![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Last modified 4 years ago
#5912 assigned defect
Crash handling tool window closeEvent after AlphaFold prediction finishes
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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: 1.3 (2021-12-08 23:08:33 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 0x00000002027ac600 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2285 in destroy
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2156 in _destroy
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 787 in remove_tool
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 353 in remove_tool
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 654 in close_request
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2251 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.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":"2022-01-13 13:06:11.00 +0800","app_version":"1.3.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.3.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.0.1 (21A559)","incident_id":"769D8285-0461-41D1-B070-F933C023C02F","name":"ChimeraX"}
{
"uptime" : 560000,
"procLaunch" : "2022-01-13 11:11:25.3889 +0800",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"procStartAbsTime" : 13478901309658,
"coalitionID" : 29623,
"osVersion" : {
"train" : "macOS 12.0.1",
"build" : "21A559",
"releaseType" : "User"
},
"captureTime" : "2022-01-13 13:06:04.2526 +0800",
"incident" : "769D8285-0461-41D1-B070-F933C023C02F",
"bug_type" : "309",
"pid" : 79870,
"procExitAbsTime" : 13643991423188,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"CAA63E76-54CA-5713-8FDF-5EBF9D05DEBC","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "47C3996C-6610-B68E-E691-B061FBA6E0C4",
"wakeTime" : 185753,
"sleepWakeUUID" : "4F10F619-D6F6-46A7-BE80-E610648BAC10",
"sip" : "enabled",
"vmRegionInfo" : "0x25ae5e6eb108 is not in any region. Bytes after previous region: 40949802512649 Bytes before following region: 64122277416696\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 600000000000-600001ed2000 [ 30.8M] rw-\/rwx SM=ZER ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x000025ae5e6eb108","rawCodes":[1,41430838849800],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000025ae5e6eb108"},
"vmregioninfo" : "0x25ae5e6eb108 is not in any region. Bytes after previous region: 40949802512649 Bytes before following region: 64122277416696\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 600000000000-600001ed2000 [ 30.8M] rw-\/rwx SM=ZER ",
"asi" : {"AppKit":["Calling windowShouldClose: on the delegate for the QNSPanel 0x7fb55f36f020"]},
"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: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_2/best_model_545.pdb
> format pdb
Chain information for best_model_545.pdb #1
---
Chain | Description
A | No description available
> select clear
Drag select of 42 residues
> mlp sel
Map values for surface "best_model_545.pdb_A SES surface": minimum -25.35,
mean -4.154, maximum 25.38
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> hide surfaces
Alignment identifier is 1/A
> select /A:169
22 atoms, 22 bonds, 1 residue, 1 model selected
> select /A:152-169
301 atoms, 302 bonds, 18 residues, 1 model selected
> select /A:147
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:147-151
86 atoms, 87 bonds, 5 residues, 1 model selected
> mlp sel
Map values for surface "best_model_545.pdb_A SES surface": minimum -25.35,
mean -4.154, maximum 25.38
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> select /A:146
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:1-146
2364 atoms, 2382 bonds, 146 residues, 1 model selected
> hide target m
> show target m
> delete sel
> select clear
Drag select of best_model_545.pdb_A SES surface, 11235 of 51156 triangles, 23
residues
> select clear
Drag select of best_model_545.pdb_A SES surface, 11235 of 51156 triangles, 23
residues
> mlp sel
Map values for surface "best_model_545.pdb_A SES surface": minimum -23.49,
mean -1.825, maximum 22.32
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> show target m
> hide target m
> show target m
> close
> open
> /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_2/best_model_545.pdb
> format pdb
Chain information for best_model_545.pdb #1
---
Chain | Description
A | No description available
> select add /A:169
22 atoms, 22 bonds, 1 residue, 1 model selected
> select add /A:167
36 atoms, 35 bonds, 2 residues, 1 model selected
> select add /A:168
60 atoms, 58 bonds, 3 residues, 1 model selected
Drag select of 12 residues
> select add /A:166
274 atoms, 76 bonds, 16 residues, 1 model selected
Drag select of 9 residues
Drag select of 6 residues
> select subtract /A:1
433 atoms, 76 bonds, 26 residues, 1 model selected
Drag select of 2 residues
> select add /A:144
417 atoms, 90 bonds, 25 residues, 1 model selected
> select add /A:143
433 atoms, 105 bonds, 26 residues, 1 model selected
> select add /A:141
455 atoms, 126 bonds, 27 residues, 1 model selected
> ui tool show Contacts
> contacts sel reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
270 contacts
atom1 atom2 overlap distance
/A LYS 141 HZ1 /A ASP 137 OD1 0.387 1.693
/A TRP 147 HE1 /A VAL 143 HG23 0.347 1.653
/A PRO 163 C /A GLU 165 H 0.325 2.375
/A VAL 143 CG2 /A TRP 147 HE1 0.318 2.382
/A ARG 159 HH21 /A PRO 20 HB3 0.317 1.683
/A TRP 147 HD1 /A VAL 143 O 0.314 2.166
/A TRP 147 HH2 /A ILE 14 CD1 0.309 2.391
/A VAL 143 O /A GLU 146 H 0.285 1.795
/A PRO 163 O /A GLU 165 H 0.277 1.803
/A TYR 169 O /A ARG 57 HH22 0.265 1.815
/A SER 151 H /A GLU 154 OE2 0.259 1.821
/A GLU 157 H /A GLU 153 O 0.252 1.828
/A THR 167 CG2 /A TYR 169 CE2 0.222 3.178
/A SER 151 HG /A GLU 154 OE2 0.215 1.865
/A SER 151 HG /A GLU 154 CD 0.184 2.516
/A SER 151 O /A ILE 155 H 0.160 1.920
/A TRP 147 NE1 /A VAL 143 CG2 0.157 3.168
/A TRP 147 CD1 /A GLU 144 HA 0.144 2.556
/A LEU 164 C /A ILE 166 H 0.143 2.557
/A LYS 141 CE /A ASP 137 OD1 0.124 3.056
/A THR 167 CG2 /A TYR 169 CZ 0.077 3.323
/A LYS 141 NZ /A ASP 137 OD1 0.066 2.639
/A GLU 156 H /A ASP 152 O 0.064 2.016
/A ILE 155 CD1 /A LEU 19 CD1 0.064 3.336
/A VAL 150 CG1 /A GLU 154 CB 0.062 3.338
/A GLU 144 C /A GLU 146 H 0.056 2.644
/A GLU 165 C /A THR 167 H 0.052 2.648
/A VAL 143 HG21 /A ALA 139 O 0.044 2.436
/A TYR 169 C /A ARG 57 HH22 0.042 2.658
/A TRP 147 HZ3 /A ILE 25 CD1 0.041 2.659
/A SER 151 C /A GLU 153 H 0.037 2.663
/A TYR 169 O /A ARG 57 NH2 0.033 2.672
/A TRP 147 CD1 /A VAL 143 O 0.032 3.148
/A ALA 158 CB /A LEU 43 O 0.028 3.152
/A VAL 143 HG23 /A ALA 140 O 0.026 2.454
/A TRP 147 CH2 /A ILE 14 CD1 0.025 3.375
/A VAL 143 HG13 /A LEU 1 CD2 0.023 2.677
/A GLU 156 O /A ARG 159 HB2 0.022 2.458
/A GLU 156 O /A GLN 160 H 0.017 2.063
/A ALA 158 HB3 /A LEU 43 O 0.015 2.465
/A TRP 147 NE1 /A VAL 143 HG23 0.012 2.613
/A SER 151 HG /A GLU 154 CG 0.010 2.690
/A TYR 169 CE2 /A THR 167 HG22 0.002 2.698
/A ALA 158 H /A GLU 154 O 0.002 2.078
/A ARG 159 HH21 /A PRO 20 CB -0.004 2.704
/A VAL 143 CG1 /A LEU 1 O -0.012 3.192
/A PRO 163 O /A GLU 165 N -0.020 2.725
/A ILE 155 O /A ARG 159 HG2 -0.026 2.506
/A ILE 155 O /A ARG 159 H -0.027 2.107
/A VAL 150 O /A SER 151 O -0.029 2.989
/A TRP 147 CD1 /A GLU 144 CA -0.029 3.429
/A THR 167 H /A GLU 165 O -0.032 2.112
/A VAL 143 HG12 /A LEU 1 O -0.033 2.513
/A ARG 159 NH2 /A PRO 20 HB3 -0.034 2.659
/A VAL 143 O /A GLU 146 N -0.037 2.742
/A TRP 147 CZ3 /A ILE 25 CD1 -0.042 3.442
/A GLU 156 O /A GLN 160 HG3 -0.044 2.524
/A LYS 141 H /A ASP 137 O -0.045 2.125
/A ASP 152 O /A GLU 156 CB -0.047 3.227
/A VAL 148 N /A GLU 146 O -0.054 2.759
/A ARG 159 NH2 /A PRO 20 O -0.062 2.767
/A VAL 143 C /A TRP 147 HD1 -0.064 2.764
/A TYR 169 O /A ARG 57 CZ -0.065 3.245
/A TRP 147 O /A ILE 149 N -0.069 2.774
/A TRP 147 HZ2 /A ALA 140 CB -0.073 2.773
/A TRP 147 HH2 /A ILE 14 HD13 -0.075 2.075
/A VAL 143 C /A GLU 146 H -0.076 2.776
/A VAL 143 O /A GLU 146 CB -0.076 3.256
/A SER 151 N /A GLU 154 OE2 -0.077 2.782
/A SER 151 OG /A GLU 154 CG -0.080 3.280
/A ILE 155 CD1 /A LEU 19 HD13 -0.082 2.782
/A LYS 161 O /A PRO 163 HD2 -0.082 2.562
/A TYR 169 CE2 /A THR 167 HG21 -0.085 2.785
/A ILE 149 H /A TRP 147 O -0.087 2.167
/A VAL 143 CG2 /A ALA 139 O -0.092 3.272
/A TRP 147 HH2 /A ILE 14 CG2 -0.094 2.794
/A GLU 142 HG3 /A GLU 138 O -0.100 2.580
/A VAL 143 O /A GLU 146 HB3 -0.102 2.582
/A TRP 147 HH2 /A ILE 14 HG23 -0.104 2.104
/A VAL 143 C /A TRP 147 CD1 -0.104 3.504
/A GLU 157 O /A LYS 161 H -0.105 2.185
/A VAL 150 O /A ILE 149 HG22 -0.106 2.586
/A TYR 169 CZ /A THR 167 HG21 -0.106 2.806
/A LYS 141 HZ1 /A ASP 137 CG -0.110 2.810
/A GLU 153 O /A GLU 157 N -0.110 2.815
/A ILE 155 O /A ARG 159 CG -0.113 3.293
/A VAL 150 O /A ILE 155 CD1 -0.123 3.303
/A TRP 147 HH2 /A ILE 14 HD12 -0.124 2.124
/A TRP 147 CH2 /A ILE 14 HG23 -0.126 2.826
/A GLU 153 O /A GLU 157 HG3 -0.126 2.606
/A VAL 150 CG1 /A GLU 154 HB2 -0.128 2.828
/A TRP 147 C /A ILE 149 H -0.130 2.830
/A VAL 150 HG12 /A GLU 154 CB -0.132 2.832
/A ILE 149 O /A SER 151 N -0.137 2.842
/A TRP 147 HH2 /A ILE 14 CB -0.141 2.841
/A ASP 152 O /A GLU 156 HB3 -0.143 2.623
/A GLU 142 HB3 /A ALA 139 O -0.144 2.624
/A VAL 143 HG13 /A LEU 1 HD21 -0.147 2.147
/A SER 151 OG /A GLU 154 HG2 -0.151 2.651
/A ILE 155 HD13 /A LEU 19 HD13 -0.152 2.152
/A TRP 147 H /A GLU 144 O -0.157 2.237
/A ILE 155 HG12 /A VAL 150 HG12 -0.159 2.159
/A LYS 161 O /A PRO 163 CD -0.163 3.343
/A VAL 150 HG12 /A GLU 154 HB2 -0.165 2.165
/A ILE 155 HG12 /A SER 151 O -0.168 2.648
/A ARG 159 HH21 /A PRO 20 C -0.171 2.871
/A SER 151 O /A GLU 154 N -0.172 2.877
/A SER 151 OG /A GLU 154 H -0.172 2.272
/A VAL 150 CG1 /A GLU 154 HB3 -0.174 2.874
/A GLU 144 OE1 /A TYR 105 HE2 -0.178 2.658
/A TRP 147 HZ2 /A LEU 5 HD12 -0.182 2.182
/A LYS 161 O /A PRO 163 N -0.182 3.287
/A TYR 169 OH /A THR 167 HG21 -0.182 2.682
/A LYS 141 HB2 /A GLU 138 O -0.183 2.663
/A LYS 141 CE /A ARG 97 O -0.184 3.364
/A TRP 147 CH2 /A ILE 14 CG2 -0.186 3.586
/A GLU 144 C /A TRP 147 H -0.187 2.887
/A TYR 169 C /A ARG 57 NH2 -0.189 3.514
/A VAL 143 O /A GLU 146 CA -0.190 3.370
/A TYR 169 CZ /A THR 167 HG22 -0.193 2.893
/A ARG 159 HH21 /A PRO 20 O -0.193 2.273
/A PRO 163 HD2 /A ALA 162 HA -0.193 2.193
/A GLU 165 O /A THR 167 N -0.195 2.900
/A VAL 150 HG13 /A GLU 154 CB -0.196 2.896
/A SER 151 OG /A GLU 154 CD -0.199 3.399
/A VAL 148 H /A GLU 146 O -0.201 2.281
/A LYS 141 CG /A ASP 137 O -0.204 3.384
/A TRP 147 CH2 /A ILE 14 HD13 -0.204 2.904
/A SER 151 O /A ILE 155 N -0.207 2.912
/A TRP 147 CZ2 /A LEU 5 HD12 -0.207 2.907
/A LYS 141 HE3 /A ARG 97 O -0.208 2.688
/A TRP 147 CZ2 /A LEU 5 CD1 -0.210 3.610
/A TRP 147 NE1 /A VAL 143 HG22 -0.211 2.836
/A ALA 158 O /A ALA 162 H -0.213 2.293
/A GLU 156 O /A GLN 160 CG -0.214 3.394
/A GLU 156 HG3 /A GLN 160 NE2 -0.215 2.840
/A SER 151 C /A GLU 154 H -0.218 2.918
/A ILE 155 HD12 /A LEU 19 CD1 -0.220 2.920
/A TRP 147 NE1 /A GLU 144 HA -0.222 2.847
/A VAL 143 CG1 /A LEU 1 CD2 -0.223 3.623
/A GLU 156 O /A ARG 159 CB -0.226 3.406
/A VAL 143 CG1 /A LEU 1 HD21 -0.227 2.927
/A ALA 158 CB /A GLU 154 O -0.228 3.408
/A LYS 141 C /A GLU 144 H -0.230 2.930
/A TRP 147 CE3 /A ILE 25 HD12 -0.231 2.931
/A ILE 166 H /A LEU 164 O -0.231 2.311
/A ILE 155 HD13 /A LEU 19 CD1 -0.231 2.931
/A LYS 141 CD /A ASP 137 OD1 -0.233 3.413
/A ARG 168 HG3 /A ILE 166 HG21 -0.235 2.235
/A LYS 141 HG2 /A ASP 137 O -0.235 2.715
/A LYS 141 C /A VAL 143 H -0.236 2.936
/A VAL 143 CG2 /A ALA 140 HA -0.240 2.940
/A SER 151 OG /A GLU 154 OE2 -0.243 2.823
/A TYR 169 OH /A PRO 53 HG3 -0.243 2.743
/A ILE 155 CD1 /A LEU 19 HD12 -0.244 2.944
/A TRP 147 HE3 /A ILE 25 HD12 -0.246 2.246
/A GLU 144 HB2 /A ALA 140 O -0.249 2.729
/A ASP 152 O /A GLU 156 N -0.249 2.954
/A VAL 150 HA /A GLU 154 OE2 -0.250 2.730
/A LYS 141 HE2 /A ASP 137 OD1 -0.251 2.731
/A TRP 147 H /A GLU 145 C -0.254 2.954
/A ILE 155 HG12 /A VAL 150 CG1 -0.254 2.954
/A SER 151 O /A GLU 154 HB2 -0.255 2.735
/A VAL 148 O /A VAL 150 N -0.261 2.966
/A GLU 142 H /A GLU 138 O -0.262 2.342
/A SER 151 N /A GLU 154 HB2 -0.262 2.887
/A VAL 150 HG12 /A ILE 155 N -0.265 2.890
/A GLU 144 N /A ALA 140 O -0.267 2.972
/A TRP 147 O /A ILE 149 HG12 -0.268 2.748
/A VAL 143 CG1 /A LEU 1 C -0.269 3.669
/A SER 151 O /A GLU 154 H -0.271 2.351
/A GLU 157 O /A LYS 161 HG2 -0.276 2.756
/A GLU 157 O /A LYS 161 CG -0.277 3.457
/A GLU 156 HA /A ARG 159 HD2 -0.277 2.277
/A VAL 143 C /A GLU 145 H -0.283 2.983
/A TRP 147 HZ3 /A ILE 25 CG1 -0.284 2.984
/A TRP 147 HZ3 /A ILE 25 HD13 -0.286 2.286
/A GLU 153 O /A GLU 157 CG -0.287 3.467
/A SER 151 O /A GLU 153 N -0.287 2.992
/A TRP 147 HZ2 /A ALA 140 HB3 -0.287 2.287
/A VAL 150 O /A ILE 155 HD12 -0.288 2.768
/A TRP 147 CE3 /A ILE 25 CD1 -0.290 3.690
/A ASP 152 O /A ILE 155 HB -0.292 2.772
/A GLU 153 C /A GLU 157 H -0.295 2.995
/A GLU 156 HG3 /A GLN 160 HE22 -0.300 2.300
/A ILE 166 C /A ARG 168 H -0.301 3.001
/A TYR 169 CD2 /A THR 167 HG22 -0.302 3.002
/A VAL 150 HG13 /A GLU 154 HB3 -0.303 2.303
/A GLU 144 O /A TRP 147 HB3 -0.305 2.785
/A ILE 155 O /A ALA 158 HB1 -0.305 2.785
/A ARG 159 NH2 /A PRO 20 C -0.305 3.630
/A SER 151 H /A GLU 154 CD -0.306 3.006
/A LYS 161 H /A ARG 159 C -0.306 3.006
/A SER 151 HG /A GLU 154 HG2 -0.308 2.308
/A ILE 166 CG2 /A ARG 168 HG3 -0.308 3.008
/A VAL 143 H /A ALA 140 C -0.308 3.008
/A GLU 156 O /A GLN 160 N -0.309 3.014
/A GLN 160 H /A GLU 157 C -0.309 3.009
/A TRP 147 CZ3 /A ILE 25 HD13 -0.312 3.012
/A TRP 147 CZ2 /A ALA 140 CB -0.313 3.713
/A ILE 149 O /A VAL 150 O -0.313 3.273
/A THR 167 CG2 /A TYR 169 OH -0.314 3.514
/A ARG 168 CG /A ILE 166 HG21 -0.315 3.015
/A TRP 147 CZ2 /A ALA 140 HB3 -0.315 3.015
/A SER 151 CB /A GLU 154 OE2 -0.316 3.496
/A GLU 153 O /A GLU 157 CB -0.319 3.499
/A ARG 159 H /A GLU 156 C -0.321 3.021
/A GLU 144 CA /A ALA 140 O -0.322 3.502
/A TRP 147 CH2 /A ILE 14 HD12 -0.322 3.022
/A GLU 157 O /A GLN 160 HB2 -0.323 2.803
/A ILE 166 O /A ARG 168 N -0.324 3.029
/A VAL 150 O /A ILE 155 HG12 -0.324 2.804
/A TRP 147 HD1 /A GLU 144 CA -0.324 3.024
/A VAL 143 CG2 /A ALA 140 O -0.325 3.505
/A ILE 155 CG1 /A VAL 150 CG1 -0.327 3.727
/A TRP 147 HH2 /A ILE 14 CG1 -0.328 3.028
/A GLU 142 H /A ALA 139 C -0.329 3.029
/A TRP 147 CZ3 /A ILE 25 HD12 -0.329 3.029
/A ARG 159 H /A GLU 157 C -0.330 3.030
/A ILE 155 O /A ARG 159 N -0.332 3.037
/A GLU 156 H /A GLU 153 C -0.332 3.032
/A TYR 169 C /A ARG 57 CZ -0.333 3.733
/A LYS 141 HD3 /A ASP 137 OD1 -0.333 2.813
/A SER 151 O /A ILE 155 CG1 -0.334 3.514
/A ARG 168 H /A ILE 166 O -0.336 2.416
/A GLU 157 HB2 /A LYS 161 HZ2 -0.337 2.337
/A VAL 143 HG13 /A LEU 1 HD23 -0.338 2.338
/A GLU 144 H /A ALA 140 O -0.338 2.418
/A VAL 143 O /A GLU 145 N -0.339 3.044
/A SER 151 O /A GLU 154 CA -0.339 3.519
/A TRP 147 HZ3 /A ILE 25 HG12 -0.339 2.339
/A ILE 155 H /A GLU 153 C -0.340 3.040
/A TRP 147 HE1 /A VAL 143 HG22 -0.340 2.340
/A ALA 158 N /A GLU 154 O -0.343 3.048
/A GLU 153 O /A GLU 156 HB2 -0.343 2.823
/A ILE 149 O /A SER 151 CA -0.346 3.526
/A GLU 144 H /A GLU 142 C -0.346 3.046
/A ALA 162 H /A ARG 159 C -0.347 3.047
/A ASP 152 C /A GLU 156 H -0.350 3.050
/A SER 151 C /A GLU 154 N -0.355 3.680
/A SER 151 OG /A GLU 154 CB -0.356 3.556
/A GLU 157 HB3 /A GLU 154 O -0.356 2.836
/A THR 167 HG21 /A TYR 169 HH -0.357 2.357
/A TRP 147 HZ2 /A LEU 5 CD1 -0.358 3.058
/A LYS 161 H /A ALA 158 C -0.360 3.060
/A ALA 162 O /A PRO 163 O -0.361 3.321
/A ALA 158 HB2 /A GLU 154 O -0.365 2.845
/A ARG 159 NH2 /A PRO 20 CB -0.365 3.690
/A LYS 141 N /A ASP 137 O -0.369 3.074
/A TYR 169 C /A ARG 57 NE -0.373 3.698
/A ILE 166 CG2 /A ARG 168 CG -0.374 3.774
/A TRP 147 CD1 /A GLU 144 N -0.374 3.699
/A VAL 148 H /A GLU 146 C -0.375 3.075
/A VAL 143 HG23 /A ALA 140 HA -0.376 2.376
/A VAL 150 O /A ILE 155 CG1 -0.380 3.560
/A LYS 141 CB /A ASP 137 O -0.382 3.562
/A ILE 155 CG1 /A VAL 150 HG12 -0.382 3.082
/A VAL 143 HG23 /A ALA 140 C -0.384 3.084
/A TRP 147 H /A GLU 146 H -0.384 2.384
/A GLU 157 O /A LYS 161 N -0.388 3.093
/A GLU 144 CB /A ALA 140 O -0.389 3.569
/A THR 167 CG2 /A TYR 169 CD2 -0.391 3.791
/A SER 151 OG /A GLU 153 HB3 -0.392 2.892
/A VAL 143 C /A TRP 147 NE1 -0.393 3.718
/A GLU 142 CG /A GLU 138 O -0.396 3.576
/A TRP 147 CH2 /A ILE 14 CB -0.397 3.797
/A SER 151 HG /A GLU 154 CB -0.397 3.097
/A ARG 159 O /A ALA 162 HB3 -0.399 2.879
/A VAL 150 CA /A GLU 154 OE2 -0.399 3.579
/A LYS 141 NZ /A ASP 137 CG -0.400 3.725
270 contacts
> select clear
Alignment identifier is 1/A
> select /A:5-7,29-35,39-42,47-50,57-68,119-146,152-161
1112 atoms, 1107 bonds, 89 pseudobonds, 68 residues, 2 models selected
> select /A:146
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:143-146
61 atoms, 60 bonds, 9 pseudobonds, 4 residues, 2 models selected
> select /A:147
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:147-150
75 atoms, 76 bonds, 7 pseudobonds, 4 residues, 2 models selected
> close
> open
> /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_539.pdb
Chain information for best_model_539.pdb #1
---
Chain | Description
A | No description available
Drag select of 9 residues
> select add /A:149
162 atoms, 18 bonds, 10 residues, 1 model selected
> select add /A:151
177 atoms, 32 bonds, 11 residues, 1 model selected
> select add /A:153
201 atoms, 55 bonds, 12 residues, 1 model selected
> select add /A:152
211 atoms, 64 bonds, 13 residues, 1 model selected
> select add /A:154
228 atoms, 80 bonds, 14 residues, 1 model selected
> select add /A:155
250 atoms, 101 bonds, 15 residues, 1 model selected
> select add /A:156
260 atoms, 110 bonds, 16 residues, 1 model selected
Drag select of 8 residues
> select add /A:156
387 atoms, 110 bonds, 23 residues, 1 model selected
> delete sel
Drag select of 2 residues
> delete sel
> mlp
Map values for surface "best_model_539.pdb_A SES surface": minimum -25.4, mean
-3.628, maximum 24.45
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
> mlp
Map values for surface "best_model_539.pdb_A SES surface": minimum -25.4, mean
-3.628, maximum 24.45
To also show corresponding color key, enter the above mlp command and add key
true
> close
> open
> /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_539.pdb
> format pdb
Chain information for best_model_539.pdb #1
---
Chain | Description
A | No description available
Drag select of 3 residues
> select clear
Drag select of 13 residues
> select add /A:157
224 atoms, 14 bonds, 14 residues, 1 model selected
> select add /A:156
234 atoms, 23 bonds, 15 residues, 1 model selected
> select add /A:159
249 atoms, 37 bonds, 16 residues, 1 model selected
> select add /A:160
268 atoms, 55 bonds, 17 residues, 1 model selected
> select add /A:163
290 atoms, 77 bonds, 18 residues, 1 model selected
> select add /A:162
314 atoms, 100 bonds, 19 residues, 1 model selected
> select add /A:161
328 atoms, 113 bonds, 20 residues, 1 model selected
> select add /A:143
347 atoms, 131 bonds, 21 residues, 1 model selected
> select add /A:142
363 atoms, 146 bonds, 22 residues, 1 model selected
> select add /A:141
387 atoms, 171 bonds, 23 residues, 1 model selected
> ui tool show Contacts
> contacts sel reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
220 contacts
atom1 atom2 overlap distance
/A TRP 141 CZ2 /A TYR 105 CE2 0.438 2.962
/A TRP 141 CH2 /A TYR 105 CE2 0.414 2.986
/A ILE 149 CG2 /A ARG 153 HE 0.413 2.287
/A LYS 155 HZ1 /A GLU 151 OE1 0.323 1.757
/A TRP 141 CE3 /A MET 96 CE 0.282 3.118
/A GLU 151 H /A GLU 147 O 0.254 1.826
/A TRP 141 CH2 /A TYR 105 CZ 0.185 3.215
/A TRP 141 CE3 /A MET 96 HE1 0.178 2.522
/A ILE 143 H /A GLU 140 O 0.163 1.917
/A ALA 152 CB /A ILE 25 HA 0.147 2.553
/A TRP 141 C /A ILE 143 H 0.146 2.554
/A GLN 154 HE22 /A GLU 150 OE1 0.122 1.958
/A ALA 152 H /A GLU 148 O 0.109 1.971
/A GLU 148 OE2 /A SER 145 HG 0.107 1.973
/A ARG 153 HE /A ILE 149 HG23 0.095 1.905
/A TRP 141 CD2 /A MET 96 CE 0.094 3.306
/A GLU 150 H /A ASP 146 O 0.093 1.987
/A THR 161 H /A ASP 21 CG 0.089 2.611
/A GLU 151 OE1 /A LYS 155 NZ 0.086 2.619
/A TRP 141 CH2 /A TYR 105 CD2 0.081 3.319
/A TRP 141 HH2 /A TYR 105 CZ 0.077 2.623
/A SER 145 C /A GLU 147 H 0.074 2.626
/A TRP 141 CD2 /A MET 96 HE3 0.070 2.630
/A GLU 148 CD /A SER 145 HG 0.070 2.630
/A GLU 150 O /A GLN 154 H 0.057 2.023
/A PRO 157 C /A GLU 159 H 0.053 2.647
/A PRO 157 O /A PRO 20 HB2 0.049 2.431
/A ILE 149 CG2 /A ARG 153 NE 0.046 3.279
/A THR 161 HB /A ASP 21 OD2 0.045 2.435
/A ARG 153 H /A ILE 149 O 0.037 2.043
/A ALA 156 HA /A GLY 44 O 0.017 2.463
/A LYS 155 HZ3 /A GLU 40 O 0.013 2.067
/A ILE 149 O /A ARG 153 HG3 0.007 2.473
/A TRP 141 CZ2 /A TYR 105 HE2 0.006 2.694
/A ILE 149 O /A ARG 153 CG -0.003 3.183
/A ARG 153 HB3 /A GLU 150 O -0.010 2.490
/A ILE 143 H /A GLU 140 C -0.022 2.722
/A GLU 148 CG /A SER 145 HG -0.025 2.725
/A ARG 153 NH2 /A ARG 18 NH2 -0.030 3.280
/A GLU 148 H /A SER 145 OG -0.036 2.136
/A ASP 146 O /A GLU 150 CB -0.036 3.216
/A TYR 163 HD2 /A ARG 48 CD -0.046 2.746
/A SER 145 OG /A GLU 148 CG -0.046 3.246
/A GLU 150 O /A GLN 154 HG2 -0.048 2.528
/A GLU 151 O /A LYS 155 H -0.050 2.130
/A TYR 163 HD2 /A ARG 48 HD3 -0.053 2.053
/A SER 145 O /A ILE 149 H -0.055 2.135
/A ALA 152 CB /A ILE 25 HG21 -0.057 2.757
/A GLU 151 OE1 /A LYS 155 CE -0.059 3.239
/A GLU 159 O /A PRO 157 HB3 -0.063 2.543
/A ILE 143 HB /A GLU 140 O -0.069 2.549
/A TRP 141 CZ3 /A MET 96 HE1 -0.073 2.773
/A ILE 160 HG13 /A ASP 21 H -0.075 2.075
/A TRP 141 CZ2 /A TYR 105 CZ -0.076 3.476
/A LYS 155 NZ /A GLU 40 HA -0.079 2.704
/A ALA 152 O /A ALA 156 H -0.082 2.162
/A LYS 155 CB /A GLY 44 HA2 -0.083 2.783
/A VAL 142 H /A GLU 140 C -0.087 2.787
/A GLU 148 O /A ALA 152 CB -0.090 3.270
/A TRP 141 CZ3 /A MET 96 CE -0.090 3.490
/A SER 145 OG /A GLU 148 HG3 -0.098 2.598
/A TYR 163 CD2 /A ARG 48 HD3 -0.103 2.803
/A ILE 160 HA /A ASP 21 HB2 -0.107 2.107
/A TRP 141 HZ3 /A ILE 14 HG22 -0.110 2.110
/A PRO 157 O /A PRO 20 CB -0.111 3.291
/A ILE 143 HD11 /A GLU 140 CG -0.114 2.814
/A GLU 147 O /A GLU 151 N -0.119 2.824
/A ILE 143 CB /A GLU 140 O -0.121 3.301
/A ILE 149 HG13 /A VAL 144 HG12 -0.122 2.122
/A GLU 148 CD /A PHE 26 HD2 -0.128 2.828
/A SER 145 H /A GLU 148 OE2 -0.128 2.208
/A ARG 153 NE /A ILE 149 HG23 -0.129 2.754
/A VAL 144 CG2 /A ILE 14 HD11 -0.131 2.831
/A GLN 154 HE22 /A GLU 150 CD -0.131 2.831
/A LYS 155 HZ3 /A GLU 40 C -0.132 2.832
/A TRP 141 HZ2 /A TYR 105 CE2 -0.134 2.834
/A GLU 151 CD /A LYS 155 HZ1 -0.135 2.835
/A ARG 153 HE /A ILE 149 HG21 -0.142 2.142
/A GLN 154 NE2 /A GLU 150 HG2 -0.143 2.768
/A TRP 141 CE3 /A MET 96 HE3 -0.148 2.848
/A THR 161 N /A ASP 21 CG -0.152 3.477
/A VAL 144 CG2 /A ILE 14 CD1 -0.153 3.553
/A ARG 153 CG /A LEU 19 HD11 -0.159 2.859
/A TRP 141 CE2 /A MET 96 HE3 -0.165 2.865
/A THR 161 CB /A ASP 21 OD2 -0.166 3.346
/A ILE 143 N /A GLU 140 O -0.167 2.872
/A TRP 141 HH2 /A TYR 105 CE2 -0.175 2.875
/A PRO 157 HD3 /A GLY 44 O -0.176 2.656
/A GLU 148 OE1 /A PHE 26 CD2 -0.178 3.358
/A LYS 155 NZ /A GLU 40 CA -0.180 3.505
/A GLU 150 O /A GLN 154 CG -0.181 3.361
/A TRP 141 CZ2 /A TYR 105 CD2 -0.184 3.584
/A ALA 152 CB /A ILE 25 CA -0.186 3.586
/A ALA 152 O /A ALA 156 N -0.188 2.893
/A ARG 153 HH22 /A ARG 18 NH2 -0.189 2.814
/A ASP 146 O /A GLU 150 HB2 -0.190 2.670
/A GLU 151 O /A LYS 155 HG3 -0.191 2.671
/A VAL 144 HG22 /A ILE 14 CD1 -0.195 2.895
/A ALA 152 O /A ALA 156 HB1 -0.195 2.675
/A ASP 146 O /A GLU 150 N -0.208 2.913
/A GLU 151 O /A GLN 154 HB2 -0.211 2.691
/A PRO 157 O /A PRO 20 CG -0.214 3.394
/A PRO 157 CB /A GLU 159 O -0.214 3.394
/A LEU 158 C /A GLU 159 HG3 -0.214 2.914
/A TYR 163 CD2 /A ARG 48 CD -0.215 3.615
/A ARG 153 NH1 /A LEU 19 HD23 -0.215 2.840
/A ARG 153 CG /A LEU 19 CD1 -0.217 3.617
/A ILE 143 O /A SER 145 N -0.224 2.929
/A LYS 155 HD3 /A LEU 43 O -0.226 2.706
/A ALA 156 CB /A PRO 23 HG3 -0.231 2.931
/A PRO 157 CD /A GLY 44 O -0.232 3.412
/A VAL 144 CG1 /A ILE 149 HG13 -0.233 2.933
/A LYS 155 CD /A LEU 43 O -0.234 3.414
/A ARG 153 HG2 /A LEU 19 CD1 -0.237 2.937
/A ILE 160 HG13 /A ASP 21 N -0.237 2.862
/A LYS 155 HZ3 /A GLU 40 CA -0.239 2.939
/A ILE 149 O /A ARG 153 N -0.242 2.947
/A ARG 153 CB /A GLU 150 O -0.244 3.424
/A GLU 148 OE1 /A PHE 26 HD2 -0.246 2.726
/A ILE 149 O /A ARG 153 CB -0.248 3.428
/A GLU 148 O /A ALA 152 N -0.251 2.956
/A ILE 149 HG12 /A ILE 25 HD11 -0.252 2.252
/A THR 161 H /A ASP 21 CB -0.254 2.954
/A GLU 147 O /A GLU 151 CB -0.254 3.434
/A ALA 156 H /A ARG 153 C -0.254 2.954
/A LEU 158 O /A GLU 159 CG -0.255 3.435
/A ALA 152 HB1 /A ILE 25 HA -0.255 2.255
/A GLU 151 O /A LYS 155 CG -0.255 3.435
/A GLN 154 NE2 /A GLU 150 OE1 -0.256 2.961
/A PRO 157 O /A PRO 20 HG3 -0.257 2.737
/A ALA 152 HB2 /A ILE 24 O -0.262 2.742
/A TRP 141 CZ3 /A ILE 14 HG22 -0.264 2.964
/A SER 145 OG /A GLU 148 CB -0.268 3.468
/A SER 145 OG /A GLU 148 CD -0.270 3.470
/A TRP 141 HZ2 /A TYR 105 HH -0.274 2.274
/A ILE 143 HD11 /A GLU 140 HG3 -0.275 2.275
/A ALA 152 O /A ALA 156 CB -0.276 3.456
/A ILE 143 CD1 /A GLU 140 HA -0.278 2.978
/A GLU 148 HB3 /A ILE 25 O -0.279 2.759
/A LYS 155 H /A ALA 152 C -0.280 2.980
/A ARG 153 H /A GLU 150 C -0.280 2.980
/A ARG 153 O /A ALA 156 HB2 -0.281 2.761
/A TRP 141 HH2 /A TYR 105 CE1 -0.281 2.981
/A GLU 150 O /A GLN 154 N -0.284 2.989
/A GLU 148 OE2 /A PHE 26 HD2 -0.286 2.766
/A ILE 160 HA /A ASP 21 CB -0.286 2.986
/A ARG 153 HG2 /A LEU 19 HD23 -0.290 2.290
/A ASP 146 O /A ILE 149 HB -0.292 2.772
/A VAL 144 HG22 /A ILE 14 HD11 -0.294 2.294
/A GLU 150 CG /A GLN 154 NE2 -0.294 3.619
/A LYS 155 HZ3 /A GLU 40 HA -0.294 2.294
/A GLU 148 OE1 /A PHE 26 CE2 -0.295 3.475
/A GLU 147 C /A GLU 151 H -0.296 2.996
/A ARG 153 HA /A LEU 19 HD13 -0.296 2.296
/A GLU 159 O /A PRO 157 CG -0.297 3.477
/A ALA 152 HB2 /A ILE 25 HG21 -0.297 2.297
/A VAL 144 CG1 /A ILE 149 CG1 -0.297 3.697
/A ILE 149 CG1 /A VAL 144 HG12 -0.298 2.998
/A GLU 150 HA /A ARG 153 HD3 -0.299 2.299
/A ILE 143 CA /A GLU 140 O -0.303 3.483
/A ALA 156 HA /A PRO 157 HD2 -0.309 2.309
/A LYS 155 HB3 /A GLY 44 HA2 -0.309 2.309
/A TYR 163 CE2 /A ARG 48 HD3 -0.312 3.012
/A GLU 150 CG /A GLN 154 HE22 -0.312 3.012
/A SER 145 O /A GLU 148 HB2 -0.312 2.792
/A ARG 153 HG2 /A LEU 19 HD11 -0.315 2.315
/A ASP 146 C /A GLU 150 H -0.318 3.018
/A ILE 160 HG22 /A ASP 21 OD1 -0.319 2.799
/A ALA 156 O /A PRO 157 O -0.319 3.279
/A GLU 148 CD /A PHE 26 CD2 -0.321 3.721
/A ALA 152 CB /A ILE 25 CG2 -0.324 3.724
/A ILE 149 HG13 /A SER 145 O -0.324 2.804
/A TRP 141 CZ3 /A VAL 144 HG22 -0.325 3.025
/A LYS 155 H /A ARG 153 C -0.326 3.026
/A GLU 148 HG3 /A SER 145 HG -0.327 2.327
/A GLU 150 H /A GLU 147 C -0.329 3.029
/A ARG 153 HG2 /A LEU 19 CD2 -0.330 3.030
/A THR 161 H /A ASP 21 HB2 -0.334 2.334
/A ALA 156 H /A GLN 154 C -0.334 3.034
/A ILE 149 O /A ARG 153 CD -0.334 3.514
/A LYS 155 NZ /A GLU 40 O -0.335 3.040
/A GLU 151 O /A LYS 155 N -0.336 3.041
/A VAL 144 HG11 /A PHE 26 HB3 -0.339 2.339
/A ALA 152 HB2 /A ILE 25 HA -0.339 2.339
/A ALA 152 O /A GLY 44 HA3 -0.346 2.826
/A LYS 155 O /A ALA 156 O -0.347 3.307
/A GLU 148 OE2 /A SER 145 OG -0.348 2.928
/A ILE 143 H /A VAL 144 H -0.349 2.349
/A GLU 147 O /A GLU 150 HB3 -0.350 2.830
/A ALA 156 CA /A GLY 44 O -0.353 3.533
/A ALA 152 HB3 /A ILE 25 HG21 -0.354 2.354
/A GLN 154 H /A GLU 151 C -0.356 3.056
/A LYS 155 C /A GLY 44 HA2 -0.359 3.059
/A ILE 160 O /A ARG 162 N -0.359 3.064
/A GLU 148 O /A ALA 152 HB1 -0.360 2.840
/A GLU 150 HA /A ARG 153 HB3 -0.362 2.362
/A ARG 153 HH21 /A ARG 18 NH2 -0.363 2.988
/A GLU 151 OE1 /A LYS 155 HE3 -0.363 2.843
/A GLU 148 CB /A SER 145 HG -0.367 3.067
/A TRP 141 HZ2 /A TYR 105 HE2 -0.368 2.368
/A GLU 159 H /A PRO 157 HB3 -0.370 2.370
/A ALA 152 O /A GLY 44 CA -0.370 3.550
/A TRP 141 CH2 /A TYR 105 CE1 -0.370 3.770
/A GLU 148 C /A ALA 152 H -0.373 3.073
/A ARG 153 H /A GLU 151 C -0.373 3.073
/A GLU 151 O /A LYS 155 CB -0.378 3.558
/A SER 145 OG /A GLU 148 N -0.381 3.106
/A LYS 155 NZ /A GLU 40 C -0.382 3.707
/A GLN 154 HE22 /A GLU 150 HG2 -0.384 2.384
/A ILE 149 C /A ARG 153 H -0.385 3.085
/A SER 145 C /A GLU 148 H -0.389 3.089
/A ILE 149 H /A GLU 147 C -0.389 3.089
/A ILE 149 HG12 /A ILE 25 CD1 -0.392 3.092
/A GLU 150 O /A GLU 151 O -0.393 3.353
/A ILE 149 CG1 /A SER 145 O -0.394 3.574
/A LYS 155 CB /A LEU 43 O -0.396 3.576
/A PRO 157 CG /A ASP 21 CB -0.398 3.798
/A ILE 143 N /A GLU 140 C -0.398 3.723
/A TRP 141 CE2 /A MET 96 CE -0.398 3.798
/A ILE 143 CG1 /A GLU 140 HA -0.399 3.099
220 contacts
> select clear
Alignment identifier is 1/A
> select /A:138
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:138-141
69 atoms, 70 bonds, 4 residues, 1 model selected
> select /A:137
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:137-141
85 atoms, 86 bonds, 5 residues, 1 model selected
> select /A:140
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:140-141
39 atoms, 40 bonds, 2 residues, 1 model selected
> ui tool show AlphaFold
> alphafold predict
> LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAVEEEWVIVSDEEIEEARQKAPLEITRY
Running AlphaFold prediction
> close
> open /Users/chenyang/Desktop/fbp1.cxs format session
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #3, grid size 128,188,163, pixel
0.681,0.684,0.68, shown at level 1.5, step 1, values float32
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #5, grid size
128,188,163, pixel 0.681,0.684,0.68, shown at level 0.412, step 1, values
float32
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #6, grid size
128,188,163, pixel 0.681,0.684,0.68, shown at level 0.208, step 1, values
float32
opened ChimeraX session
> hide #* target a
> show #1,3-6 target ab
> hide #4#!1 cartoons
> close
> open /Users/chenyang/Desktop/fbp1.cxs format session
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #3, grid size 128,188,163, pixel
0.681,0.684,0.68, shown at level 1.5, step 1, values float32
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #5, grid size
128,188,163, pixel 0.681,0.684,0.68, shown at level 0.412, step 1, values
float32
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #6, grid size
128,188,163, pixel 0.681,0.684,0.68, shown at level 0.208, step 1, values
float32
opened ChimeraX session
> close #4
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> volume style mesh
> show #!2 models
> hide #!2 models
> close
> open "/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
> 10/FBP1_R50A_refine_10.pdb"
Summary of feedback from opening /Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
10/FBP1_R50A_refine_10.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2022-01-10 Time 22:38:17 CST +0800 (1641825497.80 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/media/Elements_/BL18/2022/caoyu/good/caolab001_13/cao/output.sca
42 messages similar to the above omitted
Chain information for FBP1_R50A_refine_10.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open "/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
> 10/FBP1_R50A_refine_10_2mFo-DFc.ccp4"
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #2, grid size 128,188,163, pixel
0.681,0.684,0.68, shown at level 3.49, step 1, values float32
> volume #2 level 1.5
> volume style mesh
> transparency 50
> volume showOutlineBox true
> volume showOutlineBox false
> volume step 2
> volume step 1
> volume step 2
> volume step 1
> vop gaussian #2 sdev 2.05
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #3, grid size
128,188,163, pixel 0.681,0.684,0.68, shown at step 1, values float32
> surface dust #3 size 6.84
> undo
> close #3
> show #!2 models
> fitmap #1 inMap #2
Fit molecule FBP1_R50A_refine_10.pdb (#1) to map FBP1_R50A_refine_10_2mFo-
DFc.ccp4 (#2) using 9250 atoms
average map value = 2.813, steps = 40
shifted from previous position = 0.00374
rotated from previous position = 0.00554 degrees
atoms outside contour = 1097, contour level = 1.5
Position of FBP1_R50A_refine_10.pdb (#1) relative to FBP1_R50A_refine_10_2mFo-
DFc.ccp4 (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00001379 -0.00003225 0.00093168
0.00001379 1.00000000 -0.00009016 -0.00229194
0.00003225 0.00009016 1.00000000 -0.00586216
Axis 0.93196568 -0.33335243 0.14253467
Axis point 0.00000000 66.28018853 -22.47865262
Rotation angle (degrees) 0.00554272
Shift along axis 0.00079676
> fitmap #1 inMap #2
Fit molecule FBP1_R50A_refine_10.pdb (#1) to map FBP1_R50A_refine_10_2mFo-
DFc.ccp4 (#2) using 9250 atoms
average map value = 2.813, steps = 44
shifted from previous position = 0.00984
rotated from previous position = 0.0131 degrees
atoms outside contour = 1100, contour level = 1.5
Position of FBP1_R50A_refine_10.pdb (#1) relative to FBP1_R50A_refine_10_2mFo-
DFc.ccp4 (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00000714 0.00003105 0.00073557
0.00000713 0.99999999 0.00012920 0.00374498
-0.00003105 -0.00012920 0.99999999 0.00637562
Axis -0.97092271 0.23330833 0.05363122
Axis point 0.00000000 49.14151613 -28.07758643
Rotation angle (degrees) 0.00762419
Shift along axis 0.00050148
> close #2
> open "/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
> 10/FBP1_R50A_refine_10_2mFo-DFc.ccp4"
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #2, grid size 128,188,163, pixel
0.681,0.684,0.68, shown at level 3.49, step 1, values float32
> transparency 50
> volume style image
> volume style mesh
> volume #2 style image
> volume #2 level 1.5,0 level 3.492,0.8 level 8.163,1
> volume #2 maximumIntensityProjection true
> volume #2 region 0,0,81,127,187,81 step 1 maximumIntensityProjection false
> showOutlineBox true
> volume #2 region 0,0,0,127,187,162 step 1
> volume #2 style mesh region 0,0,0,127,187,162 step 1
> volume #2 level 1.5
> volume #2 color #00f900
> volume #2 color #fffb00
> volume #2 color #00fdff
> hide cartoons
> show atoms
> ui tool show "Color Zone"
Drag select of 1 bonds
Drag select of 3 atoms, 2 bonds, 2 FBP1_R50A_refine_10_2mFo-DFc.ccp4
> select clear
Drag select of 4 atoms, 4 bonds, 2 FBP1_R50A_refine_10_2mFo-DFc.ccp4
> select clear
Drag select of 5 atoms, 5 bonds
> color zone #2 near sel distance 4.08
> show #2.2 models
> color zone #2 near sel distance 4.08
> color single #2
> color zone #2 near sel distance 4.08
> volume splitbyzone #2
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 0 as #3.1, grid size 128,188,163,
pixel 0.681,0.684,0.68, shown at step 1, values float32
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 1 as #3.2, grid size 128,188,163,
pixel 0.681,0.684,0.68, shown at step 1, values float32
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 2 as #3.3, grid size 128,188,163,
pixel 0.681,0.684,0.68, shown at step 1, values float32
> color zone #2 near sel distance 4.08
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.2 models
> show #!3.2 models
> help help:user/tools/colorzone.html
> close
> open /Users/chenyang/Desktop/fbp1.cxs format session
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #3, grid size 128,188,163, pixel
0.681,0.684,0.68, shown at level 1.5, step 1, values float32
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #5, grid size
128,188,163, pixel 0.681,0.684,0.68, shown at level 0.412, step 1, values
float32
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #6, grid size
128,188,163, pixel 0.681,0.684,0.68, shown at level 0.208, step 1, values
float32
opened ChimeraX session
> close
> open 7cvh format mmcif fromDatabase pdb
7cvh title:
Human Fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate
[more info...]
Chain information for 7cvh #1
---
Chain | Description | UniProt
A B C D | Fructose-1,6-bisphosphatase 1 | F16P1_HUMAN
Non-standard residues in 7cvh #1
---
AMP — adenosine monophosphate
FBP — 1,6-di-O-phosphono-beta-D-fructofuranose (BETA-FRUCTOSE-1,6-DIPHOSPHATE;
FRUCTOSE-1,6-BISPHOSPHATE; 1,6-di-O-phosphono-beta-D-fructose; 1,6-di-O-
phosphono-D-fructose; 1,6-di-O-phosphono-fructose)
GRG — geranylgeranyl diphosphate
MG — magnesium ion
> open "/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
> 10/FBP1_R50A_refine_10_2mFo-DFc.ccp4"
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #2, grid size 128,188,163, pixel
0.681,0.684,0.68, shown at level 3.49, step 1, values float32
> open "/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
> 10/FBP1_R50A_refine_10.pdb"
Summary of feedback from opening /Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
10/FBP1_R50A_refine_10.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2022-01-10 Time 22:38:17 CST +0800 (1641825497.80 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/media/Elements_/BL18/2022/caoyu/good/caolab001_13/cao/output.sca
42 messages similar to the above omitted
Chain information for FBP1_R50A_refine_10.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> hide #!1 models
> volume style mesh
> volume #2 level 1.5
> volume step 2
> transparency 50
> volume zone #2 nearAtoms #3 range 4.1
> undo
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> hide #!1 models
> volume zone #2 nearAtoms #3 range 4.1
> undo
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> close
> open "/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
> 10/FBP1_R50A_refine_10.pdb"
Summary of feedback from opening /Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
10/FBP1_R50A_refine_10.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2022-01-10 Time 22:38:17 CST +0800 (1641825497.80 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/media/Elements_/BL18/2022/caoyu/good/caolab001_13/cao/output.sca
42 messages similar to the above omitted
Chain information for FBP1_R50A_refine_10.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open "/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine
> 10/FBP1_R50A_refine_10_2mFo-DFc.ccp4"
Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #2, grid size 128,188,163, pixel
0.681,0.684,0.68, shown at level 3.49, step 1, values float32
> volume zone #2 nearAtoms #1 range 4.1
> undo
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #2 nearAtoms #1 range 4.1
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume style mesh
> volume #2 level 2
> transparency 50
> ui tool show AlphaFold
No sequence chosen for AlphaFold predict
> help help:user/tools/alphafold.html
No sequence chosen for AlphaFold search
No sequence chosen for AlphaFold match
> alphafold predict
> LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAVEEEWVIVSDEEIEEARQKAPLEITRY
Running AlphaFold prediction
> ui tool show "Volume Viewer"
> transparency 0
> transparency 50
> help help:user
Chain information for best_model.pdb #3
---
Chain | Description
A | No description available
AlphaFold prediction finished
Results in /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:
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: 16 GB
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 6 days 20:22
Graphics/Displays:
Apple G13G:
Chipset Model: Apple G13G
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: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
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: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
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: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
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
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
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: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
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: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
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: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (8)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → UI |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash handling tool window closeEvent after AlphaFold prediction finishes |
follow-up: 2 comment:2 by , 4 years ago
No. Only the user can close the AlphaFold run panel by pressing its window frame close button or by quitting ChimeraX. When a prediction completes the result is downloaded automatically via an html hook, but the panel with all its log info is still shown.
comment:3 by , 4 years ago
Crashed when the user closed a tool window by clicking the close button on the window frame, probably the AlphaFold run Google Colab panel. Here is the line that crashed in ui/gui.py calling QMainWindow.removeDockWidget()
self.main_window.removeDockWidget(self.dock_widget)
And the last line of Log output shows an AlphaFold prediction result had just been returned and displayed in ChimeraX
AlphaFold prediction finished
Results in /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_3
That is why I think it was probably closing the AlphaFold Colab panel, but there is not other evidence for that.
The C++ stack trace has all kinds of crazy thread stuff, message pump stuff, .... The Colab panel is a Qt html widget and the Colab web site is no doubt running some fancy Javascript for the web page being displayed. Maybe the crash is caused by trying to close the window when some Javascript is executing.
We have seen many crash reports ending with an alphafold prediction and this may be the cause of all of them, that simply closing the panel crashes sometimes. I have never had it crash on me, and have probably closed that panel 100 times. But it may require the right timing when closing it to crash since the Colab web page must periodically be querying the Colab virtual machine Python job for new output.
This seems like a bug in Qt. But maybe there is some mandatory step we are not doing for shutting down a QWebEngineView cleanly. I doubt that but can peruse the QWebEngineView docs. It may be that we can work around the Qt bug by maybe hiding the panel, switching the URL so it is not showing the colab page, and waiting a few seconds, then closing the panel. But I have no test case to reproduce the bug so this is shooting in the dark.
comment:4 by , 4 years ago
There have been 19 ChimeraX crashes reported with QMainWindow.removeDockWidget() in the C++ stack trace going back to 2019.
Qt 5 docs says removeDockWidget just removes the widget from the window layout and does not delete it. Does not seem too dangerous.
void QMainWindow::removeDockWidget(QDockWidget *dockwidget) Removes the dockwidget from the main window layout and hides it. Note that the dockwidget is not deleted.
comment:5 by , 4 years ago
The crash report also says something about the native macOS call, maybe the one that was in process during the crash
"asi" : {"AppKit":Calling windowShouldClose: on the delegate for the QNSPanel 0x7fb55f36f020},
comment:6 by , 4 years ago
I would normally think that it's somehow a dock widget that's already dead being removed, hence the crash, but there are several Qt calls involving the dock widget just before the removeDockWidget() call, so that doesn't seem to be it.
I assume the floating tool window is actually a QNSPanel, and that Qt has registered as a delegate for that panel and therefore AppKit is handing off wndowShouldClose (i.e. close button got clicked) to it, which eventually gets down to our code with the removeDockWidget() call.
follow-up: 7 comment:7 by , 4 years ago
I am somewhat surprised that the Qt bug reporter does not have any relevant bug report about removeDockWidget. The closest I founds was an ancient Qt 4 bug https://bugreports.qt.io/browse/QTBUG-15897 This suggests to me that we may be doing something weird if only we see this kind of crash (and we have 19 reports of crashes in removeDockWidget). What are we doing I wonder with QDockWidget that is weird?
comment:8 by , 4 years ago
I experimented with not calling removeDockWidget() for a floating tool. The tool disappears but remains in the list of tools you get by clicking on other tools' title bars, and if you choose the closed tool it reappears, and closing that produces errors.
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Does Alphafold predict close its tool window when it finishes? If so, how does it go about that?