![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9177 closed defect (can't reproduce)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff85a19d340 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-06-12 11:46:26.00 -0400","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.3.1 (22E772610a)","roots_installed":0,"name":"ChimeraX","incident_id":"AA6625D7-E4A8-42C1-BA33-6E1C390DA4BC"}
{
"uptime" : 250000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 53470,
"osVersion" : {
"train" : "macOS 13.3.1",
"build" : "22E772610a",
"releaseType" : "User"
},
"captureTime" : "2023-06-12 11:46:08.6262 -0400",
"incident" : "AA6625D7-E4A8-42C1-BA33-6E1C390DA4BC",
"pid" : 56548,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-06-08 16:56:00.2203 -0400",
"procStartAbsTime" : 220016427807714,
"procExitAbsTime" : 259285065740758,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"AA534D71-249F-5C83-BDF8-8597525678D1","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1E84C152-81FD-95B6-1AA7-65E94D64DF08",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 9152,
"bridgeVersion" : {"build":"20P4252","train":"7.4"},
"sleepWakeUUID" : "E7DC04E2-54C4-46CA-AF59-0BE3F6C1F93B",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737487937512\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff9a000-7ffffff9b000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737487937512\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff9a000-7ffffff9b000 [ 4K] r-x\/r-x SM=SHM ",
"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,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
Log from Thu Jun 8 16:55:49 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
Log from Tue Jun 6 16:44:25 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open 2bbv
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #1
---
Chain | Description | UniProt
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |
Non-standard residues in 2bbv #1
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> color bychain
> style /b stick
Changed 2382 atom styles
> color /n teal
[Repeated 1 time(s)]
> hide /c
> show /c
> hide /n
> shown /n
Unknown command: shown /n
> show /n
[Repeated 1 time(s)]
> ribbon /c
[Repeated 1 time(s)]
> ribbon /n
> style /n ribbon
Expected a keyword
> select /N:4@C5'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select down
201 atoms, 222 bonds, 10 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select down
201 atoms, 222 bonds, 10 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select down
201 atoms, 222 bonds, 10 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select down
201 atoms, 222 bonds, 10 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> color sel gold
> select clear
> color sel gold
> select clear
> color sel gold
> select clear
> color sel gold
> select clear
> color sel red
> surface #1
> color /n fromatoms
> surface #1
> surface #2
No atoms specified by #2
> surface
> surface #1 hide
Expected a keyword
> hide surfaces #1
Expected ',' or a keyword
> hide surfaces
> show surfaces
> hide surfaces
> style solvent sphere
Changed 208 atom styles
> color solvent red
> sym #1
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly| 60 copies of chains A-F,N
2| icosahedral asymmetric unit| 1 copy of chains A-F,N
3| icosahedral pentamer| 5 copies of chains A-F,N
4| icosahedral 23 hexamer| 6 copies of chains A-F,N
5| icosahedral asymmetric unit, std point frame| 1 copy of chains A-F,N
6| crystal asymmetric unit, crystal frame| 5 copies of chains A-F,N
> hide #1 models
> show #1
> show #1 models
> sym #1 assembly 3 newModel false copies false
Made 5 graphical clones for 2bbv assembly 3
> sym #1 assembly 1
Made 60 graphical clones for 2bbv assembly 1
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> sym #1 assembly 1view
Assembly "1view" not found, have 1, 2, 3, 4, 5, 6
> view
> set bgColor white
> set silhouettes true
> save /Users/matthewcomstock/Desktop/2bbv.png
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/matthewcomstock/Desktop/movie1.mp4
Movie saved to /Users/matthewcomstock/Desktop/movie1.mp4
> close #2
> sym #1 assembly 3 newModel false copies false
Made 5 graphical clones for 2bbv assembly 3
> show #1 models
> view
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> surface #1
> color /n fromatoms
> style solvent sphere
Changed 208 atom styles
> color solvent red
> view
> close
> set bgColor black
> set bgColor transparent
> set silhouettes false
> open 1080 fromDatabase emdb
Summary of feedback from opening 1080 fetched from emdb
---
note | Fetching compressed map 1080 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/map/emd_1080.map.gz
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> lighting full
> volume #1 level 0.9
> volume #1 level .5
> volume #1 level .2
> volume #1 level .1
> volume #1 level 2
> volume #1 level .15
> volume #1 level 1.68
> ui mousemode right "contour level"
> volume #1 level 1.812
> volume #1 level 1.773
> volume #1 level 1.504
> volume #1 level 1.275
> volume #1 encloseVolume 1e6 step 1 color tan
> volume #1 1e5 step 1
Expected a keyword
> volume #1 1e5 step 1 color tan
Expected a keyword
> volume #1 encloseVolume 1e5 step 1
> volume #1 encloseVolume 1e4 step 1
> volume #1 encloseVolume 1e6 step 1 color tan
> set bgColor gray
> set bgColor #80808000
> set silhouettes true
> open 1grl
Summary of feedback from opening 1grl fetched from pdb
---
note | Fetching compressed mmCIF 1grl from
http://files.rcsb.org/download/1grl.cif
1grl title:
The crystal structure of the bacterial chaperonin groel At 2.8 angstroms [more
info...]
Chain information for 1grl #2
---
Chain | Description | UniProt
A B C D E F G | GROEL (HSP60 CLASS) | CH60_ECOLI 2-548
1grl mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> lighting default
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select /D:357@CG2
1 atom, 1 residue, 1 model selected
> view matrix models #2,1,0,0,44.01,0,1,0,-1.4223,0,0,1,-0.37848
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99999,-0.0041909,0.002923,44.116,0.0043018,0.99923,-0.039047,-2.5771,-0.0027571,0.039059,0.99923,-0.57913
> view matrix models
> #2,0.99572,-0.092469,0.00020636,43.966,0.092405,0.99494,-0.039468,1.1951,0.0034442,0.039318,0.99922,-0.31382
> fitmap #2 inMap #1
Fit molecule 1grl (#2) to map emdb 1080 (#1) using 29274 atoms
average map value = 1.33, steps = 104
shifted from previous position = 0.914
rotated from previous position = 20.7 degrees
atoms outside contour = 3707, contour level = 0.82501
Position of 1grl (#2) relative to emdb 1080 (#1) coordinates:
Matrix rotation and translation
0.90168809 -0.43225449 -0.01070721 39.38415285
0.43238288 0.90129381 0.02673023 18.93264110
-0.00190392 -0.02873195 0.99958534 -0.07033036
Axis -0.06401015 -0.01016007 0.99789753
Axis point -21.87968789 95.67746379 0.00000000
Rotation angle (degrees) 25.67269007
Shift along axis -2.78352503
> volume #1 transparency 0.5
> view matrix models
> #2,0.92048,-0.39074,-0.0062701,40.283,0.39076,0.92009,0.027407,17.143,-0.0049401,-0.027678,0.9996,-0.20146
> fitmap #2 inMap #1
Fit molecule 1grl (#2) to map emdb 1080 (#1) using 29274 atoms
average map value = 1.33, steps = 60
shifted from previous position = 0.0354
rotated from previous position = 2.63 degrees
atoms outside contour = 3704, contour level = 0.82501
Position of 1grl (#2) relative to emdb 1080 (#1) coordinates:
Matrix rotation and translation
0.90160406 -0.43242969 -0.01070914 39.38027615
0.43255808 0.90120994 0.02672371 18.93993563
-0.00190494 -0.02872653 0.99958549 -0.07718132
Axis -0.06397061 -0.01015704 0.99790009
Axis point -21.87911091 95.63336281 0.00000000
Rotation angle (degrees) 25.68378070
Shift along axis -2.78857344
> volume #1 transparency 0.5
> molmap #2 10
Opened 1grl map 10 as #3, grid size 63,63,41, pixel 3.33, shown at level
0.0611, step 1, values float32
> volume #3 style mesh
> volume subtract #1 #3 minRms true
Opened volume difference as #4, grid size 100,100,100, pixel 2.7, shown at
step 1, values float32
Minimum RMS scale factor for "1grl map 10 #3" above level 0.061077 is 4.5565
> volume #4 color pink transparency 0
> hide atoms
> show ribbons
> close
> set bgColor black
> set bgColor transparent
> set silhouettes false
> open 1a0m fromDatabase eds
Summary of feedback from opening 1a0m fetched from eds
---
note | Fetching map 1a0m from
http://www.ebi.ac.uk/pdbe/coordinates/files/1a0m.ccp4
Opened eds 1a0m as #1, grid size 97,101,88, pixel 0.37,0.37,0.367, shown at
level 2.28, step 1, values float32
> open 1a0m
Summary of feedback from opening 1a0m fetched from pdb
---
note | Fetching compressed mmCIF 1a0m from
http://files.rcsb.org/download/1a0m.cif
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #2
---
Chain | Description | UniProt
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16
Non-standard residues in 1a0m #2
---
NH2 — amino group
> hide ribbons
> show
> volume #1 level 1.0 style mesh
> ui mousemode right zoom
> volume zone #1 nearAtoms #2 range 2
> volume #1 level 0.5 transparency 0.6
> close
> open 1273 fromDatabase emdb
Summary of feedback from opening 1273 fetched from emdb
---
note | Fetching compressed map 1273 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1273/map/emd_1273.map.gz
Opened emdb 1273 as #1, grid size 2048,2048,76, pixel 22.5, shown at step 1,
values int8
> volume #1 region all showOutlineBox true
> close
> open 7v99
Summary of feedback from opening 7v99 fetched from pdb
---
note | Fetching compressed mmCIF 7v99 from
http://files.rcsb.org/download/7v99.cif
7v99 title:
catalytic core of human telomerase holoenzyme [more info...]
Chain information for 7v99 #1
---
Chain | Description | UniProt
A | Telomerase reverse transcriptase | TERT_HUMAN 1-1132
K | Histone H2A type 1-B/E | H2A1B_HUMAN 1-129
L | Histone H2B type 1-K | H2B1K_HUMAN 1-125
R | Telomerase RNA component |
S | Primer DNA |
> color bychain
> set bgColor white
> set bgColor #ffffff00
> lighting simple
> lighting full
> hide atoms
> show cartoons
> show atoms
> show surfaces
> nucleotides ladder
> graphics silhouettes true
> volume hide
No volumes specified
> select /R:33-334
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> hide surfaces sel
Expected ',' or a keyword
> hide sel surfaces
> color sel orange
> hide /a
> hide /a atoms
> hide /a surfaces
> hide /a ribbons
> hide /s
> hide /s all
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /s models
[Repeated 1 time(s)]
> show /s models
> show /s atoms
> hide /s atoms
> hide /s surfaces
> hide /s ribbons
> sym #1
7v99 mmCIF Assemblies
---
1| author_defined_assembly| 1 copy of chains A,K,L,R,S
> show /a surfaces
> color /r teal
> color /r orange
> color /k green
> color /l green
> color /k red
> hide sel atoms
> show sel atoms
> color sel bynucleotide
> nucleotides sel stubs
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel tube/slab shape muffler
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> nucleotides sel slab
> style nucleic & sel stick
Changed 5156 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 5156 atom styles
> nucleotides sel stubs
> nucleotides sel ladder
> color #1.4 #ff59f5ff
> hide /k atoms
> hide /l atoms
> color #1.5 #00d301ff
> color #1.5 #00da01ff
> save "/Users/matthewcomstock/OneDrive - Michigan State University/project
> analysis/230308 telomerase RNA structure/telomerase structures/7v99 chimera
> work.cxs"
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 1/R
> select sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> color sel red
> color sel orange
> save "/Users/matthewcomstock/OneDrive - Michigan State University/project
> analysis/230308 telomerase RNA structure/telomerase structures/7v99 chimera
> work.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Destroying pre-existing alignment with identifier 1/R
Alignment identifier is 1/R
> select /a
7898 atoms, 8092 bonds, 1 pseudobond, 991 residues, 2 models selected
> select /r
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> select /r sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> select sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> select /r
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> select /r :1:10
Nothing selected
> select /r:1:10
Nothing selected
> select /r:10
Nothing selected
> select /r:100
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /r:101
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /r:237
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> color sel green
> color /r:334 red
> save /Users/matthewcomstock/Desktop/image1.png supersample 3
> hide /r:start-236
> hide ribbons /r:start-236
Expected ',' or a keyword
> hide /r:start-236 ribbons
> hide /r:335-end atoms, ribbons
> show /r:335-end atoms, ribbons
> show /r:335-end atoms
> show /r:335-end
> hide /r:335-end
> show /r atoms, ribbons
> hide /r atoms, ribbons
> show /r atoms, ribbons
> hide sequence ggguug atoms, ribbon
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select /r sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> name trapping_TR sel
> name traptr sel
> color traptr red
> color traptr orange
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> name before_traptr sel
> hide before_traptr atoms, ribbons
> save /Users/matthewcomstock/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/matthewcomstock/Desktop/movie1.mp4
Movie saved to /Users/matthewcomstock/Desktop/movie1.mp4
> save "/Users/matthewcomstock/OneDrive - Michigan State University/project
> analysis/230308 telomerase RNA structure/telomerase structures/7v99 chimera
> work.cxs"
> cd "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures"
Current working directory is:
/Users/matthewcomstock/Library/CloudStorage/OneDrive-
MichiganStateUniversity/project analysis/230308 telomerase RNA
structure/telomerase structures
> select /a
7898 atoms, 8092 bonds, 1 pseudobond, 991 residues, 2 models selected
> transparency (#!1 & sel) 50
> show /s atoms, ribbons
> color /s red
> show before_traptr ribbons
> hide before_traptr ribbons
> ribbon before_traptr
> hide ribbons
> show ribbons
> hide /a ribbons
> hide before_traptr
> hide before_traptr ribbons
> before_traptr
Unknown command: before_traptr
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> hide sel
> hide sel ribbons
> hide sel ribbons, atoms
> show sel ribbons, atoms
> hide sel ribbons, atoms
> name before_traptr sel
> show before_traptr ribbons
> show before_traptr ribbons, atoms
> hide before_traptr ribbons, atoms
> show before_traptr ribbons
> show before_traptr ribbons transparency .5
Expected ',' or a keyword
> show before_traptr ribbon, transparency .5
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> transparancy before_traptr 0.5
Unknown command: transparancy before_traptr 0.5
> select before_traptr
5156 atoms, 3422 bonds, 104 pseudobonds, 243 residues, 3 models selected
> transparancy 0.5
Unknown command: transparancy 0.5
> transparency 0.5
> transparency 1
> transparency /a 50
> transparency /a 75
> transparency /a 25
> transparency /a 35
> transparency before_traptr 35
> surface before_traptr
> hide surfaces
> show /a surfaces
> show /k, /l surface
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show /k or /l surface
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show /k and /l surface
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show /l surfaces
> show /k surfaces
> hide before_traptr
> hide traptr
> hide traptr ribbons
> hide traptr ribbons, atoms
> show traptr ribbons, atoms
> /r
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
Unknown command: sequence /r
ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
> select sequence /r
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
Expected a keyword
> select /r sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> name traptr /r sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
"/r sequence
ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg":
contains extra trailing text
> name traptr sel
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> name before_traptr sel
> hide before_traptr
> hide before_traptr atoms, ribbons
> hide traptr atoms, ribbons
> lighting soft
> lighting simple
> lighting full
> lighting simple
> show /r:33:147
> show /r:33-147
> show /r:33-137
> show /r:33-147
> hide /r:33-147
> select /r:237-334
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> name traptr sel
> hide traptr
> hide traptr atoms, ribbons
> show traptr atoms, ribbons
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> select /r:163-192
643 atoms, 720 bonds, 30 residues, 1 model selected
> name beforetr1 sel
> show beforetr1 atoms, ribbons
> hide beforetr1 atoms, ribbons
> hide traptr atoms, ribbons
[Repeated 1 time(s)]
> hide traptr
> select /r:237-334
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> select /r:33-147
2426 atoms, 2702 bonds, 59 pseudobonds, 115 residues, 2 models selected
> show /r:33-147
> hide /r:33-147
> select /r:33-147
2426 atoms, 2702 bonds, 59 pseudobonds, 115 residues, 2 models selected
> name test1 sel
> show test1
> hide test1
> select test1
5156 atoms, 2702 bonds, 59 pseudobonds, 243 residues, 2 models selected
> select /r:33-147
2426 atoms, 2702 bonds, 59 pseudobonds, 115 residues, 2 models selected
> name beforetraptr1
"beforetraptr1" is not defined
> name beforetraptr1 sel
> show beforetraptr1
> hide beforetraptr1
> show beforetraptr1 atoms, ribbons
> hide beforetraptr1 atoms, ribbons
> show beforetraptr1 atoms, ribbons
> show beforetraptr1 atoms, ribbons, surfaces
> hide beforetraptr1 atoms, ribbons
> color beforetraptr1 teal
> hide beforetraptr1 surfaces
> show beforetraptr1 atoms, ribbons
> transparency beforetraptr1 50 target all
> transparency beforetraptr1 50 target All
Invalid "target" argument: Character 'A' is not an allowed target, must be one
of acrsbmpfl
> transparency beforetraptr1 50 target all
> transparency beforetraptr1 10 target all
> transparency beforetraptr1 100 target all
> color beforetraptr1 red
> color beforetraptr1 pink
> select /r:163-192
643 atoms, 720 bonds, 30 residues, 1 model selected
> select /r:163-192
643 atoms, 720 bonds, 30 residues, 1 model selected
> name beforetraptr2 sel
> show beforetraptr2 atoms, ribbons
> color beforetraptr2 pink
> save "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
——— End of log from Tue Jun 6 16:44:25 2023 ———
opened ChimeraX session
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> show traptr ribbons, atoms
> hide traptr ribbons, atoms
> show traptr ribbons, atoms
> color traptr red
> info chains
chain id /A chain_id A
chain id /K chain_id K
chain id /L chain_id L
chain id /R chain_id R
chain id /S chain_id S
> info models
model id #1 type AtomicStructure name 7v99
model id #1.1 type PseudobondGroup name "hydrogen bonds"
model id #1.2 type PseudobondGroup name "missing structure"
model id #1.3 type MolecularSurface name "7v99_A SES surface"
model id #1.4 type MolecularSurface name "7v99_K SES surface"
model id #1.5 type MolecularSurface name "7v99_L SES surface"
model id #1.6 type MolecularSurface name "7v99_R SES surface"
model id #1.7 type MolecularSurface name "7v99_S SES surface"
> info selection
atom id /R:163@P idatm_type Pac
atom id /R:163@OP1 idatm_type O3-
atom id /R:163@OP2 idatm_type O3-
atom id /R:163@O5' idatm_type O3
atom id /R:163@C5' idatm_type C3
atom id /R:163@C4' idatm_type C3
atom id /R:163@O4' idatm_type O3
atom id /R:163@C3' idatm_type C3
atom id /R:163@O3' idatm_type O3
atom id /R:163@C2' idatm_type C3
atom id /R:163@O2' idatm_type O3
atom id /R:163@C1' idatm_type C3
atom id /R:163@N9 idatm_type Npl
atom id /R:163@C8 idatm_type Car
atom id /R:163@N7 idatm_type N2
atom id /R:163@C5 idatm_type Car
atom id /R:163@C6 idatm_type C2
atom id /R:163@O6 idatm_type O2
atom id /R:163@N1 idatm_type Npl
atom id /R:163@C2 idatm_type C2
atom id /R:163@N2 idatm_type Npl
atom id /R:163@N3 idatm_type N2
atom id /R:163@C4 idatm_type Car
atom id /R:164@P idatm_type Pac
atom id /R:164@OP1 idatm_type O3-
atom id /R:164@OP2 idatm_type O3-
atom id /R:164@O5' idatm_type O3
atom id /R:164@C5' idatm_type C3
atom id /R:164@C4' idatm_type C3
atom id /R:164@O4' idatm_type O3
atom id /R:164@C3' idatm_type C3
atom id /R:164@O3' idatm_type O3
atom id /R:164@C2' idatm_type C3
atom id /R:164@O2' idatm_type O3
atom id /R:164@C1' idatm_type C3
atom id /R:164@N9 idatm_type Npl
atom id /R:164@C8 idatm_type Car
atom id /R:164@N7 idatm_type N2
atom id /R:164@C5 idatm_type Car
atom id /R:164@C6 idatm_type Car
atom id /R:164@N6 idatm_type Npl
atom id /R:164@N1 idatm_type N2
atom id /R:164@C2 idatm_type Car
atom id /R:164@N3 idatm_type N2
atom id /R:164@C4 idatm_type Car
atom id /R:165@P idatm_type Pac
atom id /R:165@OP1 idatm_type O3-
atom id /R:165@OP2 idatm_type O3-
atom id /R:165@O5' idatm_type O3
atom id /R:165@C5' idatm_type C3
atom id /R:165@C4' idatm_type C3
atom id /R:165@O4' idatm_type O3
atom id /R:165@C3' idatm_type C3
atom id /R:165@O3' idatm_type O3
atom id /R:165@C2' idatm_type C3
atom id /R:165@O2' idatm_type O3
atom id /R:165@C1' idatm_type C3
atom id /R:165@N9 idatm_type Npl
atom id /R:165@C8 idatm_type Car
atom id /R:165@N7 idatm_type N2
atom id /R:165@C5 idatm_type Car
atom id /R:165@C6 idatm_type C2
atom id /R:165@O6 idatm_type O2
atom id /R:165@N1 idatm_type Npl
atom id /R:165@C2 idatm_type C2
atom id /R:165@N2 idatm_type Npl
atom id /R:165@N3 idatm_type N2
atom id /R:165@C4 idatm_type Car
atom id /R:166@P idatm_type Pac
atom id /R:166@OP1 idatm_type O3-
atom id /R:166@OP2 idatm_type O3-
atom id /R:166@O5' idatm_type O3
atom id /R:166@C5' idatm_type C3
atom id /R:166@C4' idatm_type C3
atom id /R:166@O4' idatm_type O3
atom id /R:166@C3' idatm_type C3
atom id /R:166@O3' idatm_type O3
atom id /R:166@C2' idatm_type C3
atom id /R:166@O2' idatm_type O3
atom id /R:166@C1' idatm_type C3
atom id /R:166@N1 idatm_type Npl
atom id /R:166@C2 idatm_type C2
atom id /R:166@O2 idatm_type O2
atom id /R:166@N3 idatm_type N2
atom id /R:166@C4 idatm_type C2
atom id /R:166@N4 idatm_type Npl
atom id /R:166@C5 idatm_type C2
atom id /R:166@C6 idatm_type C2
atom id /R:167@P idatm_type Pac
atom id /R:167@OP1 idatm_type O3-
atom id /R:167@OP2 idatm_type O3-
atom id /R:167@O5' idatm_type O3
atom id /R:167@C5' idatm_type C3
atom id /R:167@C4' idatm_type C3
atom id /R:167@O4' idatm_type O3
atom id /R:167@C3' idatm_type C3
atom id /R:167@O3' idatm_type O3
atom id /R:167@C2' idatm_type C3
atom id /R:167@O2' idatm_type O3
atom id /R:167@C1' idatm_type C3
atom id /R:167@N9 idatm_type Npl
atom id /R:167@C8 idatm_type Car
atom id /R:167@N7 idatm_type N2
atom id /R:167@C5 idatm_type Car
atom id /R:167@C6 idatm_type Car
atom id /R:167@N6 idatm_type Npl
atom id /R:167@N1 idatm_type N2
atom id /R:167@C2 idatm_type Car
atom id /R:167@N3 idatm_type N2
atom id /R:167@C4 idatm_type Car
atom id /R:168@P idatm_type Pac
atom id /R:168@OP1 idatm_type O3-
atom id /R:168@OP2 idatm_type O3-
atom id /R:168@O5' idatm_type O3
atom id /R:168@C5' idatm_type C3
atom id /R:168@C4' idatm_type C3
atom id /R:168@O4' idatm_type O3
atom id /R:168@C3' idatm_type C3
atom id /R:168@O3' idatm_type O3
atom id /R:168@C2' idatm_type C3
atom id /R:168@O2' idatm_type O3
atom id /R:168@C1' idatm_type C3
atom id /R:168@N9 idatm_type Npl
atom id /R:168@C8 idatm_type Car
atom id /R:168@N7 idatm_type N2
atom id /R:168@C5 idatm_type Car
atom id /R:168@C6 idatm_type Car
atom id /R:168@N6 idatm_type Npl
atom id /R:168@N1 idatm_type N2
atom id /R:168@C2 idatm_type Car
atom id /R:168@N3 idatm_type N2
atom id /R:168@C4 idatm_type Car
atom id /R:169@P idatm_type Pac
atom id /R:169@OP1 idatm_type O3-
atom id /R:169@OP2 idatm_type O3-
atom id /R:169@O5' idatm_type O3
atom id /R:169@C5' idatm_type C3
atom id /R:169@C4' idatm_type C3
atom id /R:169@O4' idatm_type O3
atom id /R:169@C3' idatm_type C3
atom id /R:169@O3' idatm_type O3
atom id /R:169@C2' idatm_type C3
atom id /R:169@O2' idatm_type O3
atom id /R:169@C1' idatm_type C3
atom id /R:169@N9 idatm_type Npl
atom id /R:169@C8 idatm_type Car
atom id /R:169@N7 idatm_type N2
atom id /R:169@C5 idatm_type Car
atom id /R:169@C6 idatm_type Car
atom id /R:169@N6 idatm_type Npl
atom id /R:169@N1 idatm_type N2
atom id /R:169@C2 idatm_type Car
atom id /R:169@N3 idatm_type N2
atom id /R:169@C4 idatm_type Car
atom id /R:170@P idatm_type Pac
atom id /R:170@OP1 idatm_type O3-
atom id /R:170@OP2 idatm_type O3-
atom id /R:170@O5' idatm_type O3
atom id /R:170@C5' idatm_type C3
atom id /R:170@C4' idatm_type C3
atom id /R:170@O4' idatm_type O3
atom id /R:170@C3' idatm_type C3
atom id /R:170@O3' idatm_type O3
atom id /R:170@C2' idatm_type C3
atom id /R:170@O2' idatm_type O3
atom id /R:170@C1' idatm_type C3
atom id /R:170@N1 idatm_type Npl
atom id /R:170@C2 idatm_type C2
atom id /R:170@O2 idatm_type O2
atom id /R:170@N3 idatm_type N2
atom id /R:170@C4 idatm_type C2
atom id /R:170@N4 idatm_type Npl
atom id /R:170@C5 idatm_type C2
atom id /R:170@C6 idatm_type C2
atom id /R:171@P idatm_type Pac
atom id /R:171@OP1 idatm_type O3-
atom id /R:171@OP2 idatm_type O3-
atom id /R:171@O5' idatm_type O3
atom id /R:171@C5' idatm_type C3
atom id /R:171@C4' idatm_type C3
atom id /R:171@O4' idatm_type O3
atom id /R:171@C3' idatm_type C3
atom id /R:171@O3' idatm_type O3
atom id /R:171@C2' idatm_type C3
atom id /R:171@O2' idatm_type O3
atom id /R:171@C1' idatm_type C3
atom id /R:171@N9 idatm_type Npl
atom id /R:171@C8 idatm_type Car
atom id /R:171@N7 idatm_type N2
atom id /R:171@C5 idatm_type Car
atom id /R:171@C6 idatm_type Car
atom id /R:171@N6 idatm_type Npl
atom id /R:171@N1 idatm_type N2
atom id /R:171@C2 idatm_type Car
atom id /R:171@N3 idatm_type N2
atom id /R:171@C4 idatm_type Car
atom id /R:172@P idatm_type Pac
atom id /R:172@OP1 idatm_type O3-
atom id /R:172@OP2 idatm_type O3-
atom id /R:172@O5' idatm_type O3
atom id /R:172@C5' idatm_type C3
atom id /R:172@C4' idatm_type C3
atom id /R:172@O4' idatm_type O3
atom id /R:172@C3' idatm_type C3
atom id /R:172@O3' idatm_type O3
atom id /R:172@C2' idatm_type C3
atom id /R:172@O2' idatm_type O3
atom id /R:172@C1' idatm_type C3
atom id /R:172@N9 idatm_type Npl
atom id /R:172@C8 idatm_type Car
atom id /R:172@N7 idatm_type N2
atom id /R:172@C5 idatm_type Car
atom id /R:172@C6 idatm_type Car
atom id /R:172@N6 idatm_type Npl
atom id /R:172@N1 idatm_type N2
atom id /R:172@C2 idatm_type Car
atom id /R:172@N3 idatm_type N2
atom id /R:172@C4 idatm_type Car
atom id /R:173@P idatm_type Pac
atom id /R:173@OP1 idatm_type O3-
atom id /R:173@OP2 idatm_type O3-
atom id /R:173@O5' idatm_type O3
atom id /R:173@C5' idatm_type C3
atom id /R:173@C4' idatm_type C3
atom id /R:173@O4' idatm_type O3
atom id /R:173@C3' idatm_type C3
atom id /R:173@O3' idatm_type O3
atom id /R:173@C2' idatm_type C3
atom id /R:173@O2' idatm_type O3
atom id /R:173@C1' idatm_type C3
atom id /R:173@N9 idatm_type Npl
atom id /R:173@C8 idatm_type Car
atom id /R:173@N7 idatm_type N2
atom id /R:173@C5 idatm_type Car
atom id /R:173@C6 idatm_type Car
atom id /R:173@N6 idatm_type Npl
atom id /R:173@N1 idatm_type N2
atom id /R:173@C2 idatm_type Car
atom id /R:173@N3 idatm_type N2
atom id /R:173@C4 idatm_type Car
atom id /R:174@P idatm_type Pac
atom id /R:174@OP1 idatm_type O3-
atom id /R:174@OP2 idatm_type O3-
atom id /R:174@O5' idatm_type O3
atom id /R:174@C5' idatm_type C3
atom id /R:174@C4' idatm_type C3
atom id /R:174@O4' idatm_type O3
atom id /R:174@C3' idatm_type C3
atom id /R:174@O3' idatm_type O3
atom id /R:174@C2' idatm_type C3
atom id /R:174@O2' idatm_type O3
atom id /R:174@C1' idatm_type C3
atom id /R:174@N9 idatm_type Npl
atom id /R:174@C8 idatm_type Car
atom id /R:174@N7 idatm_type N2
atom id /R:174@C5 idatm_type Car
atom id /R:174@C6 idatm_type Car
atom id /R:174@N6 idatm_type Npl
atom id /R:174@N1 idatm_type N2
atom id /R:174@C2 idatm_type Car
atom id /R:174@N3 idatm_type N2
atom id /R:174@C4 idatm_type Car
atom id /R:175@P idatm_type Pac
atom id /R:175@OP1 idatm_type O3-
atom id /R:175@OP2 idatm_type O3-
atom id /R:175@O5' idatm_type O3
atom id /R:175@C5' idatm_type C3
atom id /R:175@C4' idatm_type C3
atom id /R:175@O4' idatm_type O3
atom id /R:175@C3' idatm_type C3
atom id /R:175@O3' idatm_type O3
atom id /R:175@C2' idatm_type C3
atom id /R:175@O2' idatm_type O3
atom id /R:175@C1' idatm_type C3
atom id /R:175@N9 idatm_type Npl
atom id /R:175@C8 idatm_type Car
atom id /R:175@N7 idatm_type N2
atom id /R:175@C5 idatm_type Car
atom id /R:175@C6 idatm_type Car
atom id /R:175@N6 idatm_type Npl
atom id /R:175@N1 idatm_type N2
atom id /R:175@C2 idatm_type Car
atom id /R:175@N3 idatm_type N2
atom id /R:175@C4 idatm_type Car
atom id /R:176@P idatm_type Pac
atom id /R:176@OP1 idatm_type O3-
atom id /R:176@OP2 idatm_type O3-
atom id /R:176@O5' idatm_type O3
atom id /R:176@C5' idatm_type C3
atom id /R:176@C4' idatm_type C3
atom id /R:176@O4' idatm_type O3
atom id /R:176@C3' idatm_type C3
atom id /R:176@O3' idatm_type O3
atom id /R:176@C2' idatm_type C3
atom id /R:176@O2' idatm_type O3
atom id /R:176@C1' idatm_type C3
atom id /R:176@N9 idatm_type Npl
atom id /R:176@C8 idatm_type Car
atom id /R:176@N7 idatm_type N2
atom id /R:176@C5 idatm_type Car
atom id /R:176@C6 idatm_type Car
atom id /R:176@N6 idatm_type Npl
atom id /R:176@N1 idatm_type N2
atom id /R:176@C2 idatm_type Car
atom id /R:176@N3 idatm_type N2
atom id /R:176@C4 idatm_type Car
atom id /R:177@P idatm_type Pac
atom id /R:177@OP1 idatm_type O3-
atom id /R:177@OP2 idatm_type O3-
atom id /R:177@O5' idatm_type O3
atom id /R:177@C5' idatm_type C3
atom id /R:177@C4' idatm_type C3
atom id /R:177@O4' idatm_type O3
atom id /R:177@C3' idatm_type C3
atom id /R:177@O3' idatm_type O3
atom id /R:177@C2' idatm_type C3
atom id /R:177@O2' idatm_type O3
atom id /R:177@C1' idatm_type C3
atom id /R:177@N1 idatm_type Npl
atom id /R:177@C2 idatm_type C2
atom id /R:177@O2 idatm_type O2
atom id /R:177@N3 idatm_type Npl
atom id /R:177@C4 idatm_type C2
atom id /R:177@O4 idatm_type O2
atom id /R:177@C5 idatm_type C2
atom id /R:177@C6 idatm_type C2
atom id /R:178@P idatm_type Pac
atom id /R:178@OP1 idatm_type O3-
atom id /R:178@OP2 idatm_type O3-
atom id /R:178@O5' idatm_type O3
atom id /R:178@C5' idatm_type C3
atom id /R:178@C4' idatm_type C3
atom id /R:178@O4' idatm_type O3
atom id /R:178@C3' idatm_type C3
atom id /R:178@O3' idatm_type O3
atom id /R:178@C2' idatm_type C3
atom id /R:178@O2' idatm_type O3
atom id /R:178@C1' idatm_type C3
atom id /R:178@N9 idatm_type Npl
atom id /R:178@C8 idatm_type Car
atom id /R:178@N7 idatm_type N2
atom id /R:178@C5 idatm_type Car
atom id /R:178@C6 idatm_type C2
atom id /R:178@O6 idatm_type O2
atom id /R:178@N1 idatm_type Npl
atom id /R:178@C2 idatm_type C2
atom id /R:178@N2 idatm_type Npl
atom id /R:178@N3 idatm_type N2
atom id /R:178@C4 idatm_type Car
atom id /R:179@P idatm_type Pac
atom id /R:179@OP1 idatm_type O3-
atom id /R:179@OP2 idatm_type O3-
atom id /R:179@O5' idatm_type O3
atom id /R:179@C5' idatm_type C3
atom id /R:179@C4' idatm_type C3
atom id /R:179@O4' idatm_type O3
atom id /R:179@C3' idatm_type C3
atom id /R:179@O3' idatm_type O3
atom id /R:179@C2' idatm_type C3
atom id /R:179@O2' idatm_type O3
atom id /R:179@C1' idatm_type C3
atom id /R:179@N1 idatm_type Npl
atom id /R:179@C2 idatm_type C2
atom id /R:179@O2 idatm_type O2
atom id /R:179@N3 idatm_type Npl
atom id /R:179@C4 idatm_type C2
atom id /R:179@O4 idatm_type O2
atom id /R:179@C5 idatm_type C2
atom id /R:179@C6 idatm_type C2
atom id /R:180@P idatm_type Pac
atom id /R:180@OP1 idatm_type O3-
atom id /R:180@OP2 idatm_type O3-
atom id /R:180@O5' idatm_type O3
atom id /R:180@C5' idatm_type C3
atom id /R:180@C4' idatm_type C3
atom id /R:180@O4' idatm_type O3
atom id /R:180@C3' idatm_type C3
atom id /R:180@O3' idatm_type O3
atom id /R:180@C2' idatm_type C3
atom id /R:180@O2' idatm_type O3
atom id /R:180@C1' idatm_type C3
atom id /R:180@N1 idatm_type Npl
atom id /R:180@C2 idatm_type C2
atom id /R:180@O2 idatm_type O2
atom id /R:180@N3 idatm_type N2
atom id /R:180@C4 idatm_type C2
atom id /R:180@N4 idatm_type Npl
atom id /R:180@C5 idatm_type C2
atom id /R:180@C6 idatm_type C2
atom id /R:181@P idatm_type Pac
atom id /R:181@OP1 idatm_type O3-
atom id /R:181@OP2 idatm_type O3-
atom id /R:181@O5' idatm_type O3
atom id /R:181@C5' idatm_type C3
atom id /R:181@C4' idatm_type C3
atom id /R:181@O4' idatm_type O3
atom id /R:181@C3' idatm_type C3
atom id /R:181@O3' idatm_type O3
atom id /R:181@C2' idatm_type C3
atom id /R:181@O2' idatm_type O3
atom id /R:181@C1' idatm_type C3
atom id /R:181@N9 idatm_type Npl
atom id /R:181@C8 idatm_type Car
atom id /R:181@N7 idatm_type N2
atom id /R:181@C5 idatm_type Car
atom id /R:181@C6 idatm_type Car
atom id /R:181@N6 idatm_type Npl
atom id /R:181@N1 idatm_type N2
atom id /R:181@C2 idatm_type Car
atom id /R:181@N3 idatm_type N2
atom id /R:181@C4 idatm_type Car
atom id /R:182@P idatm_type Pac
atom id /R:182@OP1 idatm_type O3-
atom id /R:182@OP2 idatm_type O3-
atom id /R:182@O5' idatm_type O3
atom id /R:182@C5' idatm_type C3
atom id /R:182@C4' idatm_type C3
atom id /R:182@O4' idatm_type O3
atom id /R:182@C3' idatm_type C3
atom id /R:182@O3' idatm_type O3
atom id /R:182@C2' idatm_type C3
atom id /R:182@O2' idatm_type O3
atom id /R:182@C1' idatm_type C3
atom id /R:182@N9 idatm_type Npl
atom id /R:182@C8 idatm_type Car
atom id /R:182@N7 idatm_type N2
atom id /R:182@C5 idatm_type Car
atom id /R:182@C6 idatm_type C2
atom id /R:182@O6 idatm_type O2
atom id /R:182@N1 idatm_type Npl
atom id /R:182@C2 idatm_type C2
atom id /R:182@N2 idatm_type Npl
atom id /R:182@N3 idatm_type N2
atom id /R:182@C4 idatm_type Car
atom id /R:183@P idatm_type Pac
atom id /R:183@OP1 idatm_type O3-
atom id /R:183@OP2 idatm_type O3-
atom id /R:183@O5' idatm_type O3
atom id /R:183@C5' idatm_type C3
atom id /R:183@C4' idatm_type C3
atom id /R:183@O4' idatm_type O3
atom id /R:183@C3' idatm_type C3
atom id /R:183@O3' idatm_type O3
atom id /R:183@C2' idatm_type C3
atom id /R:183@O2' idatm_type O3
atom id /R:183@C1' idatm_type C3
atom id /R:183@N1 idatm_type Npl
atom id /R:183@C2 idatm_type C2
atom id /R:183@O2 idatm_type O2
atom id /R:183@N3 idatm_type N2
atom id /R:183@C4 idatm_type C2
atom id /R:183@N4 idatm_type Npl
atom id /R:183@C5 idatm_type C2
atom id /R:183@C6 idatm_type C2
atom id /R:184@P idatm_type Pac
atom id /R:184@OP1 idatm_type O3-
atom id /R:184@OP2 idatm_type O3-
atom id /R:184@O5' idatm_type O3
atom id /R:184@C5' idatm_type C3
atom id /R:184@C4' idatm_type C3
atom id /R:184@O4' idatm_type O3
atom id /R:184@C3' idatm_type C3
atom id /R:184@O3' idatm_type O3
atom id /R:184@C2' idatm_type C3
atom id /R:184@O2' idatm_type O3
atom id /R:184@C1' idatm_type C3
atom id /R:184@N1 idatm_type Npl
atom id /R:184@C2 idatm_type C2
atom id /R:184@O2 idatm_type O2
atom id /R:184@N3 idatm_type Npl
atom id /R:184@C4 idatm_type C2
atom id /R:184@O4 idatm_type O2
atom id /R:184@C5 idatm_type C2
atom id /R:184@C6 idatm_type C2
atom id /R:185@P idatm_type Pac
atom id /R:185@OP1 idatm_type O3-
atom id /R:185@OP2 idatm_type O3-
atom id /R:185@O5' idatm_type O3
atom id /R:185@C5' idatm_type C3
atom id /R:185@C4' idatm_type C3
atom id /R:185@O4' idatm_type O3
atom id /R:185@C3' idatm_type C3
atom id /R:185@O3' idatm_type O3
atom id /R:185@C2' idatm_type C3
atom id /R:185@O2' idatm_type O3
atom id /R:185@C1' idatm_type C3
atom id /R:185@N9 idatm_type Npl
atom id /R:185@C8 idatm_type Car
atom id /R:185@N7 idatm_type N2
atom id /R:185@C5 idatm_type Car
atom id /R:185@C6 idatm_type C2
atom id /R:185@O6 idatm_type O2
atom id /R:185@N1 idatm_type Npl
atom id /R:185@C2 idatm_type C2
atom id /R:185@N2 idatm_type Npl
atom id /R:185@N3 idatm_type N2
atom id /R:185@C4 idatm_type Car
atom id /R:186@P idatm_type Pac
atom id /R:186@OP1 idatm_type O3-
atom id /R:186@OP2 idatm_type O3-
atom id /R:186@O5' idatm_type O3
atom id /R:186@C5' idatm_type C3
atom id /R:186@C4' idatm_type C3
atom id /R:186@O4' idatm_type O3
atom id /R:186@C3' idatm_type C3
atom id /R:186@O3' idatm_type O3
atom id /R:186@C2' idatm_type C3
atom id /R:186@O2' idatm_type O3
atom id /R:186@C1' idatm_type C3
atom id /R:186@N1 idatm_type Npl
atom id /R:186@C2 idatm_type C2
atom id /R:186@O2 idatm_type O2
atom id /R:186@N3 idatm_type N2
atom id /R:186@C4 idatm_type C2
atom id /R:186@N4 idatm_type Npl
atom id /R:186@C5 idatm_type C2
atom id /R:186@C6 idatm_type C2
atom id /R:187@P idatm_type Pac
atom id /R:187@OP1 idatm_type O3-
atom id /R:187@OP2 idatm_type O3-
atom id /R:187@O5' idatm_type O3
atom id /R:187@C5' idatm_type C3
atom id /R:187@C4' idatm_type C3
atom id /R:187@O4' idatm_type O3
atom id /R:187@C3' idatm_type C3
atom id /R:187@O3' idatm_type O3
atom id /R:187@C2' idatm_type C3
atom id /R:187@O2' idatm_type O3
atom id /R:187@C1' idatm_type C3
atom id /R:187@N1 idatm_type Npl
atom id /R:187@C2 idatm_type C2
atom id /R:187@O2 idatm_type O2
atom id /R:187@N3 idatm_type Npl
atom id /R:187@C4 idatm_type C2
atom id /R:187@O4 idatm_type O2
atom id /R:187@C5 idatm_type C2
atom id /R:187@C6 idatm_type C2
atom id /R:188@P idatm_type Pac
atom id /R:188@OP1 idatm_type O3-
atom id /R:188@OP2 idatm_type O3-
atom id /R:188@O5' idatm_type O3
atom id /R:188@C5' idatm_type C3
atom id /R:188@C4' idatm_type C3
atom id /R:188@O4' idatm_type O3
atom id /R:188@C3' idatm_type C3
atom id /R:188@O3' idatm_type O3
atom id /R:188@C2' idatm_type C3
atom id /R:188@O2' idatm_type O3
atom id /R:188@C1' idatm_type C3
atom id /R:188@N9 idatm_type Npl
atom id /R:188@C8 idatm_type Car
atom id /R:188@N7 idatm_type N2
atom id /R:188@C5 idatm_type Car
atom id /R:188@C6 idatm_type C2
atom id /R:188@O6 idatm_type O2
atom id /R:188@N1 idatm_type Npl
atom id /R:188@C2 idatm_type C2
atom id /R:188@N2 idatm_type Npl
atom id /R:188@N3 idatm_type N2
atom id /R:188@C4 idatm_type Car
atom id /R:189@P idatm_type Pac
atom id /R:189@OP1 idatm_type O3-
atom id /R:189@OP2 idatm_type O3-
atom id /R:189@O5' idatm_type O3
atom id /R:189@C5' idatm_type C3
atom id /R:189@C4' idatm_type C3
atom id /R:189@O4' idatm_type O3
atom id /R:189@C3' idatm_type C3
atom id /R:189@O3' idatm_type O3
atom id /R:189@C2' idatm_type C3
atom id /R:189@O2' idatm_type O3
atom id /R:189@C1' idatm_type C3
atom id /R:189@N9 idatm_type Npl
atom id /R:189@C8 idatm_type Car
atom id /R:189@N7 idatm_type N2
atom id /R:189@C5 idatm_type Car
atom id /R:189@C6 idatm_type C2
atom id /R:189@O6 idatm_type O2
atom id /R:189@N1 idatm_type Npl
atom id /R:189@C2 idatm_type C2
atom id /R:189@N2 idatm_type Npl
atom id /R:189@N3 idatm_type N2
atom id /R:189@C4 idatm_type Car
atom id /R:190@P idatm_type Pac
atom id /R:190@OP1 idatm_type O3-
atom id /R:190@OP2 idatm_type O3-
atom id /R:190@O5' idatm_type O3
atom id /R:190@C5' idatm_type C3
atom id /R:190@C4' idatm_type C3
atom id /R:190@O4' idatm_type O3
atom id /R:190@C3' idatm_type C3
atom id /R:190@O3' idatm_type O3
atom id /R:190@C2' idatm_type C3
atom id /R:190@O2' idatm_type O3
atom id /R:190@C1' idatm_type C3
atom id /R:190@N1 idatm_type Npl
atom id /R:190@C2 idatm_type C2
atom id /R:190@O2 idatm_type O2
atom id /R:190@N3 idatm_type N2
atom id /R:190@C4 idatm_type C2
atom id /R:190@N4 idatm_type Npl
atom id /R:190@C5 idatm_type C2
atom id /R:190@C6 idatm_type C2
atom id /R:191@P idatm_type Pac
atom id /R:191@OP1 idatm_type O3-
atom id /R:191@OP2 idatm_type O3-
atom id /R:191@O5' idatm_type O3
atom id /R:191@C5' idatm_type C3
atom id /R:191@C4' idatm_type C3
atom id /R:191@O4' idatm_type O3
atom id /R:191@C3' idatm_type C3
atom id /R:191@O3' idatm_type O3
atom id /R:191@C2' idatm_type C3
atom id /R:191@O2' idatm_type O3
atom id /R:191@C1' idatm_type C3
atom id /R:191@N1 idatm_type Npl
atom id /R:191@C2 idatm_type C2
atom id /R:191@O2 idatm_type O2
atom id /R:191@N3 idatm_type N2
atom id /R:191@C4 idatm_type C2
atom id /R:191@N4 idatm_type Npl
atom id /R:191@C5 idatm_type C2
atom id /R:191@C6 idatm_type C2
atom id /R:192@P idatm_type Pac
atom id /R:192@OP1 idatm_type O3-
atom id /R:192@OP2 idatm_type O3-
atom id /R:192@O5' idatm_type O3
atom id /R:192@C5' idatm_type C3
atom id /R:192@C4' idatm_type C3
atom id /R:192@O4' idatm_type O3
atom id /R:192@C3' idatm_type C3
atom id /R:192@O3' idatm_type O3
atom id /R:192@C2' idatm_type C3
atom id /R:192@O2' idatm_type O3
atom id /R:192@C1' idatm_type C3
atom id /R:192@N1 idatm_type Npl
atom id /R:192@C2 idatm_type C2
atom id /R:192@O2 idatm_type O2
atom id /R:192@N3 idatm_type N2
atom id /R:192@C4 idatm_type C2
atom id /R:192@N4 idatm_type Npl
atom id /R:192@C5 idatm_type C2
atom id /R:192@C6 idatm_type C2
> info selection
atom id /R:163@P idatm_type Pac
atom id /R:163@OP1 idatm_type O3-
atom id /R:163@OP2 idatm_type O3-
atom id /R:163@O5' idatm_type O3
atom id /R:163@C5' idatm_type C3
atom id /R:163@C4' idatm_type C3
atom id /R:163@O4' idatm_type O3
atom id /R:163@C3' idatm_type C3
atom id /R:163@O3' idatm_type O3
atom id /R:163@C2' idatm_type C3
atom id /R:163@O2' idatm_type O3
atom id /R:163@C1' idatm_type C3
atom id /R:163@N9 idatm_type Npl
atom id /R:163@C8 idatm_type Car
atom id /R:163@N7 idatm_type N2
atom id /R:163@C5 idatm_type Car
atom id /R:163@C6 idatm_type C2
atom id /R:163@O6 idatm_type O2
atom id /R:163@N1 idatm_type Npl
atom id /R:163@C2 idatm_type C2
atom id /R:163@N2 idatm_type Npl
atom id /R:163@N3 idatm_type N2
atom id /R:163@C4 idatm_type Car
atom id /R:164@P idatm_type Pac
atom id /R:164@OP1 idatm_type O3-
atom id /R:164@OP2 idatm_type O3-
atom id /R:164@O5' idatm_type O3
atom id /R:164@C5' idatm_type C3
atom id /R:164@C4' idatm_type C3
atom id /R:164@O4' idatm_type O3
atom id /R:164@C3' idatm_type C3
atom id /R:164@O3' idatm_type O3
atom id /R:164@C2' idatm_type C3
atom id /R:164@O2' idatm_type O3
atom id /R:164@C1' idatm_type C3
atom id /R:164@N9 idatm_type Npl
atom id /R:164@C8 idatm_type Car
atom id /R:164@N7 idatm_type N2
atom id /R:164@C5 idatm_type Car
atom id /R:164@C6 idatm_type Car
atom id /R:164@N6 idatm_type Npl
atom id /R:164@N1 idatm_type N2
atom id /R:164@C2 idatm_type Car
atom id /R:164@N3 idatm_type N2
atom id /R:164@C4 idatm_type Car
atom id /R:165@P idatm_type Pac
atom id /R:165@OP1 idatm_type O3-
atom id /R:165@OP2 idatm_type O3-
atom id /R:165@O5' idatm_type O3
atom id /R:165@C5' idatm_type C3
atom id /R:165@C4' idatm_type C3
atom id /R:165@O4' idatm_type O3
atom id /R:165@C3' idatm_type C3
atom id /R:165@O3' idatm_type O3
atom id /R:165@C2' idatm_type C3
atom id /R:165@O2' idatm_type O3
atom id /R:165@C1' idatm_type C3
atom id /R:165@N9 idatm_type Npl
atom id /R:165@C8 idatm_type Car
atom id /R:165@N7 idatm_type N2
atom id /R:165@C5 idatm_type Car
atom id /R:165@C6 idatm_type C2
atom id /R:165@O6 idatm_type O2
atom id /R:165@N1 idatm_type Npl
atom id /R:165@C2 idatm_type C2
atom id /R:165@N2 idatm_type Npl
atom id /R:165@N3 idatm_type N2
atom id /R:165@C4 idatm_type Car
atom id /R:166@P idatm_type Pac
atom id /R:166@OP1 idatm_type O3-
atom id /R:166@OP2 idatm_type O3-
atom id /R:166@O5' idatm_type O3
atom id /R:166@C5' idatm_type C3
atom id /R:166@C4' idatm_type C3
atom id /R:166@O4' idatm_type O3
atom id /R:166@C3' idatm_type C3
atom id /R:166@O3' idatm_type O3
atom id /R:166@C2' idatm_type C3
atom id /R:166@O2' idatm_type O3
atom id /R:166@C1' idatm_type C3
atom id /R:166@N1 idatm_type Npl
atom id /R:166@C2 idatm_type C2
atom id /R:166@O2 idatm_type O2
atom id /R:166@N3 idatm_type N2
atom id /R:166@C4 idatm_type C2
atom id /R:166@N4 idatm_type Npl
atom id /R:166@C5 idatm_type C2
atom id /R:166@C6 idatm_type C2
atom id /R:167@P idatm_type Pac
atom id /R:167@OP1 idatm_type O3-
atom id /R:167@OP2 idatm_type O3-
atom id /R:167@O5' idatm_type O3
atom id /R:167@C5' idatm_type C3
atom id /R:167@C4' idatm_type C3
atom id /R:167@O4' idatm_type O3
atom id /R:167@C3' idatm_type C3
atom id /R:167@O3' idatm_type O3
atom id /R:167@C2' idatm_type C3
atom id /R:167@O2' idatm_type O3
atom id /R:167@C1' idatm_type C3
atom id /R:167@N9 idatm_type Npl
atom id /R:167@C8 idatm_type Car
atom id /R:167@N7 idatm_type N2
atom id /R:167@C5 idatm_type Car
atom id /R:167@C6 idatm_type Car
atom id /R:167@N6 idatm_type Npl
atom id /R:167@N1 idatm_type N2
atom id /R:167@C2 idatm_type Car
atom id /R:167@N3 idatm_type N2
atom id /R:167@C4 idatm_type Car
atom id /R:168@P idatm_type Pac
atom id /R:168@OP1 idatm_type O3-
atom id /R:168@OP2 idatm_type O3-
atom id /R:168@O5' idatm_type O3
atom id /R:168@C5' idatm_type C3
atom id /R:168@C4' idatm_type C3
atom id /R:168@O4' idatm_type O3
atom id /R:168@C3' idatm_type C3
atom id /R:168@O3' idatm_type O3
atom id /R:168@C2' idatm_type C3
atom id /R:168@O2' idatm_type O3
atom id /R:168@C1' idatm_type C3
atom id /R:168@N9 idatm_type Npl
atom id /R:168@C8 idatm_type Car
atom id /R:168@N7 idatm_type N2
atom id /R:168@C5 idatm_type Car
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atom id /R:189@O2' idatm_type O3
atom id /R:189@C1' idatm_type C3
atom id /R:189@N9 idatm_type Npl
atom id /R:189@C8 idatm_type Car
atom id /R:189@N7 idatm_type N2
atom id /R:189@C5 idatm_type Car
atom id /R:189@C6 idatm_type C2
atom id /R:189@O6 idatm_type O2
atom id /R:189@N1 idatm_type Npl
atom id /R:189@C2 idatm_type C2
atom id /R:189@N2 idatm_type Npl
atom id /R:189@N3 idatm_type N2
atom id /R:189@C4 idatm_type Car
atom id /R:190@P idatm_type Pac
atom id /R:190@OP1 idatm_type O3-
atom id /R:190@OP2 idatm_type O3-
atom id /R:190@O5' idatm_type O3
atom id /R:190@C5' idatm_type C3
atom id /R:190@C4' idatm_type C3
atom id /R:190@O4' idatm_type O3
atom id /R:190@C3' idatm_type C3
atom id /R:190@O3' idatm_type O3
atom id /R:190@C2' idatm_type C3
atom id /R:190@O2' idatm_type O3
atom id /R:190@C1' idatm_type C3
atom id /R:190@N1 idatm_type Npl
atom id /R:190@C2 idatm_type C2
atom id /R:190@O2 idatm_type O2
atom id /R:190@N3 idatm_type N2
atom id /R:190@C4 idatm_type C2
atom id /R:190@N4 idatm_type Npl
atom id /R:190@C5 idatm_type C2
atom id /R:190@C6 idatm_type C2
atom id /R:191@P idatm_type Pac
atom id /R:191@OP1 idatm_type O3-
atom id /R:191@OP2 idatm_type O3-
atom id /R:191@O5' idatm_type O3
atom id /R:191@C5' idatm_type C3
atom id /R:191@C4' idatm_type C3
atom id /R:191@O4' idatm_type O3
atom id /R:191@C3' idatm_type C3
atom id /R:191@O3' idatm_type O3
atom id /R:191@C2' idatm_type C3
atom id /R:191@O2' idatm_type O3
atom id /R:191@C1' idatm_type C3
atom id /R:191@N1 idatm_type Npl
atom id /R:191@C2 idatm_type C2
atom id /R:191@O2 idatm_type O2
atom id /R:191@N3 idatm_type N2
atom id /R:191@C4 idatm_type C2
atom id /R:191@N4 idatm_type Npl
atom id /R:191@C5 idatm_type C2
atom id /R:191@C6 idatm_type C2
atom id /R:192@P idatm_type Pac
atom id /R:192@OP1 idatm_type O3-
atom id /R:192@OP2 idatm_type O3-
atom id /R:192@O5' idatm_type O3
atom id /R:192@C5' idatm_type C3
atom id /R:192@C4' idatm_type C3
atom id /R:192@O4' idatm_type O3
atom id /R:192@C3' idatm_type C3
atom id /R:192@O3' idatm_type O3
atom id /R:192@C2' idatm_type C3
atom id /R:192@O2' idatm_type O3
atom id /R:192@C1' idatm_type C3
atom id /R:192@N1 idatm_type Npl
atom id /R:192@C2 idatm_type C2
atom id /R:192@O2 idatm_type O2
atom id /R:192@N3 idatm_type N2
atom id /R:192@C4 idatm_type C2
atom id /R:192@N4 idatm_type Npl
atom id /R:192@C5 idatm_type C2
atom id /R:192@C6 idatm_type C2
> info traptr
1 models
#1, 7v99, shown
14582 atoms, 15404 bonds, 1419 residues, 5 chains (A,K,L,R,S)
193 hydrogen bonds, 3 missing structure
> info beforetraptr1
1 models
#1, 7v99, shown
14582 atoms, 15404 bonds, 1419 residues, 5 chains (A,K,L,R,S)
193 hydrogen bonds, 3 missing structure
> info matt
Expected a models specifier or a keyword
> color beforetraptr1 green
> color beforetraptr2 red
> name list
before_traptr sel
beforetr1 sel
beforetraptr1 sel
beforetraptr2 sel
test1 sel
trapping_TR sel
traptr sel
> select protein
9299 atoms, 9512 bonds, 1 pseudobond, 1170 residues, 2 models selected
> color test1 red
> color traptr blue
> name delete all
> name list
There are no user-defined specifier names.
> name traptr select /r:237-334
"select /r:237-334": invalid atom specifier
> name traptr selection /r:237-334
"selection /r:237-334": invalid atom specifier
> name traptr /r:237-334
> name before_traptr1 /r:33-147
> name before_traptr2 /r:163-192
> name before_traptr /r:33-192
> color /a blue
> color /a lightblue
> color /j green
> color /k green
> color /k lightgreen
> color /l lightred
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /l lightred
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /l green
> lighting soft
> color before_traptr pink
> save "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
——— End of log from Thu Jun 8 16:55:49 2023 ———
opened ChimeraX session
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> color before_traptr red
> color before_traptr pink
> lighting simple
> lighting soft
> lighting full
> lighting soft
> transparency /a 50
> transparency /a 40
> transparency /a 20
> transparency /a 10
> transparency /a 90
> transparency /a 0
> transparency /a 5
> hide /a atoms
> hide /a surfaces
> show /a surfaces
> selection /a
Unknown command: selection /a
> select /a
7898 atoms, 8092 bonds, 1 pseudobond, 991 residues, 2 models selected
> color sel byhetero
> color sel bychain
> color sel bypolymer
> rainbow sel
> color sel bychain
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> surface style #1.3 mesh
> surface style #1.3 dot
> surface style #1.3 solid
> transparency (#!1 & sel) 100
> transparency (#!1 & sel) 90
> transparency (#!1 & sel) 70
> save "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
> ui tool show "Surface Color"
> ui tool show "File History"
> ui tool show AlphaFold
> alphafold match #1/A
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold O14746 from
https://alphafold.ebi.ac.uk/files/AF-O14746-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: O14746 (chain A)
AlphaFold prediction matching 7v99
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | O14746 | TERT_HUMAN | 5.03 | 1132 | 991 | 100
Opened 1 AlphaFold model
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide target m
> show target m
> hide #!2 models
> close #2
> roll
> roll stop
Expected an axis vector or a keyword
> roll off
Expected an axis vector or a keyword
> stop
> tile 2
Expected a models specifier or a keyword
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
Unsupported scale factor (0.000000) detected on Display0
> select /R
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> select /R
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> hide beforetraptr
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> name list
before_traptr /r:33-192
before_traptr1 /r:33-147
before_traptr2 /r:163-192
beforetr1 sel
beforetraptr1 sel
test1 sel
trapping_TR sel
traptr /r:237-334
> hide before_traptr
> hide before_traptr atoms, ribbons
> hide /a
> hide /a surfaces
> hide /s atoms, ribbons
> name long_loop_hp selection /r:276-2279
"selection /r:276-2279": invalid atom specifier
> name long_loop_hp selection /r:276-279
"selection /r:276-279": invalid atom specifier
> name long_loop_hp select /r:276-279
"select /r:276-279": invalid atom specifier
> name long_loop_hp /r:276-279
> color long_loop_hp red
> save "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
> save /Users/matthewcomstock/Desktop/image1.png supersample 3
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
Log from Mon Jun 12 09:55:11 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
Log from Thu Jun 8 16:55:49 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
Log from Tue Jun 6 16:44:25 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open 2bbv
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #1
---
Chain | Description | UniProt
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |
Non-standard residues in 2bbv #1
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> color bychain
> style /b stick
Changed 2382 atom styles
> color /n teal
[Repeated 1 time(s)]
> hide /c
> show /c
> hide /n
> shown /n
Unknown command: shown /n
> show /n
[Repeated 1 time(s)]
> ribbon /c
[Repeated 1 time(s)]
> ribbon /n
> style /n ribbon
Expected a keyword
> select /N:4@C5'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select down
201 atoms, 222 bonds, 10 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select down
201 atoms, 222 bonds, 10 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select down
201 atoms, 222 bonds, 10 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select up
7817 atoms, 7813 bonds, 1208 residues, 1 model selected
> select down
201 atoms, 222 bonds, 10 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
201 atoms, 222 bonds, 10 residues, 1 model selected
> color sel gold
> select clear
> color sel gold
> select clear
> color sel gold
> select clear
> color sel gold
> select clear
> color sel red
> surface #1
> color /n fromatoms
> surface #1
> surface #2
No atoms specified by #2
> surface
> surface #1 hide
Expected a keyword
> hide surfaces #1
Expected ',' or a keyword
> hide surfaces
> show surfaces
> hide surfaces
> style solvent sphere
Changed 208 atom styles
> color solvent red
> sym #1
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly| 60 copies of chains A-F,N
2| icosahedral asymmetric unit| 1 copy of chains A-F,N
3| icosahedral pentamer| 5 copies of chains A-F,N
4| icosahedral 23 hexamer| 6 copies of chains A-F,N
5| icosahedral asymmetric unit, std point frame| 1 copy of chains A-F,N
6| crystal asymmetric unit, crystal frame| 5 copies of chains A-F,N
> hide #1 models
> show #1
> show #1 models
> sym #1 assembly 3 newModel false copies false
Made 5 graphical clones for 2bbv assembly 3
> sym #1 assembly 1
Made 60 graphical clones for 2bbv assembly 1
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> sym #1 assembly 1view
Assembly "1view" not found, have 1, 2, 3, 4, 5, 6
> view
> set bgColor white
> set silhouettes true
> save /Users/matthewcomstock/Desktop/2bbv.png
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/matthewcomstock/Desktop/movie1.mp4
Movie saved to /Users/matthewcomstock/Desktop/movie1.mp4
> close #2
> sym #1 assembly 3 newModel false copies false
Made 5 graphical clones for 2bbv assembly 3
> show #1 models
> view
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> surface #1
> color /n fromatoms
> style solvent sphere
Changed 208 atom styles
> color solvent red
> view
> close
> set bgColor black
> set bgColor transparent
> set silhouettes false
> open 1080 fromDatabase emdb
Summary of feedback from opening 1080 fetched from emdb
---
note | Fetching compressed map 1080 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/map/emd_1080.map.gz
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> lighting full
> volume #1 level 0.9
> volume #1 level .5
> volume #1 level .2
> volume #1 level .1
> volume #1 level 2
> volume #1 level .15
> volume #1 level 1.68
> ui mousemode right "contour level"
> volume #1 level 1.812
> volume #1 level 1.773
> volume #1 level 1.504
> volume #1 level 1.275
> volume #1 encloseVolume 1e6 step 1 color tan
> volume #1 1e5 step 1
Expected a keyword
> volume #1 1e5 step 1 color tan
Expected a keyword
> volume #1 encloseVolume 1e5 step 1
> volume #1 encloseVolume 1e4 step 1
> volume #1 encloseVolume 1e6 step 1 color tan
> set bgColor gray
> set bgColor #80808000
> set silhouettes true
> open 1grl
Summary of feedback from opening 1grl fetched from pdb
---
note | Fetching compressed mmCIF 1grl from
http://files.rcsb.org/download/1grl.cif
1grl title:
The crystal structure of the bacterial chaperonin groel At 2.8 angstroms [more
info...]
Chain information for 1grl #2
---
Chain | Description | UniProt
A B C D E F G | GROEL (HSP60 CLASS) | CH60_ECOLI 2-548
1grl mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> lighting default
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select /D:357@CG2
1 atom, 1 residue, 1 model selected
> view matrix models #2,1,0,0,44.01,0,1,0,-1.4223,0,0,1,-0.37848
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99999,-0.0041909,0.002923,44.116,0.0043018,0.99923,-0.039047,-2.5771,-0.0027571,0.039059,0.99923,-0.57913
> view matrix models
> #2,0.99572,-0.092469,0.00020636,43.966,0.092405,0.99494,-0.039468,1.1951,0.0034442,0.039318,0.99922,-0.31382
> fitmap #2 inMap #1
Fit molecule 1grl (#2) to map emdb 1080 (#1) using 29274 atoms
average map value = 1.33, steps = 104
shifted from previous position = 0.914
rotated from previous position = 20.7 degrees
atoms outside contour = 3707, contour level = 0.82501
Position of 1grl (#2) relative to emdb 1080 (#1) coordinates:
Matrix rotation and translation
0.90168809 -0.43225449 -0.01070721 39.38415285
0.43238288 0.90129381 0.02673023 18.93264110
-0.00190392 -0.02873195 0.99958534 -0.07033036
Axis -0.06401015 -0.01016007 0.99789753
Axis point -21.87968789 95.67746379 0.00000000
Rotation angle (degrees) 25.67269007
Shift along axis -2.78352503
> volume #1 transparency 0.5
> view matrix models
> #2,0.92048,-0.39074,-0.0062701,40.283,0.39076,0.92009,0.027407,17.143,-0.0049401,-0.027678,0.9996,-0.20146
> fitmap #2 inMap #1
Fit molecule 1grl (#2) to map emdb 1080 (#1) using 29274 atoms
average map value = 1.33, steps = 60
shifted from previous position = 0.0354
rotated from previous position = 2.63 degrees
atoms outside contour = 3704, contour level = 0.82501
Position of 1grl (#2) relative to emdb 1080 (#1) coordinates:
Matrix rotation and translation
0.90160406 -0.43242969 -0.01070914 39.38027615
0.43255808 0.90120994 0.02672371 18.93993563
-0.00190494 -0.02872653 0.99958549 -0.07718132
Axis -0.06397061 -0.01015704 0.99790009
Axis point -21.87911091 95.63336281 0.00000000
Rotation angle (degrees) 25.68378070
Shift along axis -2.78857344
> volume #1 transparency 0.5
> molmap #2 10
Opened 1grl map 10 as #3, grid size 63,63,41, pixel 3.33, shown at level
0.0611, step 1, values float32
> volume #3 style mesh
> volume subtract #1 #3 minRms true
Opened volume difference as #4, grid size 100,100,100, pixel 2.7, shown at
step 1, values float32
Minimum RMS scale factor for "1grl map 10 #3" above level 0.061077 is 4.5565
> volume #4 color pink transparency 0
> hide atoms
> show ribbons
> close
> set bgColor black
> set bgColor transparent
> set silhouettes false
> open 1a0m fromDatabase eds
Summary of feedback from opening 1a0m fetched from eds
---
note | Fetching map 1a0m from
http://www.ebi.ac.uk/pdbe/coordinates/files/1a0m.ccp4
Opened eds 1a0m as #1, grid size 97,101,88, pixel 0.37,0.37,0.367, shown at
level 2.28, step 1, values float32
> open 1a0m
Summary of feedback from opening 1a0m fetched from pdb
---
note | Fetching compressed mmCIF 1a0m from
http://files.rcsb.org/download/1a0m.cif
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #2
---
Chain | Description | UniProt
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16
Non-standard residues in 1a0m #2
---
NH2 — amino group
> hide ribbons
> show
> volume #1 level 1.0 style mesh
> ui mousemode right zoom
> volume zone #1 nearAtoms #2 range 2
> volume #1 level 0.5 transparency 0.6
> close
> open 1273 fromDatabase emdb
Summary of feedback from opening 1273 fetched from emdb
---
note | Fetching compressed map 1273 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1273/map/emd_1273.map.gz
Opened emdb 1273 as #1, grid size 2048,2048,76, pixel 22.5, shown at step 1,
values int8
> volume #1 region all showOutlineBox true
> close
> open 7v99
Summary of feedback from opening 7v99 fetched from pdb
---
note | Fetching compressed mmCIF 7v99 from
http://files.rcsb.org/download/7v99.cif
7v99 title:
catalytic core of human telomerase holoenzyme [more info...]
Chain information for 7v99 #1
---
Chain | Description | UniProt
A | Telomerase reverse transcriptase | TERT_HUMAN 1-1132
K | Histone H2A type 1-B/E | H2A1B_HUMAN 1-129
L | Histone H2B type 1-K | H2B1K_HUMAN 1-125
R | Telomerase RNA component |
S | Primer DNA |
> color bychain
> set bgColor white
> set bgColor #ffffff00
> lighting simple
> lighting full
> hide atoms
> show cartoons
> show atoms
> show surfaces
> nucleotides ladder
> graphics silhouettes true
> volume hide
No volumes specified
> select /R:33-334
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> hide surfaces sel
Expected ',' or a keyword
> hide sel surfaces
> color sel orange
> hide /a
> hide /a atoms
> hide /a surfaces
> hide /a ribbons
> hide /s
> hide /s all
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /s models
[Repeated 1 time(s)]
> show /s models
> show /s atoms
> hide /s atoms
> hide /s surfaces
> hide /s ribbons
> sym #1
7v99 mmCIF Assemblies
---
1| author_defined_assembly| 1 copy of chains A,K,L,R,S
> show /a surfaces
> color /r teal
> color /r orange
> color /k green
> color /l green
> color /k red
> hide sel atoms
> show sel atoms
> color sel bynucleotide
> nucleotides sel stubs
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel tube/slab shape muffler
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> nucleotides sel slab
> style nucleic & sel stick
Changed 5156 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 5156 atom styles
> nucleotides sel stubs
> nucleotides sel ladder
> color #1.4 #ff59f5ff
> hide /k atoms
> hide /l atoms
> color #1.5 #00d301ff
> color #1.5 #00da01ff
> save "/Users/matthewcomstock/OneDrive - Michigan State University/project
> analysis/230308 telomerase RNA structure/telomerase structures/7v99 chimera
> work.cxs"
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 1/R
> select sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> color sel red
> color sel orange
> save "/Users/matthewcomstock/OneDrive - Michigan State University/project
> analysis/230308 telomerase RNA structure/telomerase structures/7v99 chimera
> work.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Destroying pre-existing alignment with identifier 1/R
Alignment identifier is 1/R
> select /a
7898 atoms, 8092 bonds, 1 pseudobond, 991 residues, 2 models selected
> select /r
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> select /r sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> select sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> select /r
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> select /r :1:10
Nothing selected
> select /r:1:10
Nothing selected
> select /r:10
Nothing selected
> select /r:100
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /r:101
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /r:237
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> color sel green
> color /r:334 red
> save /Users/matthewcomstock/Desktop/image1.png supersample 3
> hide /r:start-236
> hide ribbons /r:start-236
Expected ',' or a keyword
> hide /r:start-236 ribbons
> hide /r:335-end atoms, ribbons
> show /r:335-end atoms, ribbons
> show /r:335-end atoms
> show /r:335-end
> hide /r:335-end
> show /r atoms, ribbons
> hide /r atoms, ribbons
> show /r atoms, ribbons
> hide sequence ggguug atoms, ribbon
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select /r sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> name trapping_TR sel
> name traptr sel
> color traptr red
> color traptr orange
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> name before_traptr sel
> hide before_traptr atoms, ribbons
> save /Users/matthewcomstock/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/matthewcomstock/Desktop/movie1.mp4
Movie saved to /Users/matthewcomstock/Desktop/movie1.mp4
> save "/Users/matthewcomstock/OneDrive - Michigan State University/project
> analysis/230308 telomerase RNA structure/telomerase structures/7v99 chimera
> work.cxs"
> cd "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures"
Current working directory is:
/Users/matthewcomstock/Library/CloudStorage/OneDrive-
MichiganStateUniversity/project analysis/230308 telomerase RNA
structure/telomerase structures
> select /a
7898 atoms, 8092 bonds, 1 pseudobond, 991 residues, 2 models selected
> transparency (#!1 & sel) 50
> show /s atoms, ribbons
> color /s red
> show before_traptr ribbons
> hide before_traptr ribbons
> ribbon before_traptr
> hide ribbons
> show ribbons
> hide /a ribbons
> hide before_traptr
> hide before_traptr ribbons
> before_traptr
Unknown command: before_traptr
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> hide sel
> hide sel ribbons
> hide sel ribbons, atoms
> show sel ribbons, atoms
> hide sel ribbons, atoms
> name before_traptr sel
> show before_traptr ribbons
> show before_traptr ribbons, atoms
> hide before_traptr ribbons, atoms
> show before_traptr ribbons
> show before_traptr ribbons transparency .5
Expected ',' or a keyword
> show before_traptr ribbon, transparency .5
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> transparancy before_traptr 0.5
Unknown command: transparancy before_traptr 0.5
> select before_traptr
5156 atoms, 3422 bonds, 104 pseudobonds, 243 residues, 3 models selected
> transparancy 0.5
Unknown command: transparancy 0.5
> transparency 0.5
> transparency 1
> transparency /a 50
> transparency /a 75
> transparency /a 25
> transparency /a 35
> transparency before_traptr 35
> surface before_traptr
> hide surfaces
> show /a surfaces
> show /k, /l surface
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show /k or /l surface
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show /k and /l surface
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show /l surfaces
> show /k surfaces
> hide before_traptr
> hide traptr
> hide traptr ribbons
> hide traptr ribbons, atoms
> show traptr ribbons, atoms
> /r
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
Unknown command: sequence /r
ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
> select sequence /r
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
Expected a keyword
> select /r sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> name traptr /r sequence
> ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg
"/r sequence
ccgaaccccgccuggaggccgcggucggcccggggcuucuccggaggcacccacugccaccgcgaagaguugggcucugucagccgcgggucucucgg":
contains extra trailing text
> name traptr sel
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> name before_traptr sel
> hide before_traptr
> hide before_traptr atoms, ribbons
> hide traptr atoms, ribbons
> lighting soft
> lighting simple
> lighting full
> lighting simple
> show /r:33:147
> show /r:33-147
> show /r:33-137
> show /r:33-147
> hide /r:33-147
> select /r:237-334
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> name traptr sel
> hide traptr
> hide traptr atoms, ribbons
> show traptr atoms, ribbons
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
> select /r:163-192
643 atoms, 720 bonds, 30 residues, 1 model selected
> name beforetr1 sel
> show beforetr1 atoms, ribbons
> hide beforetr1 atoms, ribbons
> hide traptr atoms, ribbons
[Repeated 1 time(s)]
> hide traptr
> select /r:237-334
2087 atoms, 2328 bonds, 81 pseudobonds, 98 residues, 2 models selected
> select /r:33-147
2426 atoms, 2702 bonds, 59 pseudobonds, 115 residues, 2 models selected
> show /r:33-147
> hide /r:33-147
> select /r:33-147
2426 atoms, 2702 bonds, 59 pseudobonds, 115 residues, 2 models selected
> name test1 sel
> show test1
> hide test1
> select test1
5156 atoms, 2702 bonds, 59 pseudobonds, 243 residues, 2 models selected
> select /r:33-147
2426 atoms, 2702 bonds, 59 pseudobonds, 115 residues, 2 models selected
> name beforetraptr1
"beforetraptr1" is not defined
> name beforetraptr1 sel
> show beforetraptr1
> hide beforetraptr1
> show beforetraptr1 atoms, ribbons
> hide beforetraptr1 atoms, ribbons
> show beforetraptr1 atoms, ribbons
> show beforetraptr1 atoms, ribbons, surfaces
> hide beforetraptr1 atoms, ribbons
> color beforetraptr1 teal
> hide beforetraptr1 surfaces
> show beforetraptr1 atoms, ribbons
> transparency beforetraptr1 50 target all
> transparency beforetraptr1 50 target All
Invalid "target" argument: Character 'A' is not an allowed target, must be one
of acrsbmpfl
> transparency beforetraptr1 50 target all
> transparency beforetraptr1 10 target all
> transparency beforetraptr1 100 target all
> color beforetraptr1 red
> color beforetraptr1 pink
> select /r:163-192
643 atoms, 720 bonds, 30 residues, 1 model selected
> select /r:163-192
643 atoms, 720 bonds, 30 residues, 1 model selected
> name beforetraptr2 sel
> show beforetraptr2 atoms, ribbons
> color beforetraptr2 pink
> save "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
——— End of log from Tue Jun 6 16:44:25 2023 ———
opened ChimeraX session
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> show traptr ribbons, atoms
> hide traptr ribbons, atoms
> show traptr ribbons, atoms
> color traptr red
> info chains
chain id /A chain_id A
chain id /K chain_id K
chain id /L chain_id L
chain id /R chain_id R
chain id /S chain_id S
> info models
model id #1 type AtomicStructure name 7v99
model id #1.1 type PseudobondGroup name "hydrogen bonds"
model id #1.2 type PseudobondGroup name "missing structure"
model id #1.3 type MolecularSurface name "7v99_A SES surface"
model id #1.4 type MolecularSurface name "7v99_K SES surface"
model id #1.5 type MolecularSurface name "7v99_L SES surface"
model id #1.6 type MolecularSurface name "7v99_R SES surface"
model id #1.7 type MolecularSurface name "7v99_S SES surface"
> info selection
atom id /R:163@P idatm_type Pac
atom id /R:163@OP1 idatm_type O3-
atom id /R:163@OP2 idatm_type O3-
atom id /R:163@O5' idatm_type O3
atom id /R:163@C5' idatm_type C3
atom id /R:163@C4' idatm_type C3
atom id /R:163@O4' idatm_type O3
atom id /R:163@C3' idatm_type C3
atom id /R:163@O3' idatm_type O3
atom id /R:163@C2' idatm_type C3
atom id /R:163@O2' idatm_type O3
atom id /R:163@C1' idatm_type C3
atom id /R:163@N9 idatm_type Npl
atom id /R:163@C8 idatm_type Car
atom id /R:163@N7 idatm_type N2
atom id /R:163@C5 idatm_type Car
atom id /R:163@C6 idatm_type C2
atom id /R:163@O6 idatm_type O2
atom id /R:163@N1 idatm_type Npl
atom id /R:163@C2 idatm_type C2
atom id /R:163@N2 idatm_type Npl
atom id /R:163@N3 idatm_type N2
atom id /R:163@C4 idatm_type Car
atom id /R:164@P idatm_type Pac
atom id /R:164@OP1 idatm_type O3-
atom id /R:164@OP2 idatm_type O3-
atom id /R:164@O5' idatm_type O3
atom id /R:164@C5' idatm_type C3
atom id /R:164@C4' idatm_type C3
atom id /R:164@O4' idatm_type O3
atom id /R:164@C3' idatm_type C3
atom id /R:164@O3' idatm_type O3
atom id /R:164@C2' idatm_type C3
atom id /R:164@O2' idatm_type O3
atom id /R:164@C1' idatm_type C3
atom id /R:164@N9 idatm_type Npl
atom id /R:164@C8 idatm_type Car
atom id /R:164@N7 idatm_type N2
atom id /R:164@C5 idatm_type Car
atom id /R:164@C6 idatm_type Car
atom id /R:164@N6 idatm_type Npl
atom id /R:164@N1 idatm_type N2
atom id /R:164@C2 idatm_type Car
atom id /R:164@N3 idatm_type N2
atom id /R:164@C4 idatm_type Car
atom id /R:165@P idatm_type Pac
atom id /R:165@OP1 idatm_type O3-
atom id /R:165@OP2 idatm_type O3-
atom id /R:165@O5' idatm_type O3
atom id /R:165@C5' idatm_type C3
atom id /R:165@C4' idatm_type C3
atom id /R:165@O4' idatm_type O3
atom id /R:165@C3' idatm_type C3
atom id /R:165@O3' idatm_type O3
atom id /R:165@C2' idatm_type C3
atom id /R:165@O2' idatm_type O3
atom id /R:165@C1' idatm_type C3
atom id /R:165@N9 idatm_type Npl
atom id /R:165@C8 idatm_type Car
atom id /R:165@N7 idatm_type N2
atom id /R:165@C5 idatm_type Car
atom id /R:165@C6 idatm_type C2
atom id /R:165@O6 idatm_type O2
atom id /R:165@N1 idatm_type Npl
atom id /R:165@C2 idatm_type C2
atom id /R:165@N2 idatm_type Npl
atom id /R:165@N3 idatm_type N2
atom id /R:165@C4 idatm_type Car
atom id /R:166@P idatm_type Pac
atom id /R:166@OP1 idatm_type O3-
atom id /R:166@OP2 idatm_type O3-
atom id /R:166@O5' idatm_type O3
atom id /R:166@C5' idatm_type C3
atom id /R:166@C4' idatm_type C3
atom id /R:166@O4' idatm_type O3
atom id /R:166@C3' idatm_type C3
atom id /R:166@O3' idatm_type O3
atom id /R:166@C2' idatm_type C3
atom id /R:166@O2' idatm_type O3
atom id /R:166@C1' idatm_type C3
atom id /R:166@N1 idatm_type Npl
atom id /R:166@C2 idatm_type C2
atom id /R:166@O2 idatm_type O2
atom id /R:166@N3 idatm_type N2
atom id /R:166@C4 idatm_type C2
atom id /R:166@N4 idatm_type Npl
atom id /R:166@C5 idatm_type C2
atom id /R:166@C6 idatm_type C2
atom id /R:167@P idatm_type Pac
atom id /R:167@OP1 idatm_type O3-
atom id /R:167@OP2 idatm_type O3-
atom id /R:167@O5' idatm_type O3
atom id /R:167@C5' idatm_type C3
atom id /R:167@C4' idatm_type C3
atom id /R:167@O4' idatm_type O3
atom id /R:167@C3' idatm_type C3
atom id /R:167@O3' idatm_type O3
atom id /R:167@C2' idatm_type C3
atom id /R:167@O2' idatm_type O3
atom id /R:167@C1' idatm_type C3
atom id /R:167@N9 idatm_type Npl
atom id /R:167@C8 idatm_type Car
atom id /R:167@N7 idatm_type N2
atom id /R:167@C5 idatm_type Car
atom id /R:167@C6 idatm_type Car
atom id /R:167@N6 idatm_type Npl
atom id /R:167@N1 idatm_type N2
atom id /R:167@C2 idatm_type Car
atom id /R:167@N3 idatm_type N2
atom id /R:167@C4 idatm_type Car
atom id /R:168@P idatm_type Pac
atom id /R:168@OP1 idatm_type O3-
atom id /R:168@OP2 idatm_type O3-
atom id /R:168@O5' idatm_type O3
atom id /R:168@C5' idatm_type C3
atom id /R:168@C4' idatm_type C3
atom id /R:168@O4' idatm_type O3
atom id /R:168@C3' idatm_type C3
atom id /R:168@O3' idatm_type O3
atom id /R:168@C2' idatm_type C3
atom id /R:168@O2' idatm_type O3
atom id /R:168@C1' idatm_type C3
atom id /R:168@N9 idatm_type Npl
atom id /R:168@C8 idatm_type Car
atom id /R:168@N7 idatm_type N2
atom id /R:168@C5 idatm_type Car
atom id /R:168@C6 idatm_type Car
atom id /R:168@N6 idatm_type Npl
atom id /R:168@N1 idatm_type N2
atom id /R:168@C2 idatm_type Car
atom id /R:168@N3 idatm_type N2
atom id /R:168@C4 idatm_type Car
atom id /R:169@P idatm_type Pac
atom id /R:169@OP1 idatm_type O3-
atom id /R:169@OP2 idatm_type O3-
atom id /R:169@O5' idatm_type O3
atom id /R:169@C5' idatm_type C3
atom id /R:169@C4' idatm_type C3
atom id /R:169@O4' idatm_type O3
atom id /R:169@C3' idatm_type C3
atom id /R:169@O3' idatm_type O3
atom id /R:169@C2' idatm_type C3
atom id /R:169@O2' idatm_type O3
atom id /R:169@C1' idatm_type C3
atom id /R:169@N9 idatm_type Npl
atom id /R:169@C8 idatm_type Car
atom id /R:169@N7 idatm_type N2
atom id /R:169@C5 idatm_type Car
atom id /R:169@C6 idatm_type Car
atom id /R:169@N6 idatm_type Npl
atom id /R:169@N1 idatm_type N2
atom id /R:169@C2 idatm_type Car
atom id /R:169@N3 idatm_type N2
atom id /R:169@C4 idatm_type Car
atom id /R:170@P idatm_type Pac
atom id /R:170@OP1 idatm_type O3-
atom id /R:170@OP2 idatm_type O3-
atom id /R:170@O5' idatm_type O3
atom id /R:170@C5' idatm_type C3
atom id /R:170@C4' idatm_type C3
atom id /R:170@O4' idatm_type O3
atom id /R:170@C3' idatm_type C3
atom id /R:170@O3' idatm_type O3
atom id /R:170@C2' idatm_type C3
atom id /R:170@O2' idatm_type O3
atom id /R:170@C1' idatm_type C3
atom id /R:170@N1 idatm_type Npl
atom id /R:170@C2 idatm_type C2
atom id /R:170@O2 idatm_type O2
atom id /R:170@N3 idatm_type N2
atom id /R:170@C4 idatm_type C2
atom id /R:170@N4 idatm_type Npl
atom id /R:170@C5 idatm_type C2
atom id /R:170@C6 idatm_type C2
atom id /R:171@P idatm_type Pac
atom id /R:171@OP1 idatm_type O3-
atom id /R:171@OP2 idatm_type O3-
atom id /R:171@O5' idatm_type O3
atom id /R:171@C5' idatm_type C3
atom id /R:171@C4' idatm_type C3
atom id /R:171@O4' idatm_type O3
atom id /R:171@C3' idatm_type C3
atom id /R:171@O3' idatm_type O3
atom id /R:171@C2' idatm_type C3
atom id /R:171@O2' idatm_type O3
atom id /R:171@C1' idatm_type C3
atom id /R:171@N9 idatm_type Npl
atom id /R:171@C8 idatm_type Car
atom id /R:171@N7 idatm_type N2
atom id /R:171@C5 idatm_type Car
atom id /R:171@C6 idatm_type Car
atom id /R:171@N6 idatm_type Npl
atom id /R:171@N1 idatm_type N2
atom id /R:171@C2 idatm_type Car
atom id /R:171@N3 idatm_type N2
atom id /R:171@C4 idatm_type Car
atom id /R:172@P idatm_type Pac
atom id /R:172@OP1 idatm_type O3-
atom id /R:172@OP2 idatm_type O3-
atom id /R:172@O5' idatm_type O3
atom id /R:172@C5' idatm_type C3
atom id /R:172@C4' idatm_type C3
atom id /R:172@O4' idatm_type O3
atom id /R:172@C3' idatm_type C3
atom id /R:172@O3' idatm_type O3
atom id /R:172@C2' idatm_type C3
atom id /R:172@O2' idatm_type O3
atom id /R:172@C1' idatm_type C3
atom id /R:172@N9 idatm_type Npl
atom id /R:172@C8 idatm_type Car
atom id /R:172@N7 idatm_type N2
atom id /R:172@C5 idatm_type Car
atom id /R:172@C6 idatm_type Car
atom id /R:172@N6 idatm_type Npl
atom id /R:172@N1 idatm_type N2
atom id /R:172@C2 idatm_type Car
atom id /R:172@N3 idatm_type N2
atom id /R:172@C4 idatm_type Car
atom id /R:173@P idatm_type Pac
atom id /R:173@OP1 idatm_type O3-
atom id /R:173@OP2 idatm_type O3-
atom id /R:173@O5' idatm_type O3
atom id /R:173@C5' idatm_type C3
atom id /R:173@C4' idatm_type C3
atom id /R:173@O4' idatm_type O3
atom id /R:173@C3' idatm_type C3
atom id /R:173@O3' idatm_type O3
atom id /R:173@C2' idatm_type C3
atom id /R:173@O2' idatm_type O3
atom id /R:173@C1' idatm_type C3
atom id /R:173@N9 idatm_type Npl
atom id /R:173@C8 idatm_type Car
atom id /R:173@N7 idatm_type N2
atom id /R:173@C5 idatm_type Car
atom id /R:173@C6 idatm_type Car
atom id /R:173@N6 idatm_type Npl
atom id /R:173@N1 idatm_type N2
atom id /R:173@C2 idatm_type Car
atom id /R:173@N3 idatm_type N2
atom id /R:173@C4 idatm_type Car
atom id /R:174@P idatm_type Pac
atom id /R:174@OP1 idatm_type O3-
atom id /R:174@OP2 idatm_type O3-
atom id /R:174@O5' idatm_type O3
atom id /R:174@C5' idatm_type C3
atom id /R:174@C4' idatm_type C3
atom id /R:174@O4' idatm_type O3
atom id /R:174@C3' idatm_type C3
atom id /R:174@O3' idatm_type O3
atom id /R:174@C2' idatm_type C3
atom id /R:174@O2' idatm_type O3
atom id /R:174@C1' idatm_type C3
atom id /R:174@N9 idatm_type Npl
atom id /R:174@C8 idatm_type Car
atom id /R:174@N7 idatm_type N2
atom id /R:174@C5 idatm_type Car
atom id /R:174@C6 idatm_type Car
atom id /R:174@N6 idatm_type Npl
atom id /R:174@N1 idatm_type N2
atom id /R:174@C2 idatm_type Car
atom id /R:174@N3 idatm_type N2
atom id /R:174@C4 idatm_type Car
atom id /R:175@P idatm_type Pac
atom id /R:175@OP1 idatm_type O3-
atom id /R:175@OP2 idatm_type O3-
atom id /R:175@O5' idatm_type O3
atom id /R:175@C5' idatm_type C3
atom id /R:175@C4' idatm_type C3
atom id /R:175@O4' idatm_type O3
atom id /R:175@C3' idatm_type C3
atom id /R:175@O3' idatm_type O3
atom id /R:175@C2' idatm_type C3
atom id /R:175@O2' idatm_type O3
atom id /R:175@C1' idatm_type C3
atom id /R:175@N9 idatm_type Npl
atom id /R:175@C8 idatm_type Car
atom id /R:175@N7 idatm_type N2
atom id /R:175@C5 idatm_type Car
atom id /R:175@C6 idatm_type Car
atom id /R:175@N6 idatm_type Npl
atom id /R:175@N1 idatm_type N2
atom id /R:175@C2 idatm_type Car
atom id /R:175@N3 idatm_type N2
atom id /R:175@C4 idatm_type Car
atom id /R:176@P idatm_type Pac
atom id /R:176@OP1 idatm_type O3-
atom id /R:176@OP2 idatm_type O3-
atom id /R:176@O5' idatm_type O3
atom id /R:176@C5' idatm_type C3
atom id /R:176@C4' idatm_type C3
atom id /R:176@O4' idatm_type O3
atom id /R:176@C3' idatm_type C3
atom id /R:176@O3' idatm_type O3
atom id /R:176@C2' idatm_type C3
atom id /R:176@O2' idatm_type O3
atom id /R:176@C1' idatm_type C3
atom id /R:176@N9 idatm_type Npl
atom id /R:176@C8 idatm_type Car
atom id /R:176@N7 idatm_type N2
atom id /R:176@C5 idatm_type Car
atom id /R:176@C6 idatm_type Car
atom id /R:176@N6 idatm_type Npl
atom id /R:176@N1 idatm_type N2
atom id /R:176@C2 idatm_type Car
atom id /R:176@N3 idatm_type N2
atom id /R:176@C4 idatm_type Car
atom id /R:177@P idatm_type Pac
atom id /R:177@OP1 idatm_type O3-
atom id /R:177@OP2 idatm_type O3-
atom id /R:177@O5' idatm_type O3
atom id /R:177@C5' idatm_type C3
atom id /R:177@C4' idatm_type C3
atom id /R:177@O4' idatm_type O3
atom id /R:177@C3' idatm_type C3
atom id /R:177@O3' idatm_type O3
atom id /R:177@C2' idatm_type C3
atom id /R:177@O2' idatm_type O3
atom id /R:177@C1' idatm_type C3
atom id /R:177@N1 idatm_type Npl
atom id /R:177@C2 idatm_type C2
atom id /R:177@O2 idatm_type O2
atom id /R:177@N3 idatm_type Npl
atom id /R:177@C4 idatm_type C2
atom id /R:177@O4 idatm_type O2
atom id /R:177@C5 idatm_type C2
atom id /R:177@C6 idatm_type C2
atom id /R:178@P idatm_type Pac
atom id /R:178@OP1 idatm_type O3-
atom id /R:178@OP2 idatm_type O3-
atom id /R:178@O5' idatm_type O3
atom id /R:178@C5' idatm_type C3
atom id /R:178@C4' idatm_type C3
atom id /R:178@O4' idatm_type O3
atom id /R:178@C3' idatm_type C3
atom id /R:178@O3' idatm_type O3
atom id /R:178@C2' idatm_type C3
atom id /R:178@O2' idatm_type O3
atom id /R:178@C1' idatm_type C3
atom id /R:178@N9 idatm_type Npl
atom id /R:178@C8 idatm_type Car
atom id /R:178@N7 idatm_type N2
atom id /R:178@C5 idatm_type Car
atom id /R:178@C6 idatm_type C2
atom id /R:178@O6 idatm_type O2
atom id /R:178@N1 idatm_type Npl
atom id /R:178@C2 idatm_type C2
atom id /R:178@N2 idatm_type Npl
atom id /R:178@N3 idatm_type N2
atom id /R:178@C4 idatm_type Car
atom id /R:179@P idatm_type Pac
atom id /R:179@OP1 idatm_type O3-
atom id /R:179@OP2 idatm_type O3-
atom id /R:179@O5' idatm_type O3
atom id /R:179@C5' idatm_type C3
atom id /R:179@C4' idatm_type C3
atom id /R:179@O4' idatm_type O3
atom id /R:179@C3' idatm_type C3
atom id /R:179@O3' idatm_type O3
atom id /R:179@C2' idatm_type C3
atom id /R:179@O2' idatm_type O3
atom id /R:179@C1' idatm_type C3
atom id /R:179@N1 idatm_type Npl
atom id /R:179@C2 idatm_type C2
atom id /R:179@O2 idatm_type O2
atom id /R:179@N3 idatm_type Npl
atom id /R:179@C4 idatm_type C2
atom id /R:179@O4 idatm_type O2
atom id /R:179@C5 idatm_type C2
atom id /R:179@C6 idatm_type C2
atom id /R:180@P idatm_type Pac
atom id /R:180@OP1 idatm_type O3-
atom id /R:180@OP2 idatm_type O3-
atom id /R:180@O5' idatm_type O3
atom id /R:180@C5' idatm_type C3
atom id /R:180@C4' idatm_type C3
atom id /R:180@O4' idatm_type O3
atom id /R:180@C3' idatm_type C3
atom id /R:180@O3' idatm_type O3
atom id /R:180@C2' idatm_type C3
atom id /R:180@O2' idatm_type O3
atom id /R:180@C1' idatm_type C3
atom id /R:180@N1 idatm_type Npl
atom id /R:180@C2 idatm_type C2
atom id /R:180@O2 idatm_type O2
atom id /R:180@N3 idatm_type N2
atom id /R:180@C4 idatm_type C2
atom id /R:180@N4 idatm_type Npl
atom id /R:180@C5 idatm_type C2
atom id /R:180@C6 idatm_type C2
atom id /R:181@P idatm_type Pac
atom id /R:181@OP1 idatm_type O3-
atom id /R:181@OP2 idatm_type O3-
atom id /R:181@O5' idatm_type O3
atom id /R:181@C5' idatm_type C3
atom id /R:181@C4' idatm_type C3
atom id /R:181@O4' idatm_type O3
atom id /R:181@C3' idatm_type C3
atom id /R:181@O3' idatm_type O3
atom id /R:181@C2' idatm_type C3
atom id /R:181@O2' idatm_type O3
atom id /R:181@C1' idatm_type C3
atom id /R:181@N9 idatm_type Npl
atom id /R:181@C8 idatm_type Car
atom id /R:181@N7 idatm_type N2
atom id /R:181@C5 idatm_type Car
atom id /R:181@C6 idatm_type Car
atom id /R:181@N6 idatm_type Npl
atom id /R:181@N1 idatm_type N2
atom id /R:181@C2 idatm_type Car
atom id /R:181@N3 idatm_type N2
atom id /R:181@C4 idatm_type Car
atom id /R:182@P idatm_type Pac
atom id /R:182@OP1 idatm_type O3-
atom id /R:182@OP2 idatm_type O3-
atom id /R:182@O5' idatm_type O3
atom id /R:182@C5' idatm_type C3
atom id /R:182@C4' idatm_type C3
atom id /R:182@O4' idatm_type O3
atom id /R:182@C3' idatm_type C3
atom id /R:182@O3' idatm_type O3
atom id /R:182@C2' idatm_type C3
atom id /R:182@O2' idatm_type O3
atom id /R:182@C1' idatm_type C3
atom id /R:182@N9 idatm_type Npl
atom id /R:182@C8 idatm_type Car
atom id /R:182@N7 idatm_type N2
atom id /R:182@C5 idatm_type Car
atom id /R:182@C6 idatm_type C2
atom id /R:182@O6 idatm_type O2
atom id /R:182@N1 idatm_type Npl
atom id /R:182@C2 idatm_type C2
atom id /R:182@N2 idatm_type Npl
atom id /R:182@N3 idatm_type N2
atom id /R:182@C4 idatm_type Car
atom id /R:183@P idatm_type Pac
atom id /R:183@OP1 idatm_type O3-
atom id /R:183@OP2 idatm_type O3-
atom id /R:183@O5' idatm_type O3
atom id /R:183@C5' idatm_type C3
atom id /R:183@C4' idatm_type C3
atom id /R:183@O4' idatm_type O3
atom id /R:183@C3' idatm_type C3
atom id /R:183@O3' idatm_type O3
atom id /R:183@C2' idatm_type C3
atom id /R:183@O2' idatm_type O3
atom id /R:183@C1' idatm_type C3
atom id /R:183@N1 idatm_type Npl
atom id /R:183@C2 idatm_type C2
atom id /R:183@O2 idatm_type O2
atom id /R:183@N3 idatm_type N2
atom id /R:183@C4 idatm_type C2
atom id /R:183@N4 idatm_type Npl
atom id /R:183@C5 idatm_type C2
atom id /R:183@C6 idatm_type C2
atom id /R:184@P idatm_type Pac
atom id /R:184@OP1 idatm_type O3-
atom id /R:184@OP2 idatm_type O3-
atom id /R:184@O5' idatm_type O3
atom id /R:184@C5' idatm_type C3
atom id /R:184@C4' idatm_type C3
atom id /R:184@O4' idatm_type O3
atom id /R:184@C3' idatm_type C3
atom id /R:184@O3' idatm_type O3
atom id /R:184@C2' idatm_type C3
atom id /R:184@O2' idatm_type O3
atom id /R:184@C1' idatm_type C3
atom id /R:184@N1 idatm_type Npl
atom id /R:184@C2 idatm_type C2
atom id /R:184@O2 idatm_type O2
atom id /R:184@N3 idatm_type Npl
atom id /R:184@C4 idatm_type C2
atom id /R:184@O4 idatm_type O2
atom id /R:184@C5 idatm_type C2
atom id /R:184@C6 idatm_type C2
atom id /R:185@P idatm_type Pac
atom id /R:185@OP1 idatm_type O3-
atom id /R:185@OP2 idatm_type O3-
atom id /R:185@O5' idatm_type O3
atom id /R:185@C5' idatm_type C3
atom id /R:185@C4' idatm_type C3
atom id /R:185@O4' idatm_type O3
atom id /R:185@C3' idatm_type C3
atom id /R:185@O3' idatm_type O3
atom id /R:185@C2' idatm_type C3
atom id /R:185@O2' idatm_type O3
atom id /R:185@C1' idatm_type C3
atom id /R:185@N9 idatm_type Npl
atom id /R:185@C8 idatm_type Car
atom id /R:185@N7 idatm_type N2
atom id /R:185@C5 idatm_type Car
atom id /R:185@C6 idatm_type C2
atom id /R:185@O6 idatm_type O2
atom id /R:185@N1 idatm_type Npl
atom id /R:185@C2 idatm_type C2
atom id /R:185@N2 idatm_type Npl
atom id /R:185@N3 idatm_type N2
atom id /R:185@C4 idatm_type Car
atom id /R:186@P idatm_type Pac
atom id /R:186@OP1 idatm_type O3-
atom id /R:186@OP2 idatm_type O3-
atom id /R:186@O5' idatm_type O3
atom id /R:186@C5' idatm_type C3
atom id /R:186@C4' idatm_type C3
atom id /R:186@O4' idatm_type O3
atom id /R:186@C3' idatm_type C3
atom id /R:186@O3' idatm_type O3
atom id /R:186@C2' idatm_type C3
atom id /R:186@O2' idatm_type O3
atom id /R:186@C1' idatm_type C3
atom id /R:186@N1 idatm_type Npl
atom id /R:186@C2 idatm_type C2
atom id /R:186@O2 idatm_type O2
atom id /R:186@N3 idatm_type N2
atom id /R:186@C4 idatm_type C2
atom id /R:186@N4 idatm_type Npl
atom id /R:186@C5 idatm_type C2
atom id /R:186@C6 idatm_type C2
atom id /R:187@P idatm_type Pac
atom id /R:187@OP1 idatm_type O3-
atom id /R:187@OP2 idatm_type O3-
atom id /R:187@O5' idatm_type O3
atom id /R:187@C5' idatm_type C3
atom id /R:187@C4' idatm_type C3
atom id /R:187@O4' idatm_type O3
atom id /R:187@C3' idatm_type C3
atom id /R:187@O3' idatm_type O3
atom id /R:187@C2' idatm_type C3
atom id /R:187@O2' idatm_type O3
atom id /R:187@C1' idatm_type C3
atom id /R:187@N1 idatm_type Npl
atom id /R:187@C2 idatm_type C2
atom id /R:187@O2 idatm_type O2
atom id /R:187@N3 idatm_type Npl
atom id /R:187@C4 idatm_type C2
atom id /R:187@O4 idatm_type O2
atom id /R:187@C5 idatm_type C2
atom id /R:187@C6 idatm_type C2
atom id /R:188@P idatm_type Pac
atom id /R:188@OP1 idatm_type O3-
atom id /R:188@OP2 idatm_type O3-
atom id /R:188@O5' idatm_type O3
atom id /R:188@C5' idatm_type C3
atom id /R:188@C4' idatm_type C3
atom id /R:188@O4' idatm_type O3
atom id /R:188@C3' idatm_type C3
atom id /R:188@O3' idatm_type O3
atom id /R:188@C2' idatm_type C3
atom id /R:188@O2' idatm_type O3
atom id /R:188@C1' idatm_type C3
atom id /R:188@N9 idatm_type Npl
atom id /R:188@C8 idatm_type Car
atom id /R:188@N7 idatm_type N2
atom id /R:188@C5 idatm_type Car
atom id /R:188@C6 idatm_type C2
atom id /R:188@O6 idatm_type O2
atom id /R:188@N1 idatm_type Npl
atom id /R:188@C2 idatm_type C2
atom id /R:188@N2 idatm_type Npl
atom id /R:188@N3 idatm_type N2
atom id /R:188@C4 idatm_type Car
atom id /R:189@P idatm_type Pac
atom id /R:189@OP1 idatm_type O3-
atom id /R:189@OP2 idatm_type O3-
atom id /R:189@O5' idatm_type O3
atom id /R:189@C5' idatm_type C3
atom id /R:189@C4' idatm_type C3
atom id /R:189@O4' idatm_type O3
atom id /R:189@C3' idatm_type C3
atom id /R:189@O3' idatm_type O3
atom id /R:189@C2' idatm_type C3
atom id /R:189@O2' idatm_type O3
atom id /R:189@C1' idatm_type C3
atom id /R:189@N9 idatm_type Npl
atom id /R:189@C8 idatm_type Car
atom id /R:189@N7 idatm_type N2
atom id /R:189@C5 idatm_type Car
atom id /R:189@C6 idatm_type C2
atom id /R:189@O6 idatm_type O2
atom id /R:189@N1 idatm_type Npl
atom id /R:189@C2 idatm_type C2
atom id /R:189@N2 idatm_type Npl
atom id /R:189@N3 idatm_type N2
atom id /R:189@C4 idatm_type Car
atom id /R:190@P idatm_type Pac
atom id /R:190@OP1 idatm_type O3-
atom id /R:190@OP2 idatm_type O3-
atom id /R:190@O5' idatm_type O3
atom id /R:190@C5' idatm_type C3
atom id /R:190@C4' idatm_type C3
atom id /R:190@O4' idatm_type O3
atom id /R:190@C3' idatm_type C3
atom id /R:190@O3' idatm_type O3
atom id /R:190@C2' idatm_type C3
atom id /R:190@O2' idatm_type O3
atom id /R:190@C1' idatm_type C3
atom id /R:190@N1 idatm_type Npl
atom id /R:190@C2 idatm_type C2
atom id /R:190@O2 idatm_type O2
atom id /R:190@N3 idatm_type N2
atom id /R:190@C4 idatm_type C2
atom id /R:190@N4 idatm_type Npl
atom id /R:190@C5 idatm_type C2
atom id /R:190@C6 idatm_type C2
atom id /R:191@P idatm_type Pac
atom id /R:191@OP1 idatm_type O3-
atom id /R:191@OP2 idatm_type O3-
atom id /R:191@O5' idatm_type O3
atom id /R:191@C5' idatm_type C3
atom id /R:191@C4' idatm_type C3
atom id /R:191@O4' idatm_type O3
atom id /R:191@C3' idatm_type C3
atom id /R:191@O3' idatm_type O3
atom id /R:191@C2' idatm_type C3
atom id /R:191@O2' idatm_type O3
atom id /R:191@C1' idatm_type C3
atom id /R:191@N1 idatm_type Npl
atom id /R:191@C2 idatm_type C2
atom id /R:191@O2 idatm_type O2
atom id /R:191@N3 idatm_type N2
atom id /R:191@C4 idatm_type C2
atom id /R:191@N4 idatm_type Npl
atom id /R:191@C5 idatm_type C2
atom id /R:191@C6 idatm_type C2
atom id /R:192@P idatm_type Pac
atom id /R:192@OP1 idatm_type O3-
atom id /R:192@OP2 idatm_type O3-
atom id /R:192@O5' idatm_type O3
atom id /R:192@C5' idatm_type C3
atom id /R:192@C4' idatm_type C3
atom id /R:192@O4' idatm_type O3
atom id /R:192@C3' idatm_type C3
atom id /R:192@O3' idatm_type O3
atom id /R:192@C2' idatm_type C3
atom id /R:192@O2' idatm_type O3
atom id /R:192@C1' idatm_type C3
atom id /R:192@N1 idatm_type Npl
atom id /R:192@C2 idatm_type C2
atom id /R:192@O2 idatm_type O2
atom id /R:192@N3 idatm_type N2
atom id /R:192@C4 idatm_type C2
atom id /R:192@N4 idatm_type Npl
atom id /R:192@C5 idatm_type C2
atom id /R:192@C6 idatm_type C2
> info selection
atom id /R:163@P idatm_type Pac
atom id /R:163@OP1 idatm_type O3-
atom id /R:163@OP2 idatm_type O3-
atom id /R:163@O5' idatm_type O3
atom id /R:163@C5' idatm_type C3
atom id /R:163@C4' idatm_type C3
atom id /R:163@O4' idatm_type O3
atom id /R:163@C3' idatm_type C3
atom id /R:163@O3' idatm_type O3
atom id /R:163@C2' idatm_type C3
atom id /R:163@O2' idatm_type O3
atom id /R:163@C1' idatm_type C3
atom id /R:163@N9 idatm_type Npl
atom id /R:163@C8 idatm_type Car
atom id /R:163@N7 idatm_type N2
atom id /R:163@C5 idatm_type Car
atom id /R:163@C6 idatm_type C2
atom id /R:163@O6 idatm_type O2
atom id /R:163@N1 idatm_type Npl
atom id /R:163@C2 idatm_type C2
atom id /R:163@N2 idatm_type Npl
atom id /R:163@N3 idatm_type N2
atom id /R:163@C4 idatm_type Car
atom id /R:164@P idatm_type Pac
atom id /R:164@OP1 idatm_type O3-
atom id /R:164@OP2 idatm_type O3-
atom id /R:164@O5' idatm_type O3
atom id /R:164@C5' idatm_type C3
atom id /R:164@C4' idatm_type C3
atom id /R:164@O4' idatm_type O3
atom id /R:164@C3' idatm_type C3
atom id /R:164@O3' idatm_type O3
atom id /R:164@C2' idatm_type C3
atom id /R:164@O2' idatm_type O3
atom id /R:164@C1' idatm_type C3
atom id /R:164@N9 idatm_type Npl
atom id /R:164@C8 idatm_type Car
atom id /R:164@N7 idatm_type N2
atom id /R:164@C5 idatm_type Car
atom id /R:164@C6 idatm_type Car
atom id /R:164@N6 idatm_type Npl
atom id /R:164@N1 idatm_type N2
atom id /R:164@C2 idatm_type Car
atom id /R:164@N3 idatm_type N2
atom id /R:164@C4 idatm_type Car
atom id /R:165@P idatm_type Pac
atom id /R:165@OP1 idatm_type O3-
atom id /R:165@OP2 idatm_type O3-
atom id /R:165@O5' idatm_type O3
atom id /R:165@C5' idatm_type C3
atom id /R:165@C4' idatm_type C3
atom id /R:165@O4' idatm_type O3
atom id /R:165@C3' idatm_type C3
atom id /R:165@O3' idatm_type O3
atom id /R:165@C2' idatm_type C3
atom id /R:165@O2' idatm_type O3
atom id /R:165@C1' idatm_type C3
atom id /R:165@N9 idatm_type Npl
atom id /R:165@C8 idatm_type Car
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atom id /R:186@O4' idatm_type O3
atom id /R:186@C3' idatm_type C3
atom id /R:186@O3' idatm_type O3
atom id /R:186@C2' idatm_type C3
atom id /R:186@O2' idatm_type O3
atom id /R:186@C1' idatm_type C3
atom id /R:186@N1 idatm_type Npl
atom id /R:186@C2 idatm_type C2
atom id /R:186@O2 idatm_type O2
atom id /R:186@N3 idatm_type N2
atom id /R:186@C4 idatm_type C2
atom id /R:186@N4 idatm_type Npl
atom id /R:186@C5 idatm_type C2
atom id /R:186@C6 idatm_type C2
atom id /R:187@P idatm_type Pac
atom id /R:187@OP1 idatm_type O3-
atom id /R:187@OP2 idatm_type O3-
atom id /R:187@O5' idatm_type O3
atom id /R:187@C5' idatm_type C3
atom id /R:187@C4' idatm_type C3
atom id /R:187@O4' idatm_type O3
atom id /R:187@C3' idatm_type C3
atom id /R:187@O3' idatm_type O3
atom id /R:187@C2' idatm_type C3
atom id /R:187@O2' idatm_type O3
atom id /R:187@C1' idatm_type C3
atom id /R:187@N1 idatm_type Npl
atom id /R:187@C2 idatm_type C2
atom id /R:187@O2 idatm_type O2
atom id /R:187@N3 idatm_type Npl
atom id /R:187@C4 idatm_type C2
atom id /R:187@O4 idatm_type O2
atom id /R:187@C5 idatm_type C2
atom id /R:187@C6 idatm_type C2
atom id /R:188@P idatm_type Pac
atom id /R:188@OP1 idatm_type O3-
atom id /R:188@OP2 idatm_type O3-
atom id /R:188@O5' idatm_type O3
atom id /R:188@C5' idatm_type C3
atom id /R:188@C4' idatm_type C3
atom id /R:188@O4' idatm_type O3
atom id /R:188@C3' idatm_type C3
atom id /R:188@O3' idatm_type O3
atom id /R:188@C2' idatm_type C3
atom id /R:188@O2' idatm_type O3
atom id /R:188@C1' idatm_type C3
atom id /R:188@N9 idatm_type Npl
atom id /R:188@C8 idatm_type Car
atom id /R:188@N7 idatm_type N2
atom id /R:188@C5 idatm_type Car
atom id /R:188@C6 idatm_type C2
atom id /R:188@O6 idatm_type O2
atom id /R:188@N1 idatm_type Npl
atom id /R:188@C2 idatm_type C2
atom id /R:188@N2 idatm_type Npl
atom id /R:188@N3 idatm_type N2
atom id /R:188@C4 idatm_type Car
atom id /R:189@P idatm_type Pac
atom id /R:189@OP1 idatm_type O3-
atom id /R:189@OP2 idatm_type O3-
atom id /R:189@O5' idatm_type O3
atom id /R:189@C5' idatm_type C3
atom id /R:189@C4' idatm_type C3
atom id /R:189@O4' idatm_type O3
atom id /R:189@C3' idatm_type C3
atom id /R:189@O3' idatm_type O3
atom id /R:189@C2' idatm_type C3
atom id /R:189@O2' idatm_type O3
atom id /R:189@C1' idatm_type C3
atom id /R:189@N9 idatm_type Npl
atom id /R:189@C8 idatm_type Car
atom id /R:189@N7 idatm_type N2
atom id /R:189@C5 idatm_type Car
atom id /R:189@C6 idatm_type C2
atom id /R:189@O6 idatm_type O2
atom id /R:189@N1 idatm_type Npl
atom id /R:189@C2 idatm_type C2
atom id /R:189@N2 idatm_type Npl
atom id /R:189@N3 idatm_type N2
atom id /R:189@C4 idatm_type Car
atom id /R:190@P idatm_type Pac
atom id /R:190@OP1 idatm_type O3-
atom id /R:190@OP2 idatm_type O3-
atom id /R:190@O5' idatm_type O3
atom id /R:190@C5' idatm_type C3
atom id /R:190@C4' idatm_type C3
atom id /R:190@O4' idatm_type O3
atom id /R:190@C3' idatm_type C3
atom id /R:190@O3' idatm_type O3
atom id /R:190@C2' idatm_type C3
atom id /R:190@O2' idatm_type O3
atom id /R:190@C1' idatm_type C3
atom id /R:190@N1 idatm_type Npl
atom id /R:190@C2 idatm_type C2
atom id /R:190@O2 idatm_type O2
atom id /R:190@N3 idatm_type N2
atom id /R:190@C4 idatm_type C2
atom id /R:190@N4 idatm_type Npl
atom id /R:190@C5 idatm_type C2
atom id /R:190@C6 idatm_type C2
atom id /R:191@P idatm_type Pac
atom id /R:191@OP1 idatm_type O3-
atom id /R:191@OP2 idatm_type O3-
atom id /R:191@O5' idatm_type O3
atom id /R:191@C5' idatm_type C3
atom id /R:191@C4' idatm_type C3
atom id /R:191@O4' idatm_type O3
atom id /R:191@C3' idatm_type C3
atom id /R:191@O3' idatm_type O3
atom id /R:191@C2' idatm_type C3
atom id /R:191@O2' idatm_type O3
atom id /R:191@C1' idatm_type C3
atom id /R:191@N1 idatm_type Npl
atom id /R:191@C2 idatm_type C2
atom id /R:191@O2 idatm_type O2
atom id /R:191@N3 idatm_type N2
atom id /R:191@C4 idatm_type C2
atom id /R:191@N4 idatm_type Npl
atom id /R:191@C5 idatm_type C2
atom id /R:191@C6 idatm_type C2
atom id /R:192@P idatm_type Pac
atom id /R:192@OP1 idatm_type O3-
atom id /R:192@OP2 idatm_type O3-
atom id /R:192@O5' idatm_type O3
atom id /R:192@C5' idatm_type C3
atom id /R:192@C4' idatm_type C3
atom id /R:192@O4' idatm_type O3
atom id /R:192@C3' idatm_type C3
atom id /R:192@O3' idatm_type O3
atom id /R:192@C2' idatm_type C3
atom id /R:192@O2' idatm_type O3
atom id /R:192@C1' idatm_type C3
atom id /R:192@N1 idatm_type Npl
atom id /R:192@C2 idatm_type C2
atom id /R:192@O2 idatm_type O2
atom id /R:192@N3 idatm_type N2
atom id /R:192@C4 idatm_type C2
atom id /R:192@N4 idatm_type Npl
atom id /R:192@C5 idatm_type C2
atom id /R:192@C6 idatm_type C2
> info traptr
1 models
#1, 7v99, shown
14582 atoms, 15404 bonds, 1419 residues, 5 chains (A,K,L,R,S)
193 hydrogen bonds, 3 missing structure
> info beforetraptr1
1 models
#1, 7v99, shown
14582 atoms, 15404 bonds, 1419 residues, 5 chains (A,K,L,R,S)
193 hydrogen bonds, 3 missing structure
> info matt
Expected a models specifier or a keyword
> color beforetraptr1 green
> color beforetraptr2 red
> name list
before_traptr sel
beforetr1 sel
beforetraptr1 sel
beforetraptr2 sel
test1 sel
trapping_TR sel
traptr sel
> select protein
9299 atoms, 9512 bonds, 1 pseudobond, 1170 residues, 2 models selected
> color test1 red
> color traptr blue
> name delete all
> name list
There are no user-defined specifier names.
> name traptr select /r:237-334
"select /r:237-334": invalid atom specifier
> name traptr selection /r:237-334
"selection /r:237-334": invalid atom specifier
> name traptr /r:237-334
> name before_traptr1 /r:33-147
> name before_traptr2 /r:163-192
> name before_traptr /r:33-192
> color /a blue
> color /a lightblue
> color /j green
> color /k green
> color /k lightgreen
> color /l lightred
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /l lightred
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /l green
> lighting soft
> color before_traptr pink
> save "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
——— End of log from Thu Jun 8 16:55:49 2023 ———
opened ChimeraX session
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> color before_traptr red
> color before_traptr pink
> lighting simple
[Repeated 1 time(s)]
> lighting soft
[Repeated 2 time(s)]
> lighting full
> lighting soft
[Repeated 1 time(s)]
> transparency /a 50
> transparency /a 40
> transparency /a 20
> transparency /a 10
> transparency /a 90
> transparency /a 0
> transparency /a 5
> hide /a atoms
> hide /a surfaces
> show /a surfaces
> selection /a
Unknown command: selection /a
> select /a
7898 atoms, 8092 bonds, 1 pseudobond, 991 residues, 2 models selected
> color sel byhetero
> color sel bychain
> color sel bypolymer
> rainbow sel
> color sel bychain
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> surface style #1.3 mesh
> surface style #1.3 dot
> surface style #1.3 solid
> transparency (#!1 & sel) 100
> transparency (#!1 & sel) 90
> transparency (#!1 & sel) 70
> save "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
> ui tool show "Surface Color"
> ui tool show "File History"
> ui tool show AlphaFold
> alphafold match #1/A
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold O14746 from
https://alphafold.ebi.ac.uk/files/AF-O14746-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: O14746 (chain A)
AlphaFold prediction matching 7v99
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | O14746 | TERT_HUMAN | 5.03 | 1132 | 991 | 100
Opened 1 AlphaFold model
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide target m
> show target m
> hide #!2 models
> close #2
> roll
[Repeated 1 time(s)]
> roll stop
Expected an axis vector or a keyword
> roll off
Expected an axis vector or a keyword
> stop
> tile 2
Expected a models specifier or a keyword
> select /R:33-192
3069 atoms, 3422 bonds, 104 pseudobonds, 145 residues, 3 models selected
Unsupported scale factor (0.000000) detected on Display0
[Repeated 4 time(s)]
> select /R
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> select /R
5156 atoms, 5750 bonds, 186 pseudobonds, 243 residues, 3 models selected
> hide beforetraptr
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> name list
before_traptr /r:33-192
before_traptr1 /r:33-147
before_traptr2 /r:163-192
beforetr1 sel
beforetraptr1 sel
test1 sel
trapping_TR sel
traptr /r:237-334
> hide before_traptr
> hide before_traptr atoms, ribbons
> hide /a
> hide /a surfaces
> hide /s atoms, ribbons
> name long_loop_hp selection /r:276-2279
"selection /r:276-2279": invalid atom specifier
> name long_loop_hp selection /r:276-279
"selection /r:276-279": invalid atom specifier
> name long_loop_hp select /r:276-279
"select /r:276-279": invalid atom specifier
> name long_loop_hp /r:276-279
> color long_loop_hp red
> save "/Users/matthewcomstock/Library/CloudStorage/OneDrive-
> MichiganStateUniversity/project analysis/230308 telomerase RNA
> structure/telomerase structures/7v99 chimera work.cxs"
——— End of log from Mon Jun 12 09:55:11 2023 ———
opened ChimeraX session
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
OS Loader Version: 577~129
Software:
System Software Overview:
System Version: macOS 13.3.1 (a) (22E772610a)
Kernel Version: Darwin 22.4.0
Time since boot: 18 days, 10 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Thunderbolt Display:
Display Type: LCD
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: C02HV216F2GC
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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