12980
> color #1.2 #2ec32980
> color #1.2 #2ec42980
> color #1.2 #2ec52980
> color #1.2 #2ec62980
> color #1.2 #2ec72980
> color #1.2 #2ec82980
> color #1.2 #2ece2980
> color #1.2 #2ed82980
> color #1.2 #2ede2980
> color #1.2 #2ee22980
> color #1.2 #2ee62980
> color #1.2 #2ee72980
> select clear
> style stick
Changed 70 atom styles
> style ball
Changed 70 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style ball thin
Expected a keyword
> style ball ringFill thin
Changed 70 atom styles, 12 residue ring styles
> undo
> select add /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:142@CA
2 atoms, 2 residues, 1 model selected
> ui mousemode right label
> label #1/A:143
> rename #1 angels
> select clear
> label #1/A:142
> label delete residues
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right "play map series"
> ui mousemode right "play coordinates"
> ui mousemode right minimize
> rename #1.2 ""
ID must be one or more integers separated by '.' characters
> rename #1.2 ""
No visible atoms selected
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> label sel atoms attribute element
> ui mousemode right "move label"
> ui mousemode right label
> label sel atoms attribute idatm_type
> label sel atoms text Ca
> select /A:143@N
1 atom, 1 residue, 1 model selected
> label #1/A:142
> ui mousemode right zoom
> ui mousemode right translate
> select /A:143@N
1 atom, 1 residue, 1 model selected
Height must be a positive number
> label sel atoms text N
> ui mousemode right "move label"
> select clear
> ui mousemode right label
> label #1/A:143
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> label sel atoms
> label delete residues
> ui mousemode right "move label"
> select /A:143@C
1 atom, 1 residue, 1 model selected
> label sel atoms
Drag select of , 8 of 160 triangles
> select clear
> select /A:143@O
1 atom, 1 residue, 1 model selected
> label sel atoms
> select #1.2
1 model selected
> select clear
> select /A:143@CB
1 atom, 1 residue, 1 model selected
Drag select of 6 atoms, 6 bonds
> hide sel
> ui mousemode right label
> select /A:143@CB
1 atom, 1 residue, 1 model selected
> color sel magenta
> label sel atoms text R
> ui mousemode right "move label"
> select clear
> select /A:142@CG
1 atom, 1 residue, 1 model selected
Drag select of 3 atoms, 3 bonds
> hide sel
> undo
> select add /A:142@CG
3 atoms, 2 bonds, 1 residue, 1 model selected
> select subtract /A:142@CG
2 atoms, 1 residue, 1 model selected
> select add /A:142@CG
3 atoms, 1 residue, 1 model selected
Drag select of 3 atoms, 3 bonds
> hide sel
Drag select of 3 atoms, 2 bonds
> hide sel
> hide #!1 models
> show #!1 models
> select /A:142@ND2
1 atom, 1 residue, 1 model selected
> hide sel
> select /A:142@OD1
1 atom, 1 residue, 1 model selected
> hide sel
> select /A:142@CG
1 atom, 1 residue, 1 model selected
> hide sel
> select /A:142@CB
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> ui mousemode right translate
> select add /A:144@CG
1 atom, 1 residue, 1 model selected
> select add /A:144@CB
2 atoms, 1 residue, 1 model selected
> hide sel
> select add /A:144@OD1
3 atoms, 1 residue, 1 model selected
> select add /A:144@ND2
4 atoms, 1 residue, 1 model selected
> hide sel
> select add /A:145@C
5 atoms, 2 residues, 1 model selected
> select add /A:145@O
6 atoms, 2 residues, 1 model selected
> select subtract /A:145@O
5 atoms, 2 residues, 1 model selected
> undo
> select /A:144@CA
1 atom, 1 residue, 1 model selected
> show sel
> show :144
> select add /A:144@CG
2 atoms, 1 residue, 1 model selected
> select add /A:144@OD1
3 atoms, 1 residue, 1 model selected
> select add /A:144@ND2
4 atoms, 1 residue, 1 model selected
> hide sel
> undo
> select /A:144@CG
1 atom, 1 residue, 1 model selected
> select /A:144@ND2
1 atom, 1 residue, 1 model selected
> select /A:144@OD1
1 atom, 1 residue, 1 model selected
> select add /A:144@CG
2 atoms, 1 residue, 1 model selected
> select add /A:144@ND2
3 atoms, 1 bond, 1 residue, 1 model selected
> hide sel
> select /A:144@CB
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> select add /A:145@C
1 atom, 1 residue, 1 model selected
> select add /A:145@O
2 atoms, 1 residue, 1 model selected
> select subtract /A:145@O
1 atom, 1 residue, 1 model selected
> select /A:145@O
1 atom, 1 residue, 1 model selected
> hide sel
> select /A:145@C
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> save "/Users/nitsanyehishalom/Desktop/Studys/MS.c./Thesis/Angel .cxs"
> view orient
> undo
> ui tool show "Side View"
Drag select of 9 atoms, 7 bonds
> delete sel
> save "/Users/nitsanyehishalom/Desktop/Studys/MS.c./Thesis/Angel .cxs"
> rename #1.2 ""
> rename #1.2 "-1 plane"
> rename #1.3 "+1 plane"
> rename #1.2 "+1 plane"
> rename #1.3 "-1 plane"
> select #1.2
1 model selected
> view sel
> view
> view orient
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> select clear
Need to select at least 3 atoms to define a plane
ID must be one or more integers separated by '.' characters
Need to select at least 3 atoms to define a plane
> select add /A:143@N
1 atom, 1 residue, 1 model selected
> select add /A:142@C
2 atoms, 2 residues, 1 model selected
> select add /A:142@CA
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.6 thickness 0.15
Plane 'plane' placed at [-23.40666667 26.94866667 15.07466667] with normal
[-0.55887244 -0.64599619 0.51995243] and radius 1.9
> close #1.7
> select clear
> select #1.2
1 model selected
> color #1.2 #31e72980
> color #1.2 #3be72980
> color #1.2 #47e72980
> color #1.2 #5de72980
> color #1.2 #63e72980
> color #1.2 #67e72980
> color #1.2 #69e72980
> color #1.2 #6ae72980
> color #1.2 #6ce72980
> color #1.2 #6de72980
> color #1.2 #70e72980
> color #1.2 #72e72980
> color #1.2 #74e72980
> color #1.2 #78e72980
> color #1.2 #7ae72980
> color #1.2 #7ce72980
> color #1.2 #83e72980
> color #1.2 #8ae72980
> color #1.2 #8de72980
> color #1.2 #8ee72980
> color #1.2 #8fe72980
> color #1.2 #90e72980
> color #1.2 #92e72980
> color #1.2 #93e72980
> color #1.2 #96e72980
> color #1.2 #9ae72980
> color #1.2 #9ee72980
> color #1.2 #a2e72980
> color #1.2 #a8e72980
> color #1.2 #abe72980
> color #1.2 #ace72980
> color #1.2 #a9e72980
> color #1.2 #a8e72980
> color #1.2 #a7e72980
> color #1.2 #a8e72980
> color #1.2 #a9e72980
> color #1.2 #abe72980
> color #1.2 #b1e72980
> color #1.2 #b4e72980
> color #1.2 #b6e72980
> color #1.2 #b9e72980
> color #1.2 #b8e72980
> color #1.2 #b7e72980
> color #1.2 #b6e72980
> color #1.2 #b5e72980
> color #1.2 #b4e72980
> color #1.2 #b3e72980
> color #1.2 #b2e72980
> color #1.2 #b2e52980
> color #1.2 #b2c82980
> color #1.2 #b2ae2980
> color #1.2 #b2942980
> color #1.2 #b2802980
> color #1.2 #b2652980
> color #1.2 #b25c2980
> color #1.2 #b2552980
> color #1.2 #b24c2980
> color #1.2 #b2482980
> color #1.2 #b2492980
> color #1.2 #b24a2980
> color #1.2 #b24b2980
> color #1.2 #b24c2980
> color #1.2 #b24d2980
> color #1.2 #b24e2980
> color #1.2 #b2502980
> color #1.2 #b2532980
> color #1.2 #b2582980
> color #1.2 #b25f2980
> color #1.2 #b2722980
> color #1.2 #b27c2980
> color #1.2 #b2852980
> color #1.2 #b2952980
> color #1.2 #b2a02980
> color #1.2 #b2a42980
> color #1.2 #b2ac2980
> color #1.2 #b2af2980
> color #1.2 #b2b52980
> color #1.2 #b2b72980
> color #1.2 #b2b92980
> color #1.2 #b2be2980
> color #1.2 #b2c02980
> color #1.2 #b2c22980
> color #1.2 #b2c62980
> color #1.2 #b2c72980
> color #1.2 #b2c82980
> color #1.2 #b2c92980
> color #1.2 #b2c82980
> color #1.2 #b2c72980
> color #1.2 #b2c62980
> color #1.2 #b2bf2980
> color #1.2 #b2a92980
> color #1.2 #b2982980
> color #1.2 #b2892980
> color #1.2 #b27d2980
> color #1.2 #b26c2980
> color #1.2 #b2672980
> color #1.2 #b2632980
> color #1.2 #b25b2980
> color #1.2 #b2552980
> color #1.2 #b2522980
> color #1.2 #b2502980
> color #1.2 #b24f2980
> color #1.2 #b24a2980
> color #1.2 #b2432980
> color #1.2 #b23a2980
> color #1.2 #b2322980
> color #1.2 #b22c2980
> color #1.2 #b2252980
> color #1.2 #b2262980
> color #1.2 #b2282980
> color #1.2 #b2292980
> color #1.2 #b22a2980
> color #1.2 #b22d2980
> color #1.2 #b2302980
> color #1.2 #b2362980
> color #1.2 #b2392980
> color #1.2 #b23d2980
> color #1.2 #b23e2980
> color #1.2 #b2412980
> color #1.2 #b2432980
> color #1.2 #b2492980
> color #1.2 #b2532980
> color #1.2 #b2612980
> color #1.2 #b26d2980
> color #1.2 #b2802980
> color #1.2 #b28a2980
> color #1.2 #b28f2980
> color #1.2 #b2932980
> color #1.2 #b2972980
> color #1.2 #b2a32980
> color #1.2 #b2a92980
> color #1.2 #b2af2980
> color #1.2 #b2bb2980
> color #1.2 #b2c12980
> color #1.2 #b2cc2980
> color #1.2 #b2cf2980
> color #1.2 #b2d12980
> color #1.2 #b2d32980
> color #1.2 #b2d42980
> color #1.2 #b2d62980
> color #1.2 #b2da2980
> color #1.2 #b2dd2980
> color #1.2 #b2e12980
> color #1.2 #b2e52980
> color #1.2 #b2e82980
> color #1.2 #b2e92980
> color #1.2 #b2e92a80
> color #1.2 #b2e93080
> color #1.2 #b2e93d80
> color #1.2 #b2e95980
> color #1.2 #b2e96280
> color #1.2 #b2e96c80
> color #1.2 #b2e96d80
> color #1.2 #b2e96f80
> color #1.2 #b2e97580
> color #1.2 #b2e97e80
> color #1.2 #b2e98580
> color #1.2 #b2e98e80
> color #1.2 #b2e99080
> color #1.2 #b2e99180
> color #1.2 #b2e99280
> color #1.2 #b2e99680
> color #1.2 #b2e99d80
> color #1.2 #b2e9a680
> color #1.2 #b2e9b580
> color #1.2 #b2e9b980
> color #1.2 #b2e9bb80
> color #1.2 #b2e9bc80
> color #1.2 #b2e9bb80
> color #1.2 #b2e9ba80
> color #1.2 #b2e9b980
> color #1.2 #b2e9b880
> color #1.2 #b2e9b380
> color #1.2 #b2e9ad80
> color #1.2 #b2e99f80
> color #1.2 #b2e99080
> color #1.2 #b2e98880
> color #1.2 #b2e98080
> color #1.2 #b2e96a80
> color #1.2 #b2e96580
> color #1.2 #b2e96480
> color #1.2 #b2e96380
> color #1.2 #b2e96280
> color #1.2 #b2e96080
> color #1.2 #b2e95d80
> color #1.2 #b2e95780
> color #1.2 #b2e95480
> color #1.2 #b2e94e80
> color #1.2 #b2e94780
> color #1.2 #b2e94480
> color #1.2 #bfe96b80
> color #1.2 #c2e96a80
> color #1.2 #c4e96a80
> color #1.2 #c7e96980
> color #1.2 #c9e96980
> color #1.2 #cae96880
> color #1.2 #cce96880
> color #1.2 #cde96780
> color #1.2 #d3e96480
> color #1.2 #d7e96080
> color #1.2 #dbe95a80
> color #1.2 #e4e94f80
> color #1.2 #e7e94a80
> color #1.2 #e9e84880
> color #1.2 #e9e54580
> color #1.2 #e9e44480
> color #1.2 #e9e34380
> color #1.2 #e9e24380
> color #1.2 #e9e14280
> color #1.2 #e9dc3f80
> color #1.2 #e9d93c80
> color #1.2 #e9d23780
> color #1.2 #e9d03480
> color #1.2 #e9cf3380
> color #1.2 #e9ce3280
> color #1.2 #e9cd3080
> color #1.2 #e9cd2f80
> color #1.2 #e9cc2d80
> color #1.2 #e9c92980
> color #1.2 #e9c72680
> color #1.2 #e9c62380
> color #1.2 #e9c21f80
> color #1.2 #e9c11e80
> color #1.2 #e9c01d80
> color #1.2 #e9c32380
> color #1.2 #e9c52580
> color #1.2 #e9c62880
> color #1.2 #e9c72b80
> color #1.2 #e9c92e80
> color #1.2 #e9ca3280
> color #1.2 #e9cb3380
> color #1.2 #e9cd3780
> color #1.2 #e9cf3a80
> color #1.2 #e9d03c80
> color #1.2 #e9d23f80
> color #1.2 #e9d24180
> color #1.2 #e9d34380
> color #1.2 #e9d34480
> color #1.2 #e9d44680
> color #1.2 #e9d54a80
> color #1.2 #e9d64b80
> color #1.2 #e9d64c80
> color #1.2 #e9d64d80
> color #1.2 #e9d54e80
> color #1.2 #e9d54f80
> color #1.2 #e9d55180
> color #1.2 #e9d55780
> color #1.2 #e9d55a80
> color #1.2 #e9d55e80
> color #1.2 #e9d45f80
> color #1.2 #e9d46080
> color #1.2 #e9d55f80
> color #1.2 #e9d55c80
> color #1.2 #e9d35680
> color #1.2 #e9d15080
> color #1.2 #e9ce4880
> color #1.2 #e9ca4080
> color #1.2 #e9c73780
> color #1.2 #e9c43180
> color #1.2 #e9c22d80
> color #1.2 #e9c02a80
> color #1.2 #e9bf2880
> color #1.2 #e9be2780
> color #1.2 #e9be2680
> color #1.2 #e9bd2580
> color #1.2 #e9bc2480
> color #1.2 #e9b92180
> color #1.2 #e9b71f80
> color #1.2 #e9b61d80
> color #1.2 #e9b51c80
> color #1.2 #e9b41c80
> color #1.1 #57aca09c
> color #1.1 #54aca09c
> color #1.1 #4eaca09c
> color #1.1 #47aca09c
> color #1.1 #40aca09c
> color #1.1 #3caca09c
> color #1.1 #37aca09c
> color #1.1 #36aca09c
> color #1.1 #35aca09c
> color #1.1 #33aca09c
> color #1.1 #32aca09c
> color #1.1 #30aca19c
> color #1.1 #2aaca19c
> color #1.1 #27aca29c
> color #1.1 #25aca29c
> color #1.1 #22aca39c
> color #1.1 #1faca49c
> color #1.1 #1eaca49c
> color #1.1 #1daca59c
> color #1.1 #1aaca69c
> color #1.1 #19aca69c
> color #1.1 #18aca79c
> color #1.1 #16aca79c
> color #1.1 #16aca89c
> color #1.1 #12aca99c
> color #1.1 #10acaa9c
> color #1.1 #0cacac9c
> color #1.1 #0aabac9c
> color #1.1 #09aaac9c
> color #1.1 #07aaac9c
> color #1.1 #06aaac9c
> color #1.1 #05a9ac9c
> color #1.1 #03a9ac9c
> color #1.1 #00a9ac9c
> color #1.1 #00acac9c
> color #1.1 #00aaac9c
> color #1.1 #00a9ac9c
> color #1.1 #00a6ac9c
> color #1.1 #04a5ac9c
> color #1.1 #08a4ac9c
> color #1.1 #11a3ac9c
> color #1.1 #14a2ac9c
> color #1.1 #17a1ac9c
> color #1.1 #19a1ac9c
> color #1.1 #1ba0ac9c
> color #1.1 #1ca0ac9c
> color #1.1 #1da0ac9c
> color #1.1 #1da0ac9a
> color #1.1 #1da0ac97
> color #1.1 #1da0ac93
> color #1.1 #1da0ac8d
> color #1.1 #1da0ac8c
> color #1.1 #1da0ac8b
> color #1.1 #1da0ac8a
> color #1.1 #1da0ac89
> color #1.1 #1da0ac86
> color #1.1 #1da0ac85
> color #1.1 #1da0ac83
> color #1.1 #1da0ac81
> color #1.1 #1da0ac7f
> color #1.1 #1da0ac7d
> color #1.1 #1da0ac7c
> color #1.1 #1da0ac7d
> color #1.1 #1da0ac7e
> color #1.1 #1da0ac7d
> color #1.3 #a554ac85
> color #1.3 #a555ad85
> color #1.3 #a755ae85
> color #1.3 #ab58b385
> color #1.3 #ae59b685
> color #1.3 #b15bb885
> color #1.3 #b55dbd85
> color #1.3 #bb60c385
> color #1.3 #c263ca85
> color #1.3 #c766cf85
> color #1.3 #c967d285
> color #1.3 #ca68d385
> color #1.3 #cb68d485
> color #1.3 #cd69d685
> color #1.3 #d16bda85
> color #1.3 #d36cdc85
> color #1.3 #d36cdd85
> color #1.3 #d46ddd85
> color #1.3 #d56ddf85
> color #1.3 #dd71e785
> color #1.3 #e575ee85
> color #1.3 #e977f385
> color #1.3 #e978f385
> color #1.3 #e978f384
> color #1.3 #e978f383
> color #1.3 #e978f382
> color #1.3 #e978f381
> color #1.3 #e978f380
> select clear
> save "/Users/nitsanyehishalom/Desktop/Studys/MS.c./Thesis/angels normal
> .png" width 899 height 667 supersample 4 transparentBackground true
> select /A:142@CA
1 atom, 1 residue, 1 model selected
> label sel atoms text Ca-1
> undo
> ui mousemode right label
> ui mousemode right "move label"
Drag select of 1 plane, 8 of 160 triangles
> select clear
+1 plane #1.2 to -1 plane #1.3: distance: 0.000Å; angle: 38.0°
> close #1.2-3
> select clear
> select /A:143@N
1 atom, 1 residue, 1 model selected
> select /A:142@C
1 atom, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 2 residues, 1 model selected
> select add /A:142@CA
3 atoms, 2 residues, 1 model selected
> select add /A:142@N
4 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.6 thickness 0.15
Plane 'plane' placed at [-23.85375 27.36375 15.12975] with normal [-0.55625242
-0.65928772 0.50588828] and radius 2.4
> color #1.2 #909090fd
> color #1.2 #909090f9
> color #1.2 #909090f5
> color #1.2 #909090e6
> color #1.2 #909090d8
> color #1.2 #909090d0
> color #1.2 #909090c6
> color #1.2 #909090c2
> color #1.2 #909090be
> color #1.2 #909090b9
> color #1.2 #909090b3
> color #1.2 #909090b0
> color #1.2 #909090a9
> color #1.2 #909090a5
> color #1.2 #909090a1
> color #1.2 #9090909b
> color #1.2 #90909098
> color #1.2 #90909094
> color #1.2 #90909093
> color #1.2 #90909091
> color #1.2 #90909090
> color #1.2 #9090908f
> color #1.2 #9090908e
> color #1.2 #9090908c
> color #1.2 #9090908b
> color #1.2 #90909088
> color #1.2 #90909086
> color #1.2 #90909084
> color #1.2 #90909083
> color #1.2 #90909082
> color #1.2 #90909081
> color #1.2 #90909080
> color #1.2 #9aa19280
> color #1.2 #9aa19380
> color #1.2 #9ba19480
> color #1.2 #9da19680
> color #1.2 #a1a19a80
> color #1.2 #a1a19b80
> color #1.2 #a1a09c80
> color #1.2 #a19d9e80
> color #1.2 #a19b9f80
> color #1.2 #a197a080
> color #1.2 #a18ba180
> color #1.2 #a181a180
> color #1.2 #a17ea080
> color #1.2 #a17ba080
> color #1.2 #a177a080
> color #1.2 #a176a080
> color #1.2 #a175a080
> color #1.2 #a1739f80
> color #1.2 #a1729f80
> color #1.2 #a1719f80
> color #1.2 #a16f9f80
> color #1.2 #a16e9e80
> color #1.2 #a16d9e80
> color #1.2 #a16a9e80
> color #1.2 #a1699e80
> color #1.2 #a1689e80
> color #1.2 #a1669e80
> color #1.2 #a1659e80
> color #1.2 #a1649e80
> color #1.2 #a1649f80
> color #1.2 #a1639f80
> color #1.2 #a163a080
> color #1.2 #a162a180
> color #1.2 #9f61a180
> color #1.2 #9e61a180
> color #1.2 #9d61a180
> color #1.2 #9c61a180
> color #1.2 #9c60a180
> color #1.2 #9b60a180
> color #1.2 #9b61a180
> color #1.2 #9a61a180
> color #1.2 #9b62a280
> color #1.2 #a568ac80
> color #1.2 #a669ae80
> color #1.2 #a76aaf80
> color #1.2 #a96bb180
> color #1.2 #ab6cb380
> color #1.2 #ae6eb680
> color #1.2 #b371bc80
> color #1.2 #b874c080
> color #1.2 #b975c280
> color #1.2 #bc77c580
> color #1.2 #bd77c680
> color #1.2 #bc77c580
> select clear
> select /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> select add /A:144@C
4 atoms, 2 residues, 1 model selected
> select clear
> select add /A:143@C
1 atom, 1 residue, 1 model selected
> select clear
> select add /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 1 bond, 2 residues, 1 model selected
> select add /A:144@C
4 atoms, 1 bond, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.6 thickness 0.15
Plane 'plane' placed at [-18.73925 24.56875 14.95425] with normal [0.16416778
0.24231214 0.95620802] and radius 2.3
> close #1.3
> ui mousemode right translate
> select subtract /A:144@N
3 atoms, 2 residues, 1 model selected
> select subtract /A:143@C
2 atoms, 1 residue, 1 model selected
> select subtract /A:144@C
1 atom, 1 residue, 1 model selected
> select subtract /A:144@CA
Nothing selected
> select add /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> select add /A:144@C
4 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.6 thickness 0.15
Plane 'plane' placed at [-18.73925 24.56875 14.95425] with normal [0.16416778
0.24231214 0.95620802] and radius 2.3
> color #1.3 #909090f3
> color #1.3 #909090f1
> color #1.3 #909090ea
> color #1.3 #909090df
> color #1.3 #909090d2
> color #1.3 #909090b8
> color #1.3 #909090af
> color #1.3 #909090a9
> color #1.3 #909090a4
> color #1.3 #9090909d
> color #1.3 #9090909b
> color #1.3 #90909095
> color #1.3 #90909091
> color #1.3 #9090908d
> color #1.3 #9090908a
> color #1.3 #90909089
> color #1.3 #90909088
> color #1.3 #90909087
> color #1.3 #90909084
> color #1.3 #90909083
> color #1.3 #90909081
> color #1.3 #90909080
> color #1.3 #9fa19980
> color #1.3 #9ea19880
> color #1.3 #9da19180
> color #1.3 #9da18380
> color #1.3 #9ea17480
> color #1.3 #a0a15b80
> color #1.3 #a1a15580
> color #1.3 #a1a05180
> color #1.3 #a1a04f80
> color #1.3 #a19f4e80
> color #1.3 #a19e4e80
> color #1.3 #a19e4d80
> color #1.3 #a19d4d80
> color #1.3 #a19c4c80
> color #1.3 #a19b4b80
> color #1.3 #a1994980
> color #1.3 #a1994880
> color #1.3 #a1984880
> color #1.3 #a1984780
> color #1.3 #a1974680
> color #1.3 #a1964480
> color #1.3 #a1944180
> color #1.3 #a1933e80
> color #1.3 #a1913a80
> color #1.3 #a1903880
> color #1.3 #a18f3780
> color #1.3 #a18e3480
> color #1.3 #a18e3380
> color #1.3 #a18d3180
> color #1.3 #a18c3080
> color #1.3 #a18b2e80
> color #1.3 #a1892980
> color #1.3 #a1892780
> color #1.3 #a1882680
> color #1.3 #a1882380
> color #1.3 #a1882180
> color #1.3 #a1882080
> color #1.3 #a1881e80
> color #1.3 #a1881d80
> color #1.3 #a1891d80
> color #1.3 #a1891c80
> color #1.3 #a1891b80
> color #1.3 #a18a1b80
> color #1.3 #a18a1a80
> color #1.3 #a18b1a80
> color #1.3 #a18c1a80
> color #1.3 #a18d1a80
> color #1.3 #a18e1b80
> color #1.3 #a18f1c80
> color #1.3 #a1901c80
> color #1.3 #a1901d80
> color #1.3 #a1911d80
> color #1.3 #a1921e80
> color #1.3 #a1931f80
> color #1.3 #a1941f80
> color #1.3 #a1962180
> color #1.3 #a1972280
> color #1.3 #a1982280
> color #1.3 #a19a2380
> color #1.3 #a19c2280
> color #1.3 #a19f2180
> color #1.3 #a1a12180
> color #1.3 #9da12180
> color #1.3 #9ca12280
> color #1.3 #99a12280
> color #1.3 #98a12380
> color #1.3 #97a12380
> color #1.3 #96a12480
> color #1.3 #95a12480
> color #1.3 #94a12580
> color #1.3 #a0ae2880
> color #1.3 #a2b02880
> color #1.3 #a5b42980
> color #1.3 #aab92a80
> color #1.3 #b1c12c80
> color #1.3 #b2c12c80
> ui mousemode right zoom
> ui mousemode right label
> label delete residues
> ui mousemode right "move label"
> ui mousemode right translate
> close #1.3
> select add /A:144@CB
5 atoms, 2 residues, 1 model selected
> select /A:144@C
1 atom, 1 residue, 1 model selected
> select /A:144@CA
1 atom, 1 residue, 1 model selected
> select add /A:144@CB
2 atoms, 1 residue, 1 model selected
> select add /A:144@N
3 atoms, 1 residue, 1 model selected
> select add /A:143@C
4 atoms, 2 residues, 1 model selected
> select subtract /A:144@CB
3 atoms, 2 residues, 1 model selected
> select add /A:143@O
4 atoms, 2 residues, 1 model selected
> select add /A:143@N
5 atoms, 2 residues, 1 model selected
> select clear
> ui mousemode right rotate
> select #1.1
1 model selected
> ~select #1.1
Nothing selected
> select add /A:144@N
1 atom, 1 residue, 1 model selected
> select add /A:143@C
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> select add /A:144@C
4 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.6 thickness 0.15
Plane 'plane' placed at [-18.73925 24.56875 14.95425] with normal [0.16416778
0.24231214 0.95620802] and radius 2.3
> ui mousemode right translate
> color #1.3 #aaaaaa
> color #1.3 #a9a9a9
> color #1.3 #a4a4a4
> color #1.3 #a0a0a0
> color #1.3 #979797
> color #1.3 #8e8e8e
> color #1.3 #8a8a8a
> color #1.3 #898989
> color #1.3 #888888
> color #1.3 #878787
> color #1.3 #7e7e7e
> color #1.3 #7b7b7b
> color #1.3 #787878
> color #1.3 #777777
> color #1.3 #787878
> color #1.3 #797979
> color #1.3 #7a7a7a
> color #1.3 #7c7c7c
> color #1.3 #808080
> color #1.3 #8b8b8b
> color #1.3 #929292
> color #1.3 #999999
> color #1.3 #a0a0a0
> color #1.3 #a2a2a2
> color #1.3 #a3a3a3
> color #1.3 #98a39e
> color #1.3 #99a39e
> color #1.3 #98a39a
> color #1.3 #99a38a
> color #1.3 #9aa370
> color #1.3 #9ba35c
> color #1.3 #9aa34f
> color #1.3 #9aa346
> color #1.3 #99a341
> color #1.3 #98a33f
> color #1.3 #98a33e
> color #1.3 #99a33e
> color #1.3 #99a33d
> color #1.3 #99a33c
> color #1.3 #9aa33a
> color #1.3 #9aa339
> color #1.3 #9aa338
> color #1.3 #9aa337
> color #1.3 #9ba335
> color #1.3 #9ba334
> color #1.3 #9ba333
> color #1.3 #9ba332
> color #1.3 #9ba332fe
> color #1.3 #9ba332f9
> color #1.3 #9ba332dc
> color #1.3 #9ba332cf
> color #1.3 #9ba332c5
> color #1.3 #9ba332b5
> color #1.3 #9ba332a8
> color #1.3 #9ba332a3
> color #1.3 #9ba3329d
> color #1.3 #9ba3329c
> color #1.3 #9ba3329b
> color #1.3 #9ba3329a
> color #1.3 #9ba33297
> color #1.3 #9ba33293
> color #1.3 #9ba3328b
> color #1.3 #9ba33288
> color #1.3 #9ba33282
> color #1.3 #9ba33280
> select clear
> select #1.2
1 model selected
> close #1.1
> close #1.2
> close #1.3
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 1 residue, 1 model selected
> select add /A:142@C
3 atoms, 2 residues, 1 model selected
> select add /A:142@CA
4 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.6 thickness 0.15
Plane 'plane' placed at [-22.90225 26.6145 15.27475] with normal [-0.59150966
-0.64289741 0.48662022] and radius 2.5
> select subtract /A:143@CA
3 atoms, 2 residues, 1 model selected
> select clear
> select #1.1
1 model selected
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:143@C
2 atoms, 1 residue, 1 model selected
> select add /A:144@N
3 atoms, 2 residues, 1 model selected
> select add /A:144@CA
4 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.6 thickness 0.15
Plane 'plane' placed at [-19.68625 25.13775 15.134 ] with normal [ 0.06672227
-0.73971788 0.66960108] and radius 2.5
> select /A:142@C
1 atom, 1 residue, 1 model selected
> select add /A:142@C
1 atom, 1 bond, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 1 bond, 2 residues, 1 model selected
> select add /A:143@CB
3 atoms, 1 bond, 2 residues, 1 model selected
> select add /A:143@CA
4 atoms, 1 bond, 2 residues, 1 model selected
> select clear
> select add /A:143@N
1 atom, 1 residue, 1 model selected
> select add /A:143@CA
2 atoms, 1 residue, 1 model selected
> select add /A:143@C
3 atoms, 1 residue, 1 model selected
> select clear
> select #1.1
1 model selected
> color #1.1 #9090907f
> color #1.1 #97a0a17f
> color #1.1 #98a0a17f
> color #1.1 #97a0a17f
> color #1.1 #939da17f
> color #1.1 #8693a17f
> color #1.1 #7585a17f
> color #1.1 #6677a17f
> color #1.1 #5163a17f
> color #1.1 #4d5fa17f
> color #1.1 #4b5ca17f
> color #1.1 #4b5aa17f
> color #1.1 #4e56a17f
> color #1.1 #6a54a17f
> color #1.1 #7952a17f
> color #1.1 #834fa17f
> color #1.1 #8b4ba17f
> color #1.1 #9445a17f
> color #1.1 #9744a17f
> color #1.1 #9942a17f
> color #1.1 #9b41a17f
> color #1.1 #9b40a17f
> color #1.1 #9c40a17f
> color #1.1 #9e3ea17f
> color #1.1 #a03da17f
> color #1.1 #a1399d7f
> color #1.1 #a136997f
> color #1.1 #a134967f
> color #1.1 #a1318f7f
> color #1.1 #a1308e7f
> color #1.1 #a1308d7f
> color #1.1 #a1308c7f
> color #1.1 #a1328b7f
> color #1.1 #a136887f
> color #1.1 #a138877f
> color #1.1 #a13c847f
> color #1.1 #a13d837f
> color #1.1 #a13d8380
> select #1.2
1 model selected
> color #1.2 #909090fe
> color #1.2 #909090fc
> color #1.2 #909090de
> color #1.2 #909090c9
> color #1.2 #909090a4
> color #1.2 #90909098
> color #1.2 #90909091
> color #1.2 #9090908b
> color #1.2 #90909089
> color #1.2 #90909086
> color #1.2 #90909082
> color #1.2 #9090907b
> color #1.2 #90909079
> color #1.2 #90909078
> color #1.2 #90909077
> color #1.2 #90909076
> color #1.2 #92a19576
> color #1.2 #92a19676
> color #1.2 #90a19e76
> color #1.2 #8295a176
> color #1.2 #6e82a176
> color #1.2 #5b71a176
> color #1.2 #3f55a176
> color #1.2 #394fa176
> color #1.2 #3449a176
> color #1.2 #354aa176
> color #1.2 #364ba176
> color #1.2 #384da176
> color #1.2 #4054a176
> color #1.2 #4557a176
> color #1.2 #4959a176
> color #1.2 #505ca176
> color #1.2 #535da176
> color #1.2 #555ea176
> color #1.2 #565ea176
> color #1.2 #575da176
> color #1.2 #585ea176
> color #1.2 #5c60a176
> color #1.2 #6265a176
> color #1.2 #6d6da176
> color #1.2 #8480a176
> color #1.2 #a1959076
> color #1.2 #a1948076
> color #1.2 #a1937576
> color #1.2 #a1936f76
> color #1.2 #a1936c76
> color #1.2 #a1936a76
> color #1.2 #a1936976
> color #1.2 #a1946976
> color #1.2 #a1946876
> color #1.2 #a1966576
> color #1.2 #a19a5f76
> color #1.2 #a19f5676
> color #1.2 #98a13b76
> color #1.2 #98a13a76
> color #1.2 #99a13a76
> color #1.2 #9aa13976
> color #1.2 #9ba13976
> color #1.2 #9ca13876
> color #1.2 #9da13776
> color #1.2 #9fa13576
> color #1.2 #a1a13176
> color #1.2 #a19f2d76
> color #1.2 #a19e2b76
> color #1.2 #a19d2a76
> color #1.2 #a19c2a76
> color #1.2 #a19c2a75
> select clear
> select add /A:143@C
1 atom, 1 bond, 1 residue, 1 model selected
> select add /A:143@CA
2 atoms, 1 bond, 1 residue, 1 model selected
> select add /A:143@N
3 atoms, 1 bond, 1 residue, 1 model selected
> define plane sel color #909090 padding 0.6 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 1.9
> close #1.3
> define plane sel color #909090 padding 0.8 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.1
> define plane sel color #909090 padding 1.1 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.4
> close #1.3
> define plane sel color #909090 padding 1.2 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.5
> close #1.7
> color #1.3 #90909084
> color #1.3 #9da19584
> color #1.3 #92a18e84
> color #1.3 #8ba18984
> color #1.3 #83a18284
> color #1.3 #75a17584
> color #1.3 #72a17284
> color #1.3 #6da16e84
> color #1.3 #6ba16b84
> color #1.3 #68a16884
> color #1.3 #60a16084
> color #1.3 #5da15c84
> color #1.3 #5aa15984
> color #1.3 #56a15684
> color #1.3 #50a14f84
> color #1.3 #4da14b84
> color #1.3 #4ba14884
> color #1.3 #45a14284
> color #1.3 #42a13f84
> color #1.3 #40a13d84
> color #1.3 #3fa13b84
> color #1.3 #3ea13a84
> color #1.3 #3da13a84
> color #1.3 #3da13984
> color #1.3 #3ca13784
> color #1.3 #39a13384
> color #1.3 #35a12e84
> color #1.3 #31a12884
> color #1.3 #2da12384
> color #1.3 #29a11e84
> color #1.3 #28a11d84
> color #1.3 #28a11e84
> color #1.3 #29a11e84
> color #1.3 #29a11f84
> color #1.3 #29a12084
> color #1.3 #2aa12184
> color #1.3 #2aa12284
> color #1.3 #2ca12484
> color #1.3 #2ea12684
> color #1.3 #30a12884
> color #1.3 #32a12b84
> color #1.3 #34a12c84
> color #1.3 #35a12d84
> color #1.3 #35a12e84
> color #1.3 #35a12d84
> color #1.3 #35a12c84
> color #1.3 #34a12c84
> color #1.3 #34a12b84
> color #1.3 #33a12b84
> color #1.3 #32a12a84
> color #1.3 #31a12984
> color #1.3 #30a12884
> color #1.3 #31a12984
> color #1.3 #34a12d84
> color #1.3 #38a13184
> color #1.3 #3ca13584
> color #1.3 #3fa13984
> color #1.3 #42a13c84
> color #1.3 #44a13e84
> color #1.3 #46a14084
> color #1.3 #47a14184
> color #1.3 #49a14284
> color #1.3 #49a14384
> color #1.3 #4aa14384
> color #1.3 #4ba14484
> color #1.3 #4da14684
> color #1.3 #51a14884
> color #1.3 #53a14a84
> color #1.3 #55a14b84
> color #1.3 #56a14c84
> color #1.3 #57a14d84
> color #1.3 #55a14c84
> color #1.3 #53a14a84
> color #1.3 #4ba14384
> color #1.3 #47a13f84
> color #1.3 #43a13d84
> color #1.3 #41a13b84
> color #1.3 #41a13a84
> color #1.3 #40a13a84
> color #1.3 #3ea13884
> color #1.3 #3ba13584
> color #1.3 #36a13184
> color #1.3 #32a12d84
> color #1.3 #30a12b84
> color #1.3 #2ea12a84
> color #1.3 #2ea12a85
> select #1.1
1 model selected
> color #1.1 #a13d837e
> color #1.1 #a13d8376
> color #1.1 #a13d8371
> color #1.1 #a13d8369
> color #1.1 #a13d8364
> color #1.1 #a13d8360
> color #1.1 #a13d835a
> color #1.1 #a13d8358
> color #1.1 #a13d8353
> color #1.1 #a13d8351
> color #1.1 #a13d834e
> color #1.1 #a13d834a
> color #1.1 #a13d8348
> color #1.1 #a13d8343
> color #1.1 #a13d8340
> color #1.1 #a13d833c
> color #1.1 #a13d833a
> color #1.1 #a13d8339
> color #1.1 #a13d833a
> color #1.1 #a13d833b
> color #1.1 #a13d833c
> color #1.1 #a13d833e
> color #1.1 #a13d833f
> color #1.1 #a13d8343
> color #1.1 #a13d8345
> color #1.1 #a13d8346
> color #1.1 #a13d8348
> color #1.1 #a13d8349
> color #1.1 #a13d834a
> color #1.1 #a13d834d
> color #1.1 #a13d8351
> color #1.1 #a13d8355
> color #1.1 #a13d8357
> color #1.1 #a13d8358
> color #1.1 #a13d8359
> color #1.1 #a13d8358
> color #1.1 #a13d8357
> color #1.1 #a13d8355
> color #1.1 #a13d8354
> color #1.1 #a13d8353
> color #1.1 #a13d8352
> color #1.1 #a13d8351
> color #1.1 #a13d8354
> color #1.1 #a13d835a
> color #1.1 #a13d835c
> color #1.1 #a13d835e
> color #1.1 #a13d8360
> color #1.1 #a13d8363
> color #1.1 #a13d8365
> color #1.1 #a13d8367
> color #1.1 #a13d8369
> color #1.1 #a13d8368
> color #1.1 #a13d8367
> color #1.1 #a13d8368
> color #1.1 #a13d836a
> color #1.1 #a13d836d
> color #1.1 #a13d836f
> color #1.1 #a13d8370
> color #1.1 #a13d8371
> color #1.1 #a13d8373
> color #1.1 #a13d8375
> color #1.1 #a13d8376
> color #1.1 #a13d8377
> color #1.1 #a13d8378
> color #1.1 #a13d8379
> color #1.1 #a13d837a
> color #1.1 #a13d837c
> color #1.1 #a13d8380
> ~select #1.1
Nothing selected
> ui mousemode right zoom
> ui mousemode right translate
> ui tool show Angles/Torsions
> help
> select #1.1
1 model selected
plane #1.1 to plane #1.2: distance: 0.000Å; angle: 40.4°
> select #1.2
1 model selected
> select #1.1
1 model selected
> select #1.2
1 model selected
> select #1.1
1 model selected
plane #1.2 to plane #1.3: distance: 0.000Å; angle: 48.6°
plane #1.2 to plane #1.3: distance: 0.000Å; angle: 48.6°
plane #1.1 to plane #1.2: distance: 0.000Å; angle: 40.4°
plane #1.3 to plane #1.2: distance: 0.000Å; angle: 48.6°
plane #1.2 to plane #1.1: distance: 0.000Å; angle: 40.4°
plane #1.1 to plane #1.3: distance: 0.000Å; angle: 28.1°
Choose exactly one axis or plane in table
> ui mousemode right zoom
> select clear
> ui mousemode right translate
value: array([144, 144, 144, 255], dtype=uint8) default: None
> define axis #1.2 color #909090 name normal length 10
Plane normal for plane #1.2 centered at [-19.68625 25.13775 15.134 ] with
direction [ 0.06672227 -0.73971788 0.66960108], radius 0.125817, and length 10
> close #1.2.1
Need to select at least 3 atoms to define a plane
> select add /A:143@CA
1 atom, 1 bond, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 1 bond, 1 residue, 1 model selected
> select add /A:143@C
3 atoms, 1 bond, 1 residue, 1 model selected
> define plane sel color #909090 padding 1.2 thickness 0.05
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.5
> distance /A:143@CA/A:143@N/A:143@C #1.7
Distance between plane #1.7 and 3 atoms: min 0.000Å (/A PHE 143 CA), average:
0.000Å, max 0.000Å (/A PHE 143 N)
> close #1.7
> select clear
> select #1.3
1 model selected
> hide #1.4 models
> show #1.4 models
Need to select at least one atom
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [-21.389 25.612 15.875]
> close #1.7
> select #1.2
1 model selected
> coulombic
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/nitsanyehishalom/Desktop/Studys/MS.c./Thesis/Angel .cxs"
Log from Fri Jun 23 19:45:10 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Updating list of available bundles failed: Internal Server Error
> open "/Users/nitsanyehishalom/Library/CloudStorage/OneDrive-SharedLibraries-
> Technion/Marx Ailie - Densities/GFP/Structure25.pdb" format pdb
Chain information for Structure25.pdb #1
---
Chain | Description
A B | No description available
> select backbone
1816 atoms, 1812 bonds, 454 residues, 1 model selected
> hide ~sel
> select /A:145
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
158 atoms, 161 bonds, 19 residues, 1 model selected
> hide ~sel
[Repeated 1 time(s)]
> hide ~sel ribbons
> show
> show sel
> hide sel ribbons
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
158 atoms, 161 bonds, 19 residues, 1 model selected
> select down
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 33 atoms, 32 bonds
> help
> select :144-145
30 atoms, 26 bonds, 6 residues, 1 model selected
> select :144-146
51 atoms, 48 bonds, 9 residues, 1 model selected
> select :142-143
40 atoms, 38 bonds, 6 residues, 1 model selected
> select :142-144
57 atoms, 54 bonds, 9 residues, 1 model selected
> select :142-145
70 atoms, 66 bonds, 12 residues, 1 model selected
> hide ~sel
> select clear
> dihedral true
Unknown command: dihedral true
> help
Downloading bundle ChimeraX_QScore-1.0-cp39-cp39-macosx_10_13_universal2.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip available: 22.2.2 -> 23.1.2
[notice] To update, run:
/Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
/Users/nitsanyehishalom/Downloads/ChimeraX_QScore-1.0-cp39-cp39-macosx_10_13_universal2.whl
Requirement already satisfied: ChimeraX-Core>=1.5 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-QScore==1.0) (1.5)
Installing collected packages: ChimeraX-QScore
Successfully installed ChimeraX-QScore-1.0
\---
Successfully installed ChimeraX-QScore-1.0
Installed ChimeraX-QScore (1.0)
> ui tool show "Model-map Q-Score"
> style #1 stick
Changed 3858 atom styles
> color #1 byhetero
Must select a model and map first!
[Repeated 1 time(s)]
> label #1 residues attribute phi
> undo
> angle
Missing or invalid "objects" argument: empty atom specifier
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> angle sel
Must specify exactly 3 atoms/centroids or two measurable objects (e.g.
axes/planes)
> select :143
23 atoms, 22 bonds, 3 residues, 1 model selected
> angels sel
Unknown command: angels sel
> angle sel
Must specify exactly 3 atoms/centroids or two measurable objects (e.g.
axes/planes)
> select clear
Drag select of 33 atoms, 33 bonds
> angle sel
Must specify exactly 3 atoms/centroids or two measurable objects (e.g.
axes/planes)
> select clear
> style ball
Changed 3858 atom styles
> cartoon style modeHelix tube sides 20
> ui tool show Axes/Planes/Centroids
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select /A:143@N
1 atom, 1 residue, 1 model selected
> select add /A:143@CA
2 atoms, 1 residue, 1 model selected
> select add /A:143@C
3 atoms, 1 bond, 1 residue, 1 model selected
> angle sel
Angle between /A PHE 143 N, /A PHE 143 CA, and /A PHE 143 C: 110.162
> define plane sel
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 1.3
> define centroid sel
Centroid 'centroid' placed at [-21.40533333 25.574 15.30566667]
value: None default: None
> define axis perHelix true name "helix axes"
Axis 'Structure25.pdb #!1/helix axes/chain A helix 1' centered at
[-17.27238126 -1.29708508 32.03992106] with direction [-0.74104052 0.63631348
0.21439241], radius 1.19661, and length 5.35751
Axis 'Structure25.pdb #!1/helix axes/chain A helix 2' centered at [-21.8315335
0.2968683 28.71759421] with direction [-0.80684425 0.44471499 -0.3888842 ],
radius 1.57558, and length 6.47536
Axis 'Structure25.pdb #!1/helix axes/chain A helix 3' centered at
[-24.34518934 28.46343548 23.7800401 ] with direction [ 0.64493057 -0.42416072
0.6357297 ], radius 1.53514, and length 6.54968
Axis 'Structure25.pdb #!1/helix axes/chain A helix 4' centered at
[-19.41641102 10.61622012 26.33971502] with direction [-0.36912945 -0.74637579
-0.55377488], radius 1.18606, and length 5.82732
Axis 'Structure25.pdb #!1/helix axes/chain A helix 5' centered at [-9.44334259
1.73930308 23.72302123] with direction [0.14072585 0.44156178 0.88612608],
radius 1.54016, and length 10.3001
Axis 'Structure25.pdb #!1/helix axes/chain A helix 6' centered at
[-14.67182631 6.50902984 31.34476511] with direction [-0.60790279 -0.70686576
0.3616559 ], radius 1.58684, and length 5.65226
Axis 'Structure25.pdb #!1/helix axes/chain B helix 1' centered at [-9.82953682
24.26426795 -1.730028 ] with direction [-0.84576161 0.33702053 0.41364775],
radius 1.53574, and length 9.46359
Axis 'Structure25.pdb #!1/helix axes/chain B helix 2' centered at [-29.9510665
3.57270637 0.6565128 ] with direction [ 0.90663197 -0.07806668 -0.41463727],
radius 1.54186, and length 6.44979
Axis 'Structure25.pdb #!1/helix axes/chain B helix 3' centered at
[-15.26266442 15.38447193 0.91175775] with direction [-0.02827089 0.83810341
0.54477832], radius 1.18643, and length 5.73177
Axis 'Structure25.pdb #!1/helix axes/chain B helix 4' centered at [-3.04470004
16.69078953 6.99650009] with direction [ 0.09342461 -0.47062789 -0.87737178],
radius 1.52068, and length 10.2336
Axis 'Structure25.pdb #!1/helix axes/chain B helix 5' centered at [-7.94273645
15.6876803 -2.61308687] with direction [-0.07253961 -0.86943687 0.48868961],
radius 1.5623, and length 6.20119
> select #1.2
1 model selected
> select #1.4.11
1 model selected
> close #1.2-3#1.4.1-11
Either three or four atoms must be selected!
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 1 residue, 1 model selected
> select add /A:143@C
3 atoms, 1 residue, 1 model selected
Choose exactly one axis or plane in table
> define plane sel color #909090
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 1.3
> select clear
> label hide
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> help
> label delete
> select #1.2
1 model selected
> select clear
> select /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090
Plane 'plane' placed at [-19.11866667 24.97966667 14.887 ] with normal [
0.05701853 -0.68657749 0.72481738] and radius 1.3
> select clear
value: None default: None
> define axis #1.2 name normal padding 2.5
Plane normal for plane #1.2 centered at [-21.40533333 25.574 15.30566667] with
direction [-0.48407451 -0.87205193 0.07209225], radius 0.0637005, and length
1.27401
> undo
> select #1.2.1
1 model selected
> close #1.2.1
Need to select at least 3 atoms to define a plane
[Repeated 1 time(s)]
> select /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 4 thickness 0.15
Plane 'plane' placed at [-19.11866667 24.97966667 14.887 ] with normal [
0.05701853 -0.68657749 0.72481738] and radius 5.3
> close #1.3
> select #1.2
1 model selected
> select clear
> view #1.2 zalign #1.2
> turn y 90 center #1.2
> ui tool show "Side View"
plane #1.1 to plane #1.2: distance: 0.000Å; angle: 51.4°
> close #1.1-2
> select add /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 1 residue, 1 model selected
> select add /A:143@C
3 atoms, 1 residue, 1 model selected
> define plane sel color #909090 padding 1 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.3
> close #1.1
> define plane sel color #909090 padding 1.5 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.8
> close #1.1
> define plane sel color #909090 padding 1.1 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 2.4
> close #1.1
> define plane sel color #909090 padding 0.5 thickness 0.15
Plane 'plane' placed at [-21.40533333 25.574 15.30566667] with normal
[-0.48407451 -0.87205193 0.07209225] and radius 1.8
> rename #1.1 "Ca plane"
> select subtract /A:143@C
2 atoms, 1 residue, 1 model selected
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select subtract /A:143@CA
Nothing selected
> select add /A:144@N
1 atom, 1 bond, 1 residue, 1 model selected
> select add /A:143@C
2 atoms, 1 bond, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 1 bond, 2 residues, 1 model selected
> select /A:144@N
1 atom, 1 residue, 1 model selected
> select /A:143@C
1 atom, 1 residue, 1 model selected
> select add /A:144@N
2 atoms, 2 residues, 1 model selected
> select add /A:144@CA
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.5 thickness 0.15
Plane 'plane' placed at [-19.11866667 24.97966667 14.887 ] with normal [
0.05701853 -0.68657749 0.72481738] and radius 1.8
> color #1.2 #9090909f
> color #1.2 #9090909e
> color #1.2 #9090909d
> color #1.2 #9090909b
> color #1.2 #90909096
> color #1.2 #9090908f
> color #1.2 #9090908b
> color #1.2 #90909086
> color #1.2 #90909081
> color #1.2 #9090907b
> color #1.2 #90909075
> color #1.2 #90909073
> color #1.2 #90909071
> color #1.2 #90909072
> color #1.2 #90909073
> color #1.2 #90909074
> color #1.2 #90909076
> color #1.2 #90909079
> color #1.2 #9090907b
> color #1.2 #9090907d
> color #1.2 #9090907e
> color #1.2 #90909080
> color #1.2 #a1a09680
> color #1.2 #a1a09780
> color #1.2 #a1a09880
> color #1.2 #a19d9c80
> color #1.2 #a19ba180
> color #1.2 #9d98a180
> color #1.2 #9a94a180
> color #1.2 #928ba180
> color #1.2 #8d85a180
> color #1.2 #877fa180
> color #1.2 #847ba180
> color #1.2 #7f75a180
> color #1.2 #796ea180
> color #1.2 #7064a180
> color #1.2 #6a5da180
> color #1.2 #685aa180
> color #1.2 #6254a180
> color #1.2 #5d4ea180
> color #1.2 #5b4ca180
> color #1.2 #5647a180
> color #1.2 #5344a180
> color #1.2 #5142a180
> color #1.2 #4d3ea180
> color #1.2 #4b3ca180
> color #1.2 #4839a180
> color #1.2 #4537a180
> color #1.2 #4335a180
> color #1.2 #4133a180
> color #1.2 #4032a180
> color #1.2 #3f31a180
> color #1.2 #3f32a180
> color #1.2 #3f33a180
> color #1.2 #3e33a180
> color #1.2 #3e34a180
> color #1.2 #3e35a180
> color #1.2 #3d35a180
> color #1.2 #3c36a180
> color #1.2 #3a38a180
> color #1.2 #3938a180
> color #1.2 #393ba180
> color #1.2 #3a3da180
> color #1.2 #3a3ea180
> color #1.2 #3b3fa180
> color #1.2 #3c3fa180
> color #1.2 #3c3ea180
> color #1.2 #3d3ea180
> color #1.2 #3d3da180
> color #1.2 #3e3da180
> color #1.2 #3f3ea180
> color #1.2 #423ea180
> color #1.2 #443fa180
> color #1.2 #4640a180
> color #1.2 #4740a180
> color #1.2 #4841a180
> color #1.2 #4a41a180
> color #1.2 #4c42a180
> color #1.2 #4d42a180
> color #1.2 #4e42a180
> color #1.2 #4e43a180
> color #1.2 #5649a180
> color #1.2 #6256a180
> color #1.2 #6c62a180
> color #1.2 #8781a180
> color #1.2 #9fa19e80
> color #1.2 #9aa18e80
> color #1.2 #98a18480
> color #1.2 #95a17e80
> color #1.2 #94a17d80
> color #1.2 #94a17c80
> color #1.2 #93a17a80
> color #1.2 #8fa17680
> color #1.2 #8ba17380
> color #1.2 #7aa16380
> color #1.2 #6aa15680
> color #1.2 #5aa14980
> color #1.2 #4fa14180
> color #1.2 #40a13580
> color #1.2 #39a13080
> color #1.2 #32a12b80
> color #1.2 #31a12b80
> color #1.2 #2fa12980
> color #1.2 #2ea12980
> color #1.2 #2ea12880
> color #1.2 #2da12880
> color #1.2 #2ea12880
> color #1.2 #2ea12980
> select add #1.1
3 atoms, 2 residues, 2 models selected
> color #1.1 #9ca19a
> color #1.1 #9ca19c
> color #1.1 #9ca0a1
> color #1.1 #999ca1
> color #1.1 #9498a1
> color #1.1 #8b90a1
> color #1.1 #838aa1
> color #1.1 #8088a1
> color #1.1 #7b84a1
> color #1.1 #737da1
> color #1.1 #6f79a1
> color #1.1 #6b76a1
> color #1.1 #6873a1
> color #1.1 #6671a1
> color #1.1 #6470a1
> color #1.1 #636fa1
> color #1.1 #636ea1
> color #1.1 #626da1
> color #1.1 #616da1
> color #1.1 #626da1
> color #1.1 #626ea1
> color #1.1 #636fa1
> color #1.1 #6471a1
> color #1.1 #6774a1
> color #1.1 #6876a1
> color #1.1 #6978a1
> color #1.1 #6a7aa1
> color #1.1 #6b7ca1
> color #1.1 #6f82a1
> color #1.1 #7187a1
> color #1.1 #7289a1
> color #1.1 #748da1
> color #1.1 #758ea1
> color #1.1 #7692a1
> color #1.1 #7597a1
> color #1.1 #739ba1
> color #1.1 #729da1
> color #1.1 #6fa1a0
> color #1.1 #6da19e
> color #1.1 #6da19d
> color #1.1 #6ca19b
> color #1.1 #6ba19b
> color #1.1 #6aa19b
> color #1.1 #68a19b
> color #1.1 #65a19b
> color #1.1 #5da19b
> color #1.1 #53a199
> color #1.1 #48a196
> color #1.1 #3fa194
> color #1.1 #34a192
> color #1.1 #31a192
> color #1.1 #2ba191
> color #1.1 #29a191
> color #1.1 #28a191
> color #1.1 #27a191
> color #1.1 #26a191
> color #1.1 #25a191
> color #1.1 #24a191
> color #1.1 #23a191
> color #1.1 #22a191
> color #1.1 #22a192
> color #1.1 #21a192
> color #1.1 #20a192
> color #1.1 #1fa192
> color #1.1 #1fa193
> color #1.1 #1fa193fe
> color #1.1 #1fa193f2
> color #1.1 #1fa193d7
> color #1.1 #1fa193be
> color #1.1 #1fa193b5
> color #1.1 #1fa193ac
> color #1.1 #1fa193aa
> color #1.1 #1fa193a7
> color #1.1 #1fa193a3
> color #1.1 #1fa1939f
> color #1.1 #1fa1939e
> color #1.1 #1fa1939b
> color #1.1 #1fa19399
> color #1.1 #1fa19398
> color #1.1 #1fa19397
> color #1.1 #1fa19398
> color #1.1 #1fa19399
> color #1.1 #1fa1939a
> color #1.1 #1fa1939b
> color #1.1 #1fa1939c
> select clear
> select add /A:142@C
1 atom, 1 residue, 1 model selected
> select add /A:143@N
2 atoms, 2 residues, 1 model selected
> select add /A:143@CA
3 atoms, 2 residues, 1 model selected
> select add /A:142@CA
4 atoms, 2 residues, 1 model selected
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select /A:142@C
1 atom, 1 residue, 1 model selected
> select add /A:142@CA
2 atoms, 1 residue, 1 model selected
> select add /A:143@N
3 atoms, 2 residues, 1 model selected
> define plane sel color #909090 padding 0.5 thickness 0.15
Plane 'plane' placed at [-23.40666667 26.94866667 15.07466667] with normal
[-0.55887244 -0.64599619 0.51995243] and radius 1.8
> color #1.3 #909090fe
> color #1.3 #909090e2
> color #1.3 #909090d1
> color #1.3 #909090b5
> color #1.3 #909090a4
> color #1.3 #9090909b
> color #1.3 #90909093
> color #1.3 #9090908c
> color #1.3 #9090908a
> color #1.3 #90909089
> color #1.3 #90909088
> color #1.3 #90909085
> color #1.3 #90909082
> color #1.3 #9090907e
> color #1.3 #90909078
> color #1.3 #90909077
> color #1.3 #90909073
> color #1.3 #90909072
> color #1.3 #90909073
> color #1.3 #90909074
> color #1.3 #90909075
> color #1.3 #90909076
> color #1.3 #90909077
> color #1.3 #90909078
> color #1.3 #90909079
> color #1.3 #9090907a
> color #1.3 #9090907c
> color #1.3 #9090907e
> color #1.3 #90909081
> color #1.3 #90909082
> color #1.3 #90909083
> color #1.3 #93a19083
> color #1.3 #94a18e83
> color #1.3 #96a18983
> color #1.3 #98a17f83
> color #1.3 #9ca17483
> color #1.3 #9ea16b83
> color #1.3 #9fa16683
> color #1.3 #a0a16383
> color #1.3 #9fa16283
> color #1.3 #9fa16183
> color #1.3 #9fa15f83
> color #1.3 #a1a15783
> color #1.3 #a19e4683
> color #1.3 #a19c3f83
> color #1.3 #a19a3783
> color #1.3 #a1983183
> color #1.3 #a1982f83
> color #1.3 #a1972c83
> color #1.3 #a1972b83
> color #1.3 #a1962b83
> color #1.3 #a1962a83
> color #1.3 #a1952a83
> color #1.3 #a1952983
> color #1.3 #a1922483
> color #1.3 #a1912283
> color #1.3 #a1912083
> color #1.3 #a1901f83
> color #1.3 #a18f1e83
> color #1.3 #a1901f83
> color #1.3 #a18f1f83
> color #1.3 #a1902083
> color #1.3 #a1902183
> color #1.3 #a1922483
> color #1.3 #a1942883
> color #1.3 #a1962d83
> color #1.3 #a1983183
> color #1.3 #a19a3483
> color #1.3 #a19a3583
> color #1.3 #a19b3683
> color #1.3 #a19c3783
> color #1.3 #a19d3883
> color #1.3 #a1a03e83
> color #1.3 #a1a14283
> color #1.3 #9fa14483
> color #1.3 #9ea14683
> color #1.3 #9ea14783
> color #1.3 #9ca14483
> color #1.3 #9da14583
> color #1.3 #9ea14683
> color #1.3 #a1a04883
> color #1.3 #a19b4983
> color #1.3 #a18e4b83
> color #1.3 #a1844a83
> color #1.3 #a17e4983
> color #1.3 #a1754683
> color #1.3 #a1744683
> color #1.3 #a1734583
> color #1.3 #a1744583
> color #1.3 #a1764583
> color #1.3 #a1784583
> color #1.3 #a17e4683
> color #1.3 #a1854683
> color #1.3 #a1884683
> color #1.3 #a1924583
> color #1.3 #a1964583
> color #1.3 #a1994583
> color #1.3 #a19a4683
> color #1.3 #a19c4783
> color #1.3 #a19e4983
> color #1.3 #a1a15183
> color #1.3 #a1a15b83
> color #1.3 #a1a16183
> color #1.3 #a19f7783
> color #1.3 #a19c8683
> color #1.3 #a1959783
> color #1.3 #a18fa183
> color #1.3 #9d89a183
> color #1.3 #9379a183
> color #1.3 #8c6ba183
> color #1.3 #8a68a183
> color #1.3 #865fa183
> color #1.3 #865ca183
> color #1.3 #865aa183
> color #1.3 #8653a183
> color #1.3 #864ca183
> color #1.3 #8646a183
> color #1.3 #863fa183
> color #1.3 #873ca183
> color #1.3 #873aa183
> color #1.3 #8739a183
> color #1.3 #8738a183
> color #1.3 #8838a183
> color #1.3 #8938a183
> color #1.3 #8a37a183
> color #1.3 #8d36a183
> color #1.3 #9134a183
> color #1.3 #9432a183
> color #1.3 #9831a183
> color #1.3 #9930a183
> color #1.3 #9a30a183
> color #1.3 #9a2fa183
> color #1.3 #9b30a183
> color #1.3 #9c30a183
> color #1.3 #9d31a183
> color #1.3 #9e32a183
> color #1.3 #a034a183
> color #1.3 #a135a183
> color #1.3 #a135a185
> select clear
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:143@C
2 atoms, 1 residue, 1 model selected
> select add /A:143@N
3 atoms, 1 residue, 1 model selected
> ui tool show Angles/Torsions
> select clear
> set bgColor white
> help
> select add /A:144@CB
1 atom, 1 residue, 1 model selected
> select add /A:144@CG
2 atoms, 1 residue, 1 model selected
> select add /A:144@ND2
3 atoms, 1 residue, 1 model selected
Drag select of 4 atoms, 3 bonds
> select add /A:144@CB
2 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel
Drag select of 2 atoms, 1 bonds
> hide sel
Drag select of 4 atoms, 3 bonds
> hide sel
> undo
[Repeated 4 time(s)]Drag select of Ca plane, plane, plane, 33 atoms, 33 bonds
> select /A:145@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
158 atoms, 161 bonds, 19 residues, 1 model selected
> select :142-145
70 atoms, 66 bonds, 12 residues, 1 model selected
> delete ~sel
> select clear
[Repeated 1 time(s)]
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> label sel
> label delete
> label atoms
> label :143 Ca
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label :143 CA
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label :143CA
> show label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show lable
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label /:143 residues text "{0.phi:.1f},{0.psi:.1f}"
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label :143 residues text {0.phi:.1f},{0.psi:.1f}
> label :143 residues text "Phi {0.phi:.1f},Psi {0.psi:.1f}"
> ui mousemode right label
> label delete residues
[Repeated 1 time(s)]
> label :143 residues text "Phi {0.phi:.1f},Psi {0.psi:.1f}"
> ui mousemode right "move label"
> label :143 residues text "Phi {0.phi:.1f}"
> label :143 residues text "Psi {0.psi:.1f}"
> select #1.2
1 model selected
> color #1.2 #2ea22980
> color #1.2 #2eab2980
> color #1.2 #2eb12980
> color #1.2 #2eb52980
> color #1.2 #2eb92980
> color #1.2 #2ebb2980
> color #1.2 #2ebc2980
> color #1.2 #2ebd2980
> color #1.2 #2ebe2980
> color #1.2 #2ebf2980
> color #1.2 #2ec12980
> color #1.2 #2ec32980
> color #1.2 #2ec42980
> color #1.2 #2ec52980
> color #1.2 #2ec62980
> color #1.2 #2ec72980
> color #1.2 #2ec82980
> color #1.2 #2ece2980
> color #1.2 #2ed82980
> color #1.2 #2ede2980
> color #1.2 #2ee22980
> color #1.2 #2ee62980
> color #1.2 #2ee72980
> select clear
> style stick
Changed 70 atom styles
> style ball
Changed 70 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style ball thin
Expected a keyword
> style ball ringFill thin
Changed 70 atom styles, 12 residue ring styles
> undo
> select add /A:143@CA
1 atom, 1 residue, 1 model selected
> select add /A:142@CA
2 atoms, 2 residues, 1 model selected
> ui mousemode right label
> label #1/A:143
> rename #1 angels
> select clear
[Repeated 1 time(s)]
> label #1/A:142
> label delete residues
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right "play map series"
[Repeated 1 time(s)]
> ui mousemode right "play coordinates"
[Repeated 1 time(s)]
> ui mousemode right minimize
> rename #1.2 ""
ID must be one or more integers separated by '.' characters
[Repeated 1 time(s)]
> rename #1.2 ""
No visible atoms selected
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> label sel atoms attribute element
> ui mousemode right "move label"
> ui mousemode right label
> label sel atoms attribute idatm_type
> label sel atoms text Ca
> select /A:143@N
1 atom, 1 residue, 1 model selected
> label #1/A:142
> ui mousemode right zoom
> ui mousemode right translate
> select /A:143@N
1 atom, 1 residue, 1 model selected
Height must be a positive number
> label sel atoms text N
> ui mousemode right "move label"
> select clear
> ui mousemode right label
> label #1/A:143
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
[Repeated 6 time(s)]
> select /A:143@CA
1 atom, 1 residue, 1 model selected
> label sel atoms
> label delete residues
> ui mousemode right "move label"
> select /A:143@C
1 atom, 1 residue, 1 model selected
> label sel atoms
Drag select of , 8 of 160 triangles
> select clear
> select /A:143@O
1 atom, 1 residue, 1 model selected
> label sel atoms
> select #1.2
1 model selected
> select clear
> select /A:143@CB
1 atom, 1 residue, 1 model selected
Drag select of 6 atoms, 6 bonds
> hide sel
> ui mousemode right label
> select /A:143@CB
1 atom, 1 residue, 1 model selected
> color sel magenta
> label sel atoms text R
> ui mousemode right "move label"
> select clear
[Repeated 1 time(s)]
> select /A:142@CG
1 atom, 1 residue, 1 model selected
Drag select of 3 atoms, 3 bonds
> hide sel
> undo
> select add /A:142@CG
3 atoms, 2 bonds, 1 residue, 1 model selected
> select subtract /A:142@CG
2 atoms, 1 residue, 1 model selected
> select add /A:142@CG
3 atoms, 1 residue, 1 model selected
Drag select of 3 atoms, 3 bonds
> hide sel
Drag select of 3 atoms, 2 bonds
[Repeated 1 time(s)]
> hide sel
> hide #!1 models
> show #!1 models
> select /A:142@ND2
1 atom, 1 residue, 1 model selected
> hide sel
> select /A:142@OD1
1 atom, 1 residue, 1 model selected
> hide sel
> select /A:142@CG
1 atom, 1 residue, 1 model selected
> hide sel
> select /A:142@CB
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> select add /A:144@CG
1 atom, 1 residue, 1 model selected
> select add /A:144@CB
2 atoms, 1 residue, 1 model selected
> hide sel
> select add /A:144@OD1
3 atoms, 1 residue, 1 model selected
> select add /A:144@ND2
4 atoms, 1 residue, 1 model selected
> hide sel
> select add /A:145@C
5 atoms, 2 residues, 1 model selected
> select add /A:145@O
6 atoms, 2 residues, 1 model selected
> select subtract /A:145@O
5 atoms, 2 residues, 1 model selected
> undo
[Repeated 9 time(s)]
> select /A:144@CA
1 atom, 1 residue, 1 model selected
> show sel
> show :144
> select add /A:144@CG
2 atoms, 1 residue, 1 model selected
> select add /A:144@OD1
3 atoms, 1 residue, 1 model selected
> select add /A:144@ND2
4 atoms, 1 residue, 1 model selected
> hide sel
> undo
> select /A:144@CG
1 atom, 1 residue, 1 model selected
> select /A:144@ND2
1 atom, 1 residue, 1 model selected
> select /A:144@OD1
1 atom, 1 residue, 1 model selected
> select add /A:144@CG
2 atoms, 1 residue, 1 model selected
> select add /A:144@ND2
3 atoms, 1 bond, 1 residue, 1 model selected
> hide sel
> select /A:144@CB
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> select add /A:145@C
1 atom, 1 residue, 1 model selected
> select add /A:145@O
2 atoms, 1 residue, 1 model selected
> select subtract /A:145@O
1 atom, 1 residue, 1 model selected
> select /A:145@O
1 atom, 1 residue, 1 model selected
> hide sel
> select /A:145@C
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> save "/Users/nitsanyehishalom/Desktop/Studys/MS.c./Thesis/Angel .cxs"
> view orient
> undo
> ui tool show "Side View"
Drag select of 9 atoms, 7 bonds
> delete sel
> save "/Users/nitsanyehishalom/Desktop/Studys/MS.c./Thesis/Angel .cxs"
——— End of log from Fri Jun 23 19:45:10 2023 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15G000MKAE/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.100.650
OS Loader Version: 8422.100.650
Software:
System Software Overview:
System Version: macOS 13.3.1 (a) (22E772610a)
Kernel Version: Darwin 22.4.0
Time since boot: 19 days, 8 hours, 47 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:
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: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-QScore: 1.0
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
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: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
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