![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7670 closed defect (can't reproduce)
Crash *probably* deleting MatchMaker
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000316096000 (most recent call first):
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000002026c3600 (most recent call first):
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2317 in destroy
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2185 in _destroy
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 807 in remove_tool
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 370 in remove_tool
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.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":"2022-09-26 00:41:35.00 -0400","app_version":"1.4.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.4.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.4 (21F79)","incident_id":"99C094D8-FAF1-49BF-821E-2339D69AD95E","name":"ChimeraX"}
{
"uptime" : 130000,
"procLaunch" : "2022-09-26 00:04:20.8124 -0400",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"procStartAbsTime" : 3081325974137,
"coalitionID" : 7863,
"osVersion" : {
"train" : "macOS 12.4",
"build" : "21F79",
"releaseType" : "User"
},
"captureTime" : "2022-09-26 00:41:30.1053 -0400",
"incident" : "99C094D8-FAF1-49BF-821E-2339D69AD95E",
"bug_type" : "309",
"pid" : 50786,
"procExitAbsTime" : 3134824678576,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F670C117-AF37-58D2-9FFB-6C7CC87333C6","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F5CF1F57-A60C-6341-8943-4CB0F7A3222C",
"wakeTime" : 2282,
"sleepWakeUUID" : "5B777FA7-8DAA-4EAA-ABAB-7913EF6FFDDB",
"sip" : "enabled",
"vmRegionInfo" : "0x2939c5ecef48 is not in any region. Bytes after previous region: 44847074176841 Bytes before following region: 60225005752504\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00002939c5ecef48","rawCodes":[1,45328110513992],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00002939c5ecef48"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x2939c5ecef48 is not in any region. Bytes after previous region: 44847074176841 Bytes before following region: 60225005752504\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"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: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0102.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0102.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -8.68376
Ignored bad PDB record found on line 9694
Irms 6.00161
Ignored bad PDB record found on line 9695
Irms_leg 5.42916
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0102.pdb #1
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0099.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0099.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -3.7403e-10
Ignored bad PDB record found on line 9694
Irms 30.9912
Ignored bad PDB record found on line 9695
Irms_leg 32.1051
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0099.pdb #2
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -3.15134
Ignored bad PDB record found on line 9694
Irms 7.20646
Ignored bad PDB record found on line 9695
Irms_leg 5.64961
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb #3
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0072.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0072.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -5.50336
Ignored bad PDB record found on line 9694
Irms 8.74348
Ignored bad PDB record found on line 9695
Irms_leg 7.85585
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0072.pdb #4
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0054.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0054.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 1
Ignored bad PDB record found on line 9692
Fnat 0.214286
Ignored bad PDB record found on line 9693
I_sc -2.75225
Ignored bad PDB record found on line 9694
Irms 2.53004
Ignored bad PDB record found on line 9695
Irms_leg 2.49518
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0054.pdb #5
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -6.41876e-10
Ignored bad PDB record found on line 9694
Irms 25.284
Ignored bad PDB record found on line 9695
Irms_leg 25.6332
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb #6
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> select #*/d,e
21648 atoms, 21876 bonds, 1386 residues, 6 models selected
> show sel surfaces
> select #*/L:24-42,57-69, 107-138
5172 atoms, 5220 bonds, 354 residues, 6 models selected
> select #*/L
18378 atoms, 18612 bonds, 1206 residues, 6 models selected
> color sel dark gray
> select #*/L:24-42,57-69, 107-138
5172 atoms, 5220 bonds, 354 residues, 6 models selected
> color sel light sea green
> select #*/H
17994 atoms, 18222 bonds, 6 pseudobonds, 1224 residues, 12 models selected
> color (#!1-6 & sel) light gray
> select #*/H:24-42,57-69, 107-138
4914 atoms, 4986 bonds, 342 residues, 6 models selected
> color sel cornflower blue
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> close #6
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> select #*/e:73-83
795 atoms, 795 bonds, 55 residues, 5 models selected
> color (#!1-5 & sel) hot pink
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> close #4
> show #!3 models
> close #3
> show #!2 models
> close #2
> show #!1 models
> close #1
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0540.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0540.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -3.39389
Ignored bad PDB record found on line 9694
Irms 10.4088
Ignored bad PDB record found on line 9695
Irms_leg 9.35688
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0540.pdb #1
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0527.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0527.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -7.57227
Ignored bad PDB record found on line 9694
Irms 9.69897
Ignored bad PDB record found on line 9695
Irms_leg 8.63842
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0527.pdb #2
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0919.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0919.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -4.9249
Ignored bad PDB record found on line 9694
Irms 5.70901
Ignored bad PDB record found on line 9695
Irms_leg 5.0121
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0919.pdb #3
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1868.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1868.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -1.66877
Ignored bad PDB record found on line 9694
Irms 8.06501
Ignored bad PDB record found on line 9695
Irms_leg 6.59623
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1868.pdb #4
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1315.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1315.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -3.91601
Ignored bad PDB record found on line 9694
Irms 8.62544
Ignored bad PDB record found on line 9695
Irms_leg 6.97779
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1315.pdb #6
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -3.15134
Ignored bad PDB record found on line 9694
Irms 7.20646
Ignored bad PDB record found on line 9695
Irms_leg 5.64961
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb #7
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2054.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2054.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 1
Ignored bad PDB record found on line 9692
Fnat 0.142857
Ignored bad PDB record found on line 9693
I_sc -3.35916
Ignored bad PDB record found on line 9694
Irms 4.17874
Ignored bad PDB record found on line 9695
Irms_leg 3.50091
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2054.pdb #8
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0803.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0803.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -1.79567
Ignored bad PDB record found on line 9694
Irms 9.3712
Ignored bad PDB record found on line 9695
Irms_leg 8.43876
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0803.pdb #9
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0536.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0536.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0.0714286
Ignored bad PDB record found on line 9693
I_sc -7.42132
Ignored bad PDB record found on line 9694
Irms 5.30965
Ignored bad PDB record found on line 9695
Irms_leg 4.13428
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0536.pdb #10
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2402.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2402.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 1
Ignored bad PDB record found on line 9692
Fnat 0.214286
Ignored bad PDB record found on line 9693
I_sc -3.91057
Ignored bad PDB record found on line 9694
Irms 2.87454
Ignored bad PDB record found on line 9695
Irms_leg 2.49698
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2402.pdb #11
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1958.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1958.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -5.78107
Ignored bad PDB record found on line 9694
Irms 11.442
Ignored bad PDB record found on line 9695
Irms_leg 9.85159
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1958.pdb #12
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2795.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2795.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -0.000177861
Ignored bad PDB record found on line 9694
Irms 10.1235
Ignored bad PDB record found on line 9695
Irms_leg 9.88136
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2795.pdb #13
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -6.41876e-10
Ignored bad PDB record found on line 9694
Irms 25.284
Ignored bad PDB record found on line 9695
Irms_leg 25.6332
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb #14
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0290.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0290.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -0.839759
Ignored bad PDB record found on line 9694
Irms 8.39478
Ignored bad PDB record found on line 9695
Irms_leg 7.69343
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0290.pdb #15
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0174.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0174.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -9.31914
Ignored bad PDB record found on line 9694
Irms 6.58641
Ignored bad PDB record found on line 9695
Irms_leg 6.15729
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0174.pdb #16
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1523.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1523.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -3.87471
Ignored bad PDB record found on line 9694
Irms 4.90735
Ignored bad PDB record found on line 9695
Irms_leg 4.55731
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1523.pdb #17
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2500.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2500.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 1
Ignored bad PDB record found on line 9692
Fnat 0.214286
Ignored bad PDB record found on line 9693
I_sc -5.25695
Ignored bad PDB record found on line 9694
Irms 3.36464
Ignored bad PDB record found on line 9695
Irms_leg 2.93762
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2500.pdb #18
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2541.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2541.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -2.77925
Ignored bad PDB record found on line 9694
Irms 7.79606
Ignored bad PDB record found on line 9695
Irms_leg 6.07049
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2541.pdb #19
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2949.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2949.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0.0714286
Ignored bad PDB record found on line 9693
I_sc -2.79016
Ignored bad PDB record found on line 9694
Irms 5.82414
Ignored bad PDB record found on line 9695
Irms_leg 4.64252
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2949.pdb #20
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1895.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1895.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -4.94088
Ignored bad PDB record found on line 9694
Irms 9.19857
Ignored bad PDB record found on line 9695
Irms_leg 8.2817
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1895.pdb #21
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0935.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0935.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -5.00562
Ignored bad PDB record found on line 9694
Irms 11.0117
Ignored bad PDB record found on line 9695
Irms_leg 10.1688
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0935.pdb #22
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> open
> /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0219.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0219.pdb
---
warnings | Ignored bad PDB record found on line 9691
CAPRI_rank 0
Ignored bad PDB record found on line 9692
Fnat 0
Ignored bad PDB record found on line 9693
I_sc -1.07733
Ignored bad PDB record found on line 9694
Irms 9.12215
Ignored bad PDB record found on line 9695
Irms_leg 7.35583
651 messages similar to the above omitted
Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0219.pdb #23
---
Chain | Description
H | No description available
L | No description available
d | No description available
e | No description available
> select #*/H
68977 atoms, 69851 bonds, 23 pseudobonds, 4692 residues, 46 models selected
> color (#!1-4,6-23 & sel) light gray
> select #*/H:24-42,57-69, 107-138
18837 atoms, 19113 bonds, 1311 residues, 23 models selected
> color (#!1-4,6-23 & sel) cornflower blue
> select #*/L
70449 atoms, 71346 bonds, 4623 residues, 23 models selected
> color (#!1-4,6-23 & sel) dark gray
> select #*/d,e
82984 atoms, 83858 bonds, 5313 residues, 23 models selected
> show sel & #!1-4,6-23 surfaces
> select #*/e:73-83
3657 atoms, 3657 bonds, 253 residues, 23 models selected
> color (#!1-4,6-23 & sel) hot pink
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!23 models
> show #!1 models
> close #1
> show #!2 models
> close #2
> show #!3 models
> close #3
> show #!4 models
> close #4
> show #!5 models
> close #5
> show #!6 models
> close #6
> show #!7 models
> close #7
> show #!8 models
> hide #!8 models
> show #!9 models
> close #9
> show #!10 models
> close #10
> show #!11 models
> close #11
> show #!12 models
> close #12
> show #!13 models
> close #13
> show #!14 models
> close #14
> show #!15 models
> close #15
> show #!16 models
> hide #!16 models
> show #!17 models
> show #!18 models
> hide #!17 models
> hide #!18 models
> show #!19 models
> close #19
> show #!20 models
> close #20
> show #!21 models
> close #21
> show #!22 models
> close #22
> show #!23 models
> close #23
> show #!8 models
> show #!16 models
> show #!17 models
> show #!18 models
> hide #!8 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!16 models
> hide #!17 models
> close #16
> show #!8 models
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/tyr.com_0001_16678.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/tyr.com_0001_16678.pdb
---
warnings | Ignored bad PDB record found on line 3646
CAPRI_rank 2
Ignored bad PDB record found on line 3647
Fnat 0.5
Ignored bad PDB record found on line 3648
I_sc -6.552
Ignored bad PDB record found on line 3649
Irms 3.05
Ignored bad PDB record found on line 3650
Irms_leg 2.298
7 messages similar to the above omitted
Chain information for tyr.com_0001_16678.pdb #1
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/tyr.com_0001_01731.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/tyr.com_0001_01731.pdb
---
warnings | Ignored bad PDB record found on line 3646
CAPRI_rank 1
Ignored bad PDB record found on line 3647
Fnat 0.25
Ignored bad PDB record found on line 3648
I_sc -10.157
Ignored bad PDB record found on line 3649
Irms 4.479
Ignored bad PDB record found on line 3650
Irms_leg 2.184
7 messages similar to the above omitted
Chain information for tyr.com_0001_01731.pdb #2
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_14925.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_14925.pdb
---
warnings | Ignored bad PDB record found on line 3649
CAPRI_rank 1.84467e+19
Ignored bad PDB record found on line 3650
I_sc -9.313
Ignored bad PDB record found on line 3651
Irms 4.856
Ignored bad PDB record found on line 3652
cen_rms 16.873
Ignored bad PDB record found on line 3653
rms 19.691
5 messages similar to the above omitted
Chain information for trp.com_0001_14925.pdb #3
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_10073.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_10073.pdb
---
warnings | Ignored bad PDB record found on line 3649
CAPRI_rank 1.84467e+19
Ignored bad PDB record found on line 3650
I_sc -6.418
Ignored bad PDB record found on line 3651
Irms 4.645
Ignored bad PDB record found on line 3652
cen_rms 16.076
Ignored bad PDB record found on line 3653
rms 14.999
5 messages similar to the above omitted
Chain information for trp.com_0001_10073.pdb #4
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_01950.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_01950.pdb
---
warnings | Ignored bad PDB record found on line 3649
CAPRI_rank 1.84467e+19
Ignored bad PDB record found on line 3650
I_sc -6.506
Ignored bad PDB record found on line 3651
Irms 2.166
Ignored bad PDB record found on line 3652
cen_rms 16.366
Ignored bad PDB record found on line 3653
rms 6.561
5 messages similar to the above omitted
Chain information for trp.com_0001_01950.pdb #5
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/thr.com_0001_13336.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/thr.com_0001_13336.pdb
---
warnings | Ignored bad PDB record found on line 3639
CAPRI_rank 1
Ignored bad PDB record found on line 3640
Fnat 0.25
Ignored bad PDB record found on line 3641
I_sc -7.846
Ignored bad PDB record found on line 3642
Irms 2.789
Ignored bad PDB record found on line 3643
Irms_leg 2.637
7 messages similar to the above omitted
Chain information for thr.com_0001_13336.pdb #6
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/thr.com_0001_11240.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/thr.com_0001_11240.pdb
---
warnings | Ignored bad PDB record found on line 3639
CAPRI_rank 3
Ignored bad PDB record found on line 3640
Fnat 1
Ignored bad PDB record found on line 3641
I_sc -7.449
Ignored bad PDB record found on line 3642
Irms 0.812
Ignored bad PDB record found on line 3643
Irms_leg 0.734
7 messages similar to the above omitted
Chain information for thr.com_0001_11240.pdb #7
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/phe.com_0001_18061.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/phe.com_0001_18061.pdb
---
warnings | Ignored bad PDB record found on line 3645
CAPRI_rank 0
Ignored bad PDB record found on line 3646
Fnat 0
Ignored bad PDB record found on line 3647
I_sc -7.161
Ignored bad PDB record found on line 3648
Irms 7.124
Ignored bad PDB record found on line 3649
Irms_leg 5.407
7 messages similar to the above omitted
Chain information for phe.com_0001_18061.pdb #9
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/phe.com_0001_01987.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/phe.com_0001_01987.pdb
---
warnings | Ignored bad PDB record found on line 3645
CAPRI_rank 0
Ignored bad PDB record found on line 3646
Fnat 0
Ignored bad PDB record found on line 3647
I_sc -11.661
Ignored bad PDB record found on line 3648
Irms 3.555
Ignored bad PDB record found on line 3649
Irms_leg 2.975
7 messages similar to the above omitted
Chain information for phe.com_0001_01987.pdb #10
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/lys.com_0001_09032.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/lys.com_0001_09032.pdb
---
warnings | Ignored bad PDB record found on line 3647
CAPRI_rank 0
Ignored bad PDB record found on line 3648
Fnat 0.2
Ignored bad PDB record found on line 3649
I_sc -8.942
Ignored bad PDB record found on line 3650
Irms 3.773
Ignored bad PDB record found on line 3651
Irms_leg 4.029
7 messages similar to the above omitted
Chain information for lys.com_0001_09032.pdb #11
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/lys.com_0001_06272.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/lys.com_0001_06272.pdb
---
warnings | Ignored bad PDB record found on line 3647
CAPRI_rank 2
Ignored bad PDB record found on line 3648
Fnat 0.6
Ignored bad PDB record found on line 3649
I_sc -9.019
Ignored bad PDB record found on line 3650
Irms 2.253
Ignored bad PDB record found on line 3651
Irms_leg 1.996
7 messages similar to the above omitted
Chain information for lys.com_0001_06272.pdb #12
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/asp.com_0001_04115.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/asp.com_0001_04115.pdb
---
warnings | Ignored bad PDB record found on line 3637
CAPRI_rank 0
Ignored bad PDB record found on line 3638
Fnat 0
Ignored bad PDB record found on line 3639
I_sc -6.118
Ignored bad PDB record found on line 3640
Irms 6.421
Ignored bad PDB record found on line 3641
Irms_leg 7.418
7 messages similar to the above omitted
Chain information for asp.com_0001_04115.pdb #13
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_13296.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_13296.pdb
---
warnings | Ignored bad PDB record found on line 3649
CAPRI_rank 2
Ignored bad PDB record found on line 3650
Fnat 0.5
Ignored bad PDB record found on line 3651
I_sc -8.83
Ignored bad PDB record found on line 3652
Irms 2.89
Ignored bad PDB record found on line 3653
Irms_leg 3.157
7 messages similar to the above omitted
Chain information for arg.com_0001_13296.pdb #14
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_13266.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_13266.pdb
---
warnings | Ignored bad PDB record found on line 3649
CAPRI_rank 2
Ignored bad PDB record found on line 3650
Fnat 0.5
Ignored bad PDB record found on line 3651
I_sc -8.657
Ignored bad PDB record found on line 3652
Irms 2.394
Ignored bad PDB record found on line 3653
Irms_leg 1.696
7 messages similar to the above omitted
Chain information for arg.com_0001_13266.pdb #15
---
Chain | Description
d | No description available
e | No description available
> open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_12389.pdb
Summary of feedback from opening
/Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_12389.pdb
---
warnings | Ignored bad PDB record found on line 3649
CAPRI_rank 1
Ignored bad PDB record found on line 3650
Fnat 0.25
Ignored bad PDB record found on line 3651
I_sc -10.654
Ignored bad PDB record found on line 3652
Irms 4.412
Ignored bad PDB record found on line 3653
Irms_leg 3.808
7 messages similar to the above omitted
Chain information for arg.com_0001_12389.pdb #16
---
Chain | Description
d | No description available
e | No description available
> hide #1 models
> show #1 models
> ui tool show Matchmaker
> matchmaker #8/d to #1/d pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker tyr.com_0001_16678.pdb, chain d (#1) with
CD3de_3giz_L_oriH1H2_dummy_H3_0002_2054.pdb, chain d (#8), sequence alignment
score = 512
RMSD between 68 pruned atom pairs is 0.828 angstroms; (across all 108 pairs:
3.137)
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 8 MB
Memory: 8 GB
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 6 days 21:08
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash *probably* deleting MatchMaker |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Recent changes to not directly connect delete to the OK/Apply signal may well have fixed this.