Opened 2 years ago

Closed 2 years ago

#9245 closed defect (can't reproduce)

Crash in chain.existing_residues

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

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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===== 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
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    Sphinx: 5.1.1
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    urllib3: 1.26.13
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Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Sequence
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in chain.existing_residues

comment:2 by Eric Pettersen, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed

Possibly already fixed; would definitely need the PDB file to reproduce.

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