![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15755 closed defect (can't reproduce)
Crash in QTimer event callback
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00007ff84944db40 (most recent call first):
File ???
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{
"uptime" : 140000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 1707,
"osVersion" : {
"train" : "macOS 14.1",
"build" : "23B74",
"releaseType" : "User"
},
"captureTime" : "2024-08-09 17:58:00.3150 -0400",
"codeSigningMonitor" : 0,
"incident" : "826AF9D8-131C-40DF-AC20-396324F04D95",
"pid" : 39557,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-09 15:46:26.5246 -0400",
"procStartAbsTime" : 139816424321882,
"procExitAbsTime" : 147709964354217,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"91518230-79F8-5D14-8F16-2578D280AEDD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FDC29741-6154-3BE4-FA2A-E996A55D5BE5",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 390,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sleepWakeUUID" : "6F695788-045B-4617-BF12-5E9F06C3EC83",
"sip" : "enabled",
"vmRegionInfo" : "0x19b5d8840 is not in any region. Bytes after previous region: 440031297 Bytes before following region: 105546214700992\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 180ab2000-181233000 [ 7684K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffe7edcd000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000000019b5d8840","rawCodes":[1,6901565504],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000019b5d8840"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":39557},
"vmregioninfo" : "0x19b5d8840 is not in any region. Bytes after previous region: 440031297 Bytes before following region: 105546214700992\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 180ab2000-181233000 [ 7684K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffe7edcd000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20243005epac2_sur1_Zhao_binding_site_models/lig_Epac2_Zhao_2013_binding_site_AlphaFoldQ8WZA2_v4.pdb"
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20243005epac2_sur1_Zhao_binding_site_models/lig_Epac2_Zhao_2013_binding_site_AlphaFoldQ8WZA2_v4.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for lig_Epac2_Zhao_2013_binding_site_AlphaFoldQ8WZA2_v4.pdb
#1
---
Chain | Description
A | No description available
> set bgColor white
> close
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking
> Models/20242905_epac2_sur1_whole_dock/EPAC2_AF_lig.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20242905_epac2_sur1_whole_dock/EPAC2_AF_lig.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for EPAC2_AF_lig.pdb #1
---
Chain | Description
A | No description available
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking
> Models/20242905_epac2_sur1_whole_dock/SUR1_7s5v_rec.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20242905_epac2_sur1_whole_dock/SUR1_7s5v_rec.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for SUR1_7s5v_rec.pdb #2
---
Chain | Description
E | No description available
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color light gray
> ui tool show "Show Sequence Viewer"
> interfaces
0 buried areas:
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/E
Alignment identifier is 2/E
> hide #1 models
> view
> select
> #2/E:35-50,72-98,109-129,134-156,168-191,225-229,232-239,260-272,285-295,297-328,349-352,357-402,415-423,425-433,436-456,459-461,466-499,501-512,516-564,574-586,591-600,606-615,720-727,784-788,796-805,809-813,818-820,832-843,862-873,891-896,914-921,924-929,999-1006,1010-1032,1038-1041,1069-1072,1080-1105,1110-1115,1118-1134,1136-1154,1162-1165,1169-1194,1197-1209,1211-1217,1220-1271,1279-1294,1296-1320,1385-1392,1415-1418,1436-1440,1449-1456,1461-1464,1477-1479,1485-1497,1514-1527,1563-1567,1573-1577
7674 atoms, 7748 bonds, 794 residues, 1 model selected
> select #2/E:5
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/E:5-168
1436 atoms, 1474 bonds, 2 pseudobonds, 152 residues, 2 models selected
> select
> #2/E:35-50,72-98,109-129,134-156,168-191,225-229,232-239,260-272,285-295,297-328,349-352,357-402,415-423,425-433,436-456,459-461,466-499,501-512,516-564,574-586,591-600,606-615,720-727,784-788,796-805,809-813,818-820,832-843,862-873,891-896,914-921,924-929,999-1006,1010-1032,1038-1041,1069-1072,1080-1105,1110-1115,1118-1134,1136-1154,1162-1165,1169-1194,1197-1209,1211-1217,1220-1271,1279-1294,1296-1320,1385-1392,1415-1418,1436-1440,1449-1456,1461-1464,1477-1479,1485-1497,1514-1527,1563-1567,1573-1577
7674 atoms, 7748 bonds, 794 residues, 1 model selected
> select clear
> select #2/E:860-861
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/E:860
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select 882
Expected an objects specifier or a keyword
> select SUR1_7s5v_rec.pdb 882
Expected an objects specifier or a keyword
> select #2 882
Expected a keyword
> select #2 r882
Expected a keyword
> select #2/E:861
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:861
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/E:878-879
26 atoms, 25 bonds, 2 residues, 1 model selected
> select #2/E:878-879
26 atoms, 25 bonds, 2 residues, 1 model selected
> select #2/E:882
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/E:882
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel red
> close #1#2
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency Models/SUR1_Frequency.cif"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/SUR1_Frequency.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
notes | Fetching CCD ADP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif
Chain information for SUR1_Frequency.cif #1
---
Chain | Description
E | No description available
> close #1
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking
> Models/20242905_epac2_sur1_whole_dock/SUR1_7s5v_rec.pdb" format pdb
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20242905_epac2_sur1_whole_dock/SUR1_7s5v_rec.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for SUR1_7s5v_rec.pdb #1
---
Chain | Description
E | No description available
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> undo
> set bgColor white
Alignment identifier is 1/E
> select
> /E:709-713,771-773,850-853,883-887,899-904,907-912,1346-1348,1350-1353,1362-1365,1374-1379,1397-1400,1402-1404,1423-1425,1502-1506,1532-1536,1549-1552,1557-1561
708 atoms, 700 bonds, 75 residues, 1 model selected
> select
> /E:35-50,72-98,109-129,134-156,168-191,225-229,232-239,260-272,285-295,297-328,349-352,357-402,415-423,425-433,436-456,459-461,466-499,501-512,516-564,574-586,591-600,606-615,720-727,784-788,796-805,809-813,818-820,832-843,862-873,891-896,914-921,924-929,999-1006,1010-1032,1038-1041,1069-1072,1080-1105,1110-1115,1118-1134,1136-1154,1162-1165,1169-1194,1197-1209,1211-1217,1220-1271,1279-1294,1296-1320,1385-1392,1415-1418,1436-1440,1449-1456,1461-1464,1477-1479,1485-1497,1514-1527,1563-1567,1573-1577
7674 atoms, 7748 bonds, 794 residues, 1 model selected
> select
> /E:35-50,72-98,109-129,134-156,168-191,225-229,232-239,260-272,285-295,297-328,349-352,357-402,415-423,425-433,436-456,459-461,466-499,501-512,516-564,574-586,591-600,606-615,720-727,784-788,796-805,809-813,818-820,832-843,862-873,891-896,914-921,924-929,999-1006,1010-1032,1038-1041,1069-1072,1080-1105,1110-1115,1118-1134,1136-1154,1162-1165,1169-1194,1197-1209,1211-1217,1220-1271,1279-1294,1296-1320,1385-1392,1415-1418,1436-1440,1449-1456,1461-1464,1477-1479,1485-1497,1514-1527,1563-1567,1573-1577
7674 atoms, 7748 bonds, 794 residues, 1 model selected
> select /E:160-163
18 atoms, 16 bonds, 1 pseudobond, 2 residues, 2 models selected
> select
> /E:35-50,72-98,109-129,134-156,168-191,225-229,232-239,260-272,285-295,297-328,349-352,357-402,415-423,425-433,436-456,459-461,466-499,501-512,516-564,574-586,591-600,606-615,720-727,784-788,796-805,809-813,818-820,832-843,862-873,891-896,914-921,924-929,999-1006,1010-1032,1038-1041,1069-1072,1080-1105,1110-1115,1118-1134,1136-1154,1162-1165,1169-1194,1197-1209,1211-1217,1220-1271,1279-1294,1296-1320,1385-1392,1415-1418,1436-1440,1449-1456,1461-1464,1477-1479,1485-1497,1514-1527,1563-1567,1573-1577
7674 atoms, 7748 bonds, 794 residues, 1 model selected
> select /E:160-218
573 atoms, 581 bonds, 1 pseudobond, 57 residues, 2 models selected
> select clear
> color white
> select /E:599
17 atoms, 16 bonds, 1 residue, 1 model selected
> select
> /E:35-50,72-98,109-129,134-156,168-191,225-229,232-239,260-272,285-295,297-328,349-352,357-402,415-423,425-433,436-456,459-461,466-499,501-512,516-564,574-586,591-600,606-615,720-727,784-788,796-805,809-813,818-820,832-843,862-873,891-896,914-921,924-929,999-1006,1010-1032,1038-1041,1069-1072,1080-1105,1110-1115,1118-1134,1136-1154,1162-1165,1169-1194,1197-1209,1211-1217,1220-1271,1279-1294,1296-1320,1385-1392,1415-1418,1436-1440,1449-1456,1461-1464,1477-1479,1485-1497,1514-1527,1563-1567,1573-1577
7674 atoms, 7748 bonds, 794 residues, 1 model selected
> select /E:599-677
245 atoms, 244 bonds, 1 pseudobond, 25 residues, 2 models selected
> select
> /E:35-50,72-98,109-129,134-156,168-191,225-229,232-239,260-272,285-295,297-328,349-352,357-402,415-423,425-433,436-456,459-461,466-499,501-512,516-564,574-586,591-600,606-615,720-727,784-788,796-805,809-813,818-820,832-843,862-873,891-896,914-921,924-929,999-1006,1010-1032,1038-1041,1069-1072,1080-1105,1110-1115,1118-1134,1136-1154,1162-1165,1169-1194,1197-1209,1211-1217,1220-1271,1279-1294,1296-1320,1385-1392,1415-1418,1436-1440,1449-1456,1461-1464,1477-1479,1485-1497,1514-1527,1563-1567,1573-1577
7674 atoms, 7748 bonds, 794 residues, 1 model selected
Position Coverage for "Copy of structure helices"
---
Alignment | 31-46,58-84,95-115,120-142,152-175,209-213,216-223,244-256,261-271,273-304,312-315,320-365,378-386,388-396,399-419,422-424,429-462,464-475,479-527,537-549,554-563,569-578,629-636,669-673,681-690,694-698,703-705,717-728,747-758,776-781,799-806,809-814,832-839,843-865,871-874,884-887,895-920,925-930,933-949,951-969,977-980,984-1009,1012-1024,1026-1032,1035-1086,1094-1109,1111-1135,1200-1207,1230-1233,1251-1255,1264-1271,1276-1279,1292-1294,1300-1312,1329-1342,1378-1382,1388-1392
chain E | 35-50,62-88,99-119,124-146,156-179,213-217,220-227,248-260,265-275,277-308,316-319,324-369,382-390,392-400,403-423,426-428,433-466,468-479,483-531,541-553,558-567,573-582,633-640,673-677,685-694,698-702,707-709,721-732,751-762,780-785,803-810,813-818,836-843,847-869,875-878,888-891,899-924,929-934,937-953,955-973,981-984,988-1013,1016-1028,1030-1036,1039-1090,1098-1113,1115-1139,1204-1211,1234-1237,1255-1259,1268-1275,1280-1283,1296-1298,1304-1316,1333-1346,1382-1386,1392-1396
/E | VAL 35-ILE 50,HIS 72-GLY 98,MET 109-GLU 129,PRO 134-VAL 156,LEU 168-ILE 191,LEU 225-GLY 229,TRP 232-LYS 239,ALA 260-ASP 272,ALA 285-ALA 295,GLY 297-LEU 328,SER 349-PHE 352,TYR 357-HIS 402,ALA 415-ALA 423,ASP 425-PHE 433,CYS 436-ILE 456,VAL 459-ALA 461,ALA 466-GLN 499,ASN 501-LEU 512,GLU 516-VAL 564,PRO 574-ILE 586,LEU 591-SER 600,VAL 606-LEU 615,LYS 720-ALA 727,VAL 784-ILE 788,LYS 796-ALA 805,GLN 809-ASP 813,GLY 818-GLN 820,GLY 832-ALA 843,ILE 862-ILE 873,LEU 891-HIS 896,LEU 914-GLU 921,LEU 924-LYS 929,ARG 999-SER 1006,ILE 1010-TYR 1032,THR 1038-ALA 1041,THR 1069-CYS 1072,LEU 1080-ILE 1105,MET 1110-THR 1115,LEU 1118-GLN 1134,ILE 1136-LEU 1154,PRO 1162-LEU 1165,LEU 1169-ASP 1194,GLN 1197-GLU 1209,LEU 1211-PHE 1217,GLU 1220-SER 1271,GLY 1279-TYR 1294,ASN 1296-LYS 1320,LYS 1385-PHE 1392,LEU 1415-LEU 1418,ILE 1436-LEU 1440,SER 1449-GLU 1456,LYS 1461-VAL 1464,GLU 1477-GLY 1479,GLY 1485-VAL 1497,MET 1514-ALA 1527,PRO 1563-LEU 1567,VAL 1573-PHE 1577
> select /E:410
9 atoms, 8 bonds, 1 residue, 1 model selected
> select
> /E:35-50,72-98,109-129,134-156,168-191,225-229,232-239,260-272,285-295,297-328,349-352,357-402,415-423,425-433,436-456,459-461,466-499,501-512,516-564,574-586,591-600,606-615,720-727,784-788,796-805,809-813,818-820,832-843,862-873,891-896,914-921,924-929,999-1006,1010-1032,1038-1041,1069-1072,1080-1105,1110-1115,1118-1134,1136-1154,1162-1165,1169-1194,1197-1209,1211-1217,1220-1271,1279-1294,1296-1320,1385-1392,1415-1418,1436-1440,1449-1456,1461-1464,1477-1479,1485-1497,1514-1527,1563-1567,1573-1577
7674 atoms, 7748 bonds, 794 residues, 1 model selected
> select /E:410-555
1415 atoms, 1437 bonds, 146 residues, 1 model selected
> select :49
12 atoms, 12 bonds, 1 residue, 1 model selected
> select :599-677
245 atoms, 244 bonds, 1 pseudobond, 25 residues, 2 models selected
> select :599-677, 735
253 atoms, 251 bonds, 1 pseudobond, 26 residues, 2 models selected
> select :599-6792, 735
8020 atoms, 8139 bonds, 4 pseudobonds, 836 residues, 2 models selected
> select :599-692, 735
391 atoms, 394 bonds, 1 pseudobond, 41 residues, 2 models selected
> select :599-677, 681, 683-684, 686, 689-692
326 atoms, 325 bonds, 1 pseudobond, 33 residues, 2 models selected
> select :599-677, 681, 683-684, 686, 689-692, 696, 701, 703, 706, 708, 715,
> 716, 717, 721, 722, 725, 728
449 atoms, 439 bonds, 1 pseudobond, 45 residues, 2 models selected
> select :599-677, 681, 683-684, 686, 689-692, 696, 701, 703, 706, 708, 715,
> 716, 717, 721, 722, 725, 728-730, 732-741, 766-770, 772
624 atoms, 616 bonds, 2 pseudobonds, 63 residues, 2 models selected
> select :599-677, 681, 683-684, 686, 689-692, 696, 701, 703, 706, 708, 715,
> 716, 717, 721, 722, 725, 728-730, 732-741, 766-770, 772, 774-776, 778-781,
> 785-786
722 atoms, 713 bonds, 2 pseudobonds, 72 residues, 2 models selected
> select :599-677, 681, 683-684, 686, 689-692, 696, 701, 703, 706, 708, 715,
> 716, 717, 721, 722, 725, 728-730, 732-741, 766-770, 772, 774-776, 778-781,
> 785-786, 778-781, 785-786, 789, 790, 791, 793, 794-797
808 atoms, 800 bonds, 2 pseudobonds, 80 residues, 2 models selected
> select :599-677, 681, 683-684, 686, 689-692, 696, 701, 703, 706, 708, 715,
> 716, 717, 721, 722, 725, 728-730, 732-741, 766-770, 772, 774-776, 778-781,
> 785-786, 778-781, 785-786, 789, 790, 791, 793, 794-798, 800-801, 804, 809,
> 811, 813-814, 816-817, 820, 822, 825-829, 831, 834-835
1028 atoms, 1011 bonds, 2 pseudobonds, 100 residues, 2 models selected
> select :599-677, 681, 683-684, 686, 689-692, 696, 701, 703, 706, 708, 715,
> 716, 717, 721, 722, 725, 728-730, 732-741, 766-770, 772, 774-776, 778-781,
> 785-786, 778-781, 785-786, 789, 790, 791, 793, 794-798, 800-801, 804, 809,
> 811, 813-814, 816-817, 820, 822, 825-829, 831, 834-835, 846-847, 849, 855,
> 860-882, 889-890, 892, 896, 898-899, 904, 905, 910, 915-916, 918-919, 920,
> 922, 924, 926-927, 931, 934, 935-944, 997-1004
1725 atoms, 1702 bonds, 3 pseudobonds, 165 residues, 2 models selected
> label (#!1 & sel) attribute name
> rename #1.2 "binding residues"
> color (#!1 & sel) cyan
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> select ~sel & ##selected
11688 atoms, 11942 bonds, 5 pseudobonds, 1232 residues, 2 models selected
> label (#!1 & sel) attribute name
> hide #1.2 models
> show #1.2 models
> select clear
> undo
> label (#!1 & sel) atoms attribute name
> undo
> ~label (#!1 & sel) residues
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
>
Incomplete command: build
> hide #!1 models
> show #!1 models
> close #1.2
> close #1.1
> log metadata #1
The model has no metadata
> log chains #1
Chain information for SUR1_7s5v_rec.pdb #1
---
Chain | Description
E | No description available
> name frozen "interacting residues" sel
Not registering illegal selector name "interacting residues"
> help help:user/menu.html#named-selections
> name frozen interactors sel
> select interactors
1725 atoms, 1702 bonds, 165 residues, 1 model selected
> select clear
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_interacting_residues.pdb" relModel #1
> show surfaces
> select interactors
1725 atoms, 1702 bonds, 165 residues, 1 model selected
> color (#!1 & sel) cyan
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_interacting_residues.pdb"
> color #1.1 #ffd1aaff
> color (#!1 & sel) cyan
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> select : 860
9 atoms, 8 bonds, 1 residue, 1 model selected
> name frozen most_frequent sel
> select : 860, 882, 877, 864, 998, 873, 867, 875, 878, 826, 881, 997, 999,
> 1000
168 atoms, 163 bonds, 14 residues, 1 model selected
> name frozen most_frequent sel
> color (#!1 & sel) red
> select : 860, 882, 877, 864, 998
60 atoms, 57 bonds, 5 residues, 1 model selected
> name frozen most_frequent sel
> color (#!1 & sel) red
> select : 873, 867, 875, 878, 826, 881, 997, 999, 1000
108 atoms, 102 bonds, 9 residues, 1 model selected
> color (#!1 & sel) orange red
> name frozen most_frequent_2 sel
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> name frozen most_frequent_3 sel
> color (#!1 & sel) yellow
> select : 619, 600, 604, 865, 607, 608, 620, 791, 862, 601, 730, 1002, 1003,
> 786, 816, 828, 870, 871
158 atoms, 146 bonds, 18 residues, 1 model selected
> color (#!1 & sel) yellow
> name frozen most_frequent_4 sel
> select most_frequent_3
13413 atoms, 141 bonds, 1397 residues, 1 model selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> name frozen most_frequent_3 sel
> color (#!1 & sel) orange
> select : 610, 776, 778, 790, 827, 863, 874, 767, 772, 781, 866, 602, 605,
> 621, 820, 829, 793, 612, 617, 689, 725, 780
245 atoms, 232 bonds, 22 residues, 1 model selected
> name frozen most_frequent_5 sel
> color (#!1 & sel) lime
> select : 618, 774, 785, 796, 846, 872, 943, 944, 616, 676, 703, 766, 769,
> 770, 794, 795, 797, 825, 609, 677, 691, 708, 732, 801, 804, 847, 849, 937,
> 938, 942, 606, 613, 683, 684, 706, 715, 716, 717, 721, 728, 729, 733-738,
> 741, 768, 798, 831, 835, 889, 919, 934, 936, 940
570 atoms, 540 bonds, 57 residues, 1 model selected
> name frozen least_frequent_2 sel
> color (#!1 & sel) blue
> select : 681, 686, 690, 692, 696, 701, 722, 739, 740, 775, 779, 789, 800,
> 809, 811, 813, 814, 834, 855, 890, 892, 896, 898, 899, 904, 905, 910, 915,
> 916, 918, 920, 922, 924, 926, 927, 931, 935, 941, 953
416 atoms, 392 bonds, 38 residues, 1 model selected
> name frozen least_frequent sel
> color (#!1 & sel) light gray
> color (#!1 & sel) gray
> color (#!1 & sel) cornflower blue
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/AmyDeLury/Desktop/movie1.mp4
Movie saved to /Users/AmyDeLury/Desktop/movie1.mp4
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> hide #1.1 models
> show sel surfaces
> hide #1.1 models
> surface (#!1 & sel)
> select interactors
1725 atoms, 1702 bonds, 165 residues, 1 model selected
> show sel surfaces
> select ~sel & ##selected
11688 atoms, 11942 bonds, 1232 residues, 1 model selected
> name frozen non-interactor sel
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 11688 atom styles
> cartoon hide (#!1 & sel)
> select interactors
1725 atoms, 1702 bonds, 165 residues, 1 model selected
> show sel surfaces
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_interacting_residue_surface.pdb"
> save /Users/AmyDeLury/Desktop/image3.png supersample 3
> select most_frequent
13413 atoms, 57 bonds, 1397 residues, 1 model selected
Alignment identifier is 1/E
> select clear
> select most_frequent
13413 atoms, 57 bonds, 1397 residues, 1 model selected
> select : 860, 882, 877, 864, 998
60 atoms, 57 bonds, 5 residues, 1 model selected
> select up
460 atoms, 464 bonds, 46 residues, 2 models selected
> select up
2223 atoms, 2262 bonds, 225 residues, 2 models selected
> select up
2430 atoms, 2472 bonds, 247 residues, 2 models selected
> select up
7795 atoms, 7914 bonds, 813 residues, 2 models selected
> select down
2430 atoms, 2472 bonds, 247 residues, 2 models selected
> select down
2223 atoms, 2262 bonds, 225 residues, 2 models selected
> select down
460 atoms, 464 bonds, 46 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select down
60 atoms, 57 bonds, 5 residues, 2 models selected
> select : 873, 867, 875, 878, 826, 881, 997, 999, 1000
108 atoms, 102 bonds, 9 residues, 1 model selected
> color (#!1 & sel) orange
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> color (#!1 & sel) yellow
> select : 610, 776, 778, 790, 827, 863, 874, 767, 772, 781, 866, 602, 605,
> 621, 820, 829, 793, 612, 617, 689, 725, 780
245 atoms, 232 bonds, 22 residues, 1 model selected
> color (#!1 & sel) lime
> select : 618, 774, 785, 796, 846, 872, 943, 944, 616, 676, 703, 766, 769,
> 770, 794, 795, 797, 825, 609, 677, 691, 708, 732, 801, 804, 847, 849, 937,
> 938, 942, 606, 613, 683, 684, 706, 715, 716, 717, 721, 728, 729, 733-738,
> 741, 768, 798, 831, 835, 889, 919, 934, 936, 940
570 atoms, 540 bonds, 57 residues, 1 model selected
> color (#!1 & sel) blue
> select : 681, 686, 690, 692, 696, 701, 722, 739, 740, 775, 779, 789, 800,
> 809, 811, 813, 814, 834, 855, 890, 892, 896, 898, 899, 904, 905, 910, 915,
> 916, 918, 920, 922, 924, 926, 927, 931, 935, 941, 953
416 atoms, 392 bonds, 38 residues, 1 model selected
> color (#!1 & sel) hot pink
> color (#!1 & sel) purple
> ui tool show "Color Actions"
> color sel purple
> save /Users/AmyDeLury/Desktop/image4.png supersample 3
> select clear
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> select : 618, 774, 785, 796, 846, 872, 943, 944, 616, 676, 703, 766, 769,
> 770, 794, 795, 797, 825, 609, 677, 691, 708, 732, 801, 804, 847, 849, 937,
> 938, 942, 606, 613, 683, 684, 706, 715, 716, 717, 721, 728, 729, 733-738,
> 741, 768, 798, 831, 835, 889, 919, 934, 936, 940
570 atoms, 540 bonds, 57 residues, 1 model selected
> select : 873, 867, 875, 878, 826, 881, 997, 999, 1000
108 atoms, 102 bonds, 9 residues, 1 model selected
> select up
575 atoms, 577 bonds, 57 residues, 2 models selected
> select up
2223 atoms, 2262 bonds, 225 residues, 2 models selected
> select down
575 atoms, 577 bonds, 57 residues, 2 models selected
> select down
108 atoms, 102 bonds, 9 residues, 2 models selected
> select : 873, 867, 875, 878, 826, 881, 997, 999, 1000
108 atoms, 102 bonds, 9 residues, 1 model selected
> select : 873, 867, 875, 878, 826, 881, 997, 999, 1000
108 atoms, 102 bonds, 9 residues, 1 model selected
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> select : 610, 776, 778, 790, 827, 863, 874, 767, 772, 781, 866, 602, 605,
> 621, 820, 829, 793, 612, 617, 689, 725, 780
245 atoms, 232 bonds, 22 residues, 1 model selected
> select up
1293 atoms, 1307 bonds, 136 residues, 2 models selected
> select up
5044 atoms, 5126 bonds, 523 residues, 2 models selected
> select : 610, 776, 778, 790, 827, 863, 874, 767, 772, 781, 866, 602, 605,
> 621, 820, 829, 793, 612, 617, 689, 725, 780
245 atoms, 232 bonds, 22 residues, 1 model selected
> select up
1293 atoms, 1307 bonds, 136 residues, 2 models selected
> select up
5044 atoms, 5126 bonds, 523 residues, 2 models selected
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> select up
739 atoms, 743 bonds, 77 residues, 2 models selected
> select : 619, 600, 604, 865, 607, 608, 620, 791, 862, 601, 730, 1002, 1003,
> 786, 816, 828, 870, 871
158 atoms, 146 bonds, 18 residues, 1 model selected
> select up
1232 atoms, 1244 bonds, 130 residues, 2 models selected
> select : 610, 776, 778, 790, 827, 863, 874, 767, 772, 781, 866, 602, 605,
> 621, 820, 829, 793, 612, 617, 689, 725, 780
245 atoms, 232 bonds, 22 residues, 1 model selected
> select up
1293 atoms, 1307 bonds, 136 residues, 2 models selected
> select up
5044 atoms, 5126 bonds, 523 residues, 2 models selected
> select : 619, 600, 604, 865, 607, 608, 620, 791, 862, 601, 730, 1002, 1003,
> 786, 816, 828, 870, 871
158 atoms, 146 bonds, 18 residues, 1 model selected
> select up
1232 atoms, 1244 bonds, 130 residues, 2 models selected
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> select : 619, 600, 604, 865, 607, 608, 620, 791, 862, 601, 730, 1002, 1003,
> 786, 816, 828, 870, 871
158 atoms, 146 bonds, 18 residues, 1 model selected
> color (#!1 & sel) lime
> select : 619, 600, 604, 865, 607, 608, 620, 791, 862, 601, 730, 1002, 1003,
> 786, 816, 828, 870, 871
158 atoms, 146 bonds, 18 residues, 1 model selected
> color (#!1 & sel) cyan
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> select interactors
1725 atoms, 1702 bonds, 165 residues, 1 model selected
> select ~sel & ##selected
11688 atoms, 11942 bonds, 1232 residues, 1 model selected
> surface (#!1 & sel)
> select ~sel & ##selected
1725 atoms, 1702 bonds, 165 residues, 1 model selected
> surface (#!1 & sel)
> select
13413 atoms, 13644 bonds, 1397 residues, 1 model selected
> surface (#!1 & sel)
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> undo
> redo
> select interactors
1725 atoms, 1702 bonds, 165 residues, 1 model selected
> select ~sel & ##selected
11688 atoms, 11942 bonds, 1232 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> save /Users/AmyDeLury/Desktop/image3.png supersample 3
> select
13413 atoms, 13644 bonds, 1397 residues, 1 model selected
> surface (#!1 & sel)
> save /Users/AmyDeLury/Desktop/image4.png supersample 3
> ui windowfill toggle
> ui tool show "Basic Actions"
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue-white-red :min : :max white:
> key blue:min white: red:max white: white:
> key blue:min white: red:max white: white: white:
> key blue:min white: red: white: white: white:
> key blue:min white: red: white: white: #ff2600:
> key blue:min white: red: white: #ff9300: #ff2600:
> key blue:min white: red: #fffb00: #ff9300: #ff2600:
> key blue:min white: #00fdff: #fffb00: #ff9300: #ff2600:
> key blue:min white: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #00f900: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #00fdff: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #00fdff: #00f900: #fffb00: #ff9300: #ff2600: white:
> key blue:min #00fdff: #00f900: #fffb00: #ff9300: #ff2600: #ff2600:
> key blue:min #00fdff: #00f900: #fffb00: #ff9300: #ff9300: #ff2600:
> key blue:min #00fdff: #00f900: #fffb00: #fffb00: #ff9300: #ff2600:
> key blue:min #00fdff: #00f900: #fffb00: #fffb00: #ff9300: #ff2600: white:
> key blue:min #00fdff: #00f900: #fffb00: #fffb00: #ff9300: #ff2600: #ff2600:
> key blue:min #00fdff: #00f900: #fffb00: #fffb00: #ff9300: #ff9300: #ff2600:
> key blue:min #00fdff: #00f900: #fffb00: #fffb00: #fffb00: #ff9300: #ff2600:
> key blue:min #00fdff: #00f900: #fffb00: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #00fdff: #00f900: #0433ff: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #00fdff: #00f900: #00fdff: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #00fdff: #0433ff: #00fdff: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #ff2600: #0433ff: #00fdff: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #942192: #0433ff: #00fdff: #00f900: #fffb00: #ff9300: #ff2600:
> key #fffffa:min #942192: #0433ff: #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> ui mousemode right translate
> select clear
> save /Users/AmyDeLury/Desktop/image5.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/AmyDeLury/Desktop/movie2.mp4
Movie saved to /Users/AmyDeLury/Desktop/movie2.mp4
> select interactors
1725 atoms, 1702 bonds, 165 residues, 1 model selected
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/Models/SUR1_Interacting_Residues_All_Models.pdb" selectedOnly true
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/Models/SUR1_Interacting_Residues_All_Models.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/Models/SUR1_Interacting_Residues_All_Models.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 VAL E 35 PHE E 45 1
11
Start residue of secondary structure not found: HELIX 2 2 PRO E 46 ILE E 50 1
5
Start residue of secondary structure not found: HELIX 3 3 HIS E 72 GLY E 98 1
27
Start residue of secondary structure not found: HELIX 4 4 MET E 109 GLU E 129
1 21
Start residue of secondary structure not found: HELIX 5 5 PRO E 134 LEU E 137
1 4
31 messages similar to the above omitted
End residue of secondary structure not found: HELIX 38 38 LYS E 796 ALA E 805
1 10
Start residue of secondary structure not found: HELIX 40 40 GLY E 818 GLN E
820 1 3
Start residue of secondary structure not found: HELIX 41 41 GLY E 832 ALA E
843 1 12
Start residue of secondary structure not found: HELIX 43 43 LEU E 891 HIS E
896 1 6
Start residue of secondary structure not found: HELIX 44 44 LEU E 914 GLU E
921 1 8
End residue of secondary structure not found: HELIX 45 45 LEU E 924 LYS E 929
1 6
End residue of secondary structure not found: HELIX 46 46 ARG E 999 SER E 1006
1 8
Start residue of secondary structure not found: HELIX 47 47 ILE E 1010 TYR E
1032 1 23
Start residue of secondary structure not found: HELIX 48 48 THR E 1038 ALA E
1041 1 4
Start residue of secondary structure not found: HELIX 49 49 THR E 1069 CYS E
1072 1 4
Start residue of secondary structure not found: HELIX 50 50 LEU E 1080 ILE E
1105 1 26
Start residue of secondary structure not found: HELIX 51 51 MET E 1110 THR E
1115 1 6
43 messages similar to the above omitted
Chain information for SUR1_Interacting_Residues_All_Models.pdb #3
---
Chain | Description
E | No description available
> close session
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_interacting_residue_surface.pdb" format pdb
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/SUR1_interacting_residue_surface.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for SUR1_interacting_residue_surface.pdb #1
---
Chain | Description
E | No description available
> ui tool show Log
> close
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_interacting_residue_surface.pdb" format pdb
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/SUR1_interacting_residue_surface.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for SUR1_interacting_residue_surface.pdb #1
---
Chain | Description
E | No description available
> close
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/Models/SUR1_Interacting_Residues_All_Models.pdb" format pdb
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/Models/SUR1_Interacting_Residues_All_Models.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 VAL E 35 PHE E 45 1
11
Start residue of secondary structure not found: HELIX 2 2 PRO E 46 ILE E 50 1
5
Start residue of secondary structure not found: HELIX 3 3 HIS E 72 GLY E 98 1
27
Start residue of secondary structure not found: HELIX 4 4 MET E 109 GLU E 129
1 21
Start residue of secondary structure not found: HELIX 5 5 PRO E 134 LEU E 137
1 4
31 messages similar to the above omitted
End residue of secondary structure not found: HELIX 38 38 LYS E 796 ALA E 805
1 10
Start residue of secondary structure not found: HELIX 40 40 GLY E 818 GLN E
820 1 3
Start residue of secondary structure not found: HELIX 41 41 GLY E 832 ALA E
843 1 12
Start residue of secondary structure not found: HELIX 43 43 LEU E 891 HIS E
896 1 6
Start residue of secondary structure not found: HELIX 44 44 LEU E 914 GLU E
921 1 8
End residue of secondary structure not found: HELIX 45 45 LEU E 924 LYS E 929
1 6
End residue of secondary structure not found: HELIX 46 46 ARG E 999 SER E 1006
1 8
Start residue of secondary structure not found: HELIX 47 47 ILE E 1010 TYR E
1032 1 23
Start residue of secondary structure not found: HELIX 48 48 THR E 1038 ALA E
1041 1 4
Start residue of secondary structure not found: HELIX 49 49 THR E 1069 CYS E
1072 1 4
Start residue of secondary structure not found: HELIX 50 50 LEU E 1080 ILE E
1105 1 26
Start residue of secondary structure not found: HELIX 51 51 MET E 1110 THR E
1115 1 6
43 messages similar to the above omitted
Chain information for SUR1_Interacting_Residues_All_Models.pdb #1
---
Chain | Description
E | No description available
> hide #!1 models
> show #!1 models
> close #1
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/Models/SUR1_Interacting_Residues_All_Models.pdb" format pdb
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/Models/SUR1_Interacting_Residues_All_Models.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 VAL E 35 PHE E 45 1
11
Start residue of secondary structure not found: HELIX 2 2 PRO E 46 ILE E 50 1
5
Start residue of secondary structure not found: HELIX 3 3 HIS E 72 GLY E 98 1
27
Start residue of secondary structure not found: HELIX 4 4 MET E 109 GLU E 129
1 21
Start residue of secondary structure not found: HELIX 5 5 PRO E 134 LEU E 137
1 4
31 messages similar to the above omitted
End residue of secondary structure not found: HELIX 38 38 LYS E 796 ALA E 805
1 10
Start residue of secondary structure not found: HELIX 40 40 GLY E 818 GLN E
820 1 3
Start residue of secondary structure not found: HELIX 41 41 GLY E 832 ALA E
843 1 12
Start residue of secondary structure not found: HELIX 43 43 LEU E 891 HIS E
896 1 6
Start residue of secondary structure not found: HELIX 44 44 LEU E 914 GLU E
921 1 8
End residue of secondary structure not found: HELIX 45 45 LEU E 924 LYS E 929
1 6
End residue of secondary structure not found: HELIX 46 46 ARG E 999 SER E 1006
1 8
Start residue of secondary structure not found: HELIX 47 47 ILE E 1010 TYR E
1032 1 23
Start residue of secondary structure not found: HELIX 48 48 THR E 1038 ALA E
1041 1 4
Start residue of secondary structure not found: HELIX 49 49 THR E 1069 CYS E
1072 1 4
Start residue of secondary structure not found: HELIX 50 50 LEU E 1080 ILE E
1105 1 26
Start residue of secondary structure not found: HELIX 51 51 MET E 1110 THR E
1115 1 6
43 messages similar to the above omitted
Chain information for SUR1_Interacting_Residues_All_Models.pdb #1
---
Chain | Description
E | No description available
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/AmyDeLury/Downloads/UB (University at Buffalo)/Lab
> Rotations/Klein Lab Rotation/Epac2-SUR1
> project/20240719_Shibisaki_model/Balanced Models/model.000.00.pdb" format
> pdb
Summary of feedback from opening /Users/AmyDeLury/Downloads/UB (University at
Buffalo)/Lab Rotations/Klein Lab Rotation/Epac2-SUR1
project/20240719_Shibisaki_model/Balanced Models/model.000.00.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for model.000.00.pdb
---
Chain | Description
1.2/A | No description available
1.1/E | No description available
> close
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/Models/SUR1_Interacting_Residues_All_Models.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/Models/SUR1_Interacting_Residues_All_Models.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 VAL E 35 PHE E 45 1
11
Start residue of secondary structure not found: HELIX 2 2 PRO E 46 ILE E 50 1
5
Start residue of secondary structure not found: HELIX 3 3 HIS E 72 GLY E 98 1
27
Start residue of secondary structure not found: HELIX 4 4 MET E 109 GLU E 129
1 21
Start residue of secondary structure not found: HELIX 5 5 PRO E 134 LEU E 137
1 4
31 messages similar to the above omitted
End residue of secondary structure not found: HELIX 38 38 LYS E 796 ALA E 805
1 10
Start residue of secondary structure not found: HELIX 40 40 GLY E 818 GLN E
820 1 3
Start residue of secondary structure not found: HELIX 41 41 GLY E 832 ALA E
843 1 12
Start residue of secondary structure not found: HELIX 43 43 LEU E 891 HIS E
896 1 6
Start residue of secondary structure not found: HELIX 44 44 LEU E 914 GLU E
921 1 8
End residue of secondary structure not found: HELIX 45 45 LEU E 924 LYS E 929
1 6
End residue of secondary structure not found: HELIX 46 46 ARG E 999 SER E 1006
1 8
Start residue of secondary structure not found: HELIX 47 47 ILE E 1010 TYR E
1032 1 23
Start residue of secondary structure not found: HELIX 48 48 THR E 1038 ALA E
1041 1 4
Start residue of secondary structure not found: HELIX 49 49 THR E 1069 CYS E
1072 1 4
Start residue of secondary structure not found: HELIX 50 50 LEU E 1080 ILE E
1105 1 26
Start residue of secondary structure not found: HELIX 51 51 MET E 1110 THR E
1115 1 6
43 messages similar to the above omitted
Chain information for SUR1_Interacting_Residues_All_Models.pdb #1
---
Chain | Description
E | No description available
> set bgColor white
> select : 860, 882, 877, 864, 998
60 atoms, 57 bonds, 5 residues, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> select
1725 atoms, 1702 bonds, 48 pseudobonds, 165 residues, 2 models selected
> show sel surfaces
> select : 860, 882, 877, 864, 998
60 atoms, 57 bonds, 5 residues, 1 model selected
> color (#!1 & sel) red
> ui tool show "Color Actions"
> ui tool show "Render/Select by Attribute"
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue-white-red :min : :max white:
> key blue:min white: red:max white: white:
> key blue:min white: red:max white: white: white:
> key blue:min white: red:max white: white: white: white:
> key blue:min white: red:max white: white: white: white: white:
> key blue:min white: red:max white: white: white: white:
> key blue:min white: red:max white: white: white: #ff2600:
> key blue:min white: red:max white: white: #ff9300: #ff2600:
> key blue:min white: red:max white: white: #ff9300: #ff2600:m
> key blue:min white: red:max white: white: #ff9300: #ff2600:ma
> key blue:min white: red:max white: white: #ff9300: #ff2600:max
> key blue:min white: red: white: white: #ff9300: #ff2600:max
> key blue:min white: red: white: #fffb00: #ff9300: #ff2600:max
> key blue:min white: red: #ff40ff: #fffb00: #ff9300: #ff2600:max
> key blue:min white: red: #00f900: #fffb00: #ff9300: #ff2600:max
> key blue:min white: #ff40ff: #00f900: #fffb00: #ff9300: #ff2600:max
> key blue:min white: #00fdff: #00f900: #fffb00: #ff9300: #ff2600:max
> key blue:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: #ff2600:max
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: #ff2600:max
> ui mousemode right translate
> select : 873, 867, 875, 878, 826, 881, 997, 999, 1000
108 atoms, 102 bonds, 9 residues, 1 model selected
> name frozen most_interactions_2 sel
> color (#!1 & sel) orange
> select : 860, 882, 877, 864, 998
60 atoms, 57 bonds, 5 residues, 1 model selected
> name frozen most_interactions sel
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> color (#!1 & sel) yellow
> select : 619, 600, 604, 865, 607, 608, 620, 791, 862, 601, 730, 1002, 1003,
> 786, 816, 828, 870, 871
158 atoms, 146 bonds, 18 residues, 1 model selected
> color (#!1 & sel) lime
> select : 610, 776, 778, 790, 827, 863, 874, 767, 772, 781, 866, 602, 605,
> 621, 820, 829, 793, 612, 617, 689, 725, 780
245 atoms, 232 bonds, 1 pseudobond, 22 residues, 2 models selected
> color (#!1 & sel) cyan
> select : 618, 774, 785, 796, 846, 872, 943, 944, 616, 676, 703, 766, 769,
> 770, 794, 795, 797, 825, 609, 677, 691, 708, 732, 801, 804, 847, 849, 937,
> 938, 942, 606, 613, 683, 684, 706, 715, 716, 717, 721, 728, 729, 733-738,
> 741, 768, 798, 831, 835, 889, 919, 934, 936, 940
570 atoms, 540 bonds, 7 pseudobonds, 57 residues, 2 models selected
> color (#!1 & sel) blue
> select : 681, 686, 690, 692, 696, 701, 722, 739, 740, 775, 779, 789, 800,
> 809, 811, 813, 814, 834, 855, 890, 892, 896, 898, 899, 904, 905, 910, 915,
> 916, 918, 920, 922, 924, 926, 927, 931, 935, 941, 953
416 atoms, 392 bonds, 15 pseudobonds, 38 residues, 2 models selected
> color (#!1 & sel) purple
> name frozen least_interactions sel
> select : 618, 774, 785, 796, 846, 872, 943, 944, 616, 676, 703, 766, 769,
> 770, 794, 795, 797, 825, 609, 677, 691, 708, 732, 801, 804, 847, 849, 937,
> 938, 942, 606, 613, 683, 684, 706, 715, 716, 717, 721, 728, 729, 733-738,
> 741, 768, 798, 831, 835, 889, 919, 934, 936, 940
570 atoms, 540 bonds, 7 pseudobonds, 57 residues, 2 models selected
> name frozen least_interactions_2 sel
> select : 610, 776, 778, 790, 827, 863, 874, 767, 772, 781, 866, 602, 605,
> 621, 820, 829, 793, 612, 617, 689, 725, 780
245 atoms, 232 bonds, 1 pseudobond, 22 residues, 2 models selected
> name frozen mod_interactions_3 sel
> select : 619, 600, 604, 865, 607, 608, 620, 791, 862, 601, 730, 1002, 1003,
> 786, 816, 828, 870, 871
158 atoms, 146 bonds, 18 residues, 1 model selected
> name frozen mod_interactions_4 sel
> select up
1506 atoms, 1485 bonds, 146 residues, 2 models selected
> select up
1630 atoms, 1609 bonds, 157 residues, 2 models selected
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> name frozen mod_interactions_5 sel
> select least_interactions
1725 atoms, 392 bonds, 15 pseudobonds, 165 residues, 2 models selected
> 681, 686, 690, 692, 696, 701, 722, 739, 740, 775, 779, 789, 800, 809, 811,
> 813, 814, 834, 855, 890, 892, 896, 898, 899, 904, 905, 910, 915, 916, 918,
> 920, 922, 924, 926, 927, 931, 935, 941, 953, 939, 868
Unknown command: 681, 686, 690, 692, 696, 701, 722, 739, 740, 775, 779, 789,
800, 809, 811, 813, 814, 834, 855, 890, 892, 896, 898, 899, 904, 905, 910,
915, 916, 918, 920, 922, 924, 926, 927, 931, 935, 941, 953, 939, 868
> select : 681, 686, 690, 692, 696, 701, 722, 739, 740, 775, 779, 789, 800,
> 809, 811, 813, 814, 834, 855, 890, 892, 896, 898, 899, 904, 905, 910, 915,
> 916, 918, 920, 922, 924, 926, 927, 931, 935, 941, 953, 939, 868
434 atoms, 408 bonds, 15 pseudobonds, 40 residues, 2 models selected
> color (#!1 & sel) purple
> name frozen least_interactions sel
[Repeated 1 time(s)]
> select clear
> save /Users/AmyDeLury/Desktop/image6.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/AmyDeLury/Desktop/movie3.mp4
Movie saved to /Users/AmyDeLury/Desktop/movie3.mp4
> ui tool show "Color Key"
> ui mousemode right "color key"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: #ff2600:max:
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: "#ff2600:max: "
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: "#ff2600:max:
> 2"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: "#ff2600:max:
> 25"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: "#ff2600:max:
> 25-"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: "#ff2600:max:
> 25-3"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300: "#ff2600:max:
> 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300:2 "#ff2600:max:
> 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300:21 "#ff2600:max:
> 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300:21-
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300:21-2
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00: #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00:1 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00:15 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00:1 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00:16 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00:16- #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00:16-2 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900: #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900:1 #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900:11 #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900:11- #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900:11-1 #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900:11-15 #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff:1 #00f900:11-15 #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff: #00f900:11-15 #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff:6 #00f900:11-15 #fffb00:16-20 #ff9300:21-24
> "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff:6- #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff:6-1 #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 "#ff2600:max: 25-30"
> key #942192:min #0433ff: #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 "#ff2600:max: 25-30"
> key #942192:min #0433ff:2 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 "#ff2600:max: 25-30"
> key #942192:min #0433ff:2- #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 "#ff2600:max: 25-30"
> key #942192:min #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 "#ff2600:max: 25-30"
> key #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 "#ff2600:max: 25-30"
> ui mousemode right translate
> ui tool show "Color Key"
> ui mousemode right "color key"
> key pos 0.587981,0.0913929
> key colorTreatment distinct
> key size 0.26000,0.05000
> key size 0.27000,0.05000
> key size 0.28000,0.05000
> key size 0.29000,0.05000
> key size 0.30000,0.05000
> key size 0.31000,0.05000
> key size 0.32000,0.05000
> key size 0.33000,0.05000
> key size 0.34000,0.05000
> key colorTreatment blended
> key colorTreatment distinct
> key size 0.35000,0.05000
> key size 0.36000,0.05000
> key size 0.37000,0.05000
> key size 0.38000,0.05000
> key size 0.39000,0.05000
> key size 0.40000,0.05000
> key size 0.41000,0.05000
> key size 0.42000,0.05000
Key is partially or completely offscreen
> key size 0.43000,0.05000
Key is partially or completely offscreen
> key pos 0.248698,0.111668 size 0.454901,0.0500602
> key pos 0.649444,0.0983467 size 0.663274,0.0289296
Key is partially or completely offscreen
> key pos 0.24932,0.122635 size 0.539038,0.0399963
> key pos 0.113087,0.151735 size 0.172625,0.0518874
> key pos 0.052181,0.13701 size 0.909869,0.0521346
> key #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 #ff2600:25-30
> key pos 0.289445,0.16735 size 0.0234136,0.0138647
> undo
[Repeated 1 time(s)]
> key pos 0.0568993,0.150345
> key pos 0.064363,0.122445 size 0.9066,0.039791
> save /Users/AmyDeLury/Desktop/image7.png supersample 3
> select clear
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/AmyDeLury/Desktop/movie1.mp4
Movie saved to /Users/AmyDeLury/Desktop/movie1.mp4
> key pos 0.489272,0.685173 size 0.0457635,0.000841559
> undo
[Repeated 1 time(s)]
> key pos 0.0453024,0.209633 size 0.431949,0.0159848
> key pos 0.593498,0.218223 size 0.0626279,0.238406
> key pos 0.635423,0.672672 size 0.0177695,0.233187
> key pos 0.862758,0.171001 size 0.048077,0.719719
> key pos 0.0764587,0.0997615 size 0.089914,0.820889
> key pos 0.104062,0.0982014 size 0.862562,0.0649709
> key pos 0.192543,0.0485344 size 0.00299954,0.0853665
> key pos 0.0461562,0.0436275 size 0.926514,0.0706813
> key pos 0.725076,0.464065 size 0.0398139,0.0104461
> key pos 0.599932,0.299986 size 0.130748,0.0365107
> key pos 0.0752269,0.0715386 size 0.889836,0.0822679
> select clear
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
[Repeated 1 time(s)]
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/Models/SUR1_Interacting_Residues_All_Models.pdb"
> close #1
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Sur1_7s5v.pdb"
Sur1_7s5v.pdb title:
Human katp channel In open conformation, focused on sur [more info...]
Chain information for Sur1_7s5v.pdb #1
---
Chain | Description | UniProt
E | sulfonylurea receptor 1 | ABCC8_HUMAN 3-1582
Non-standard residues in Sur1_7s5v.pdb #1
---
ADP \u2014 adenosine-5'-diphosphate
ATP \u2014 adenosine-5'-triphosphate
MG \u2014 magnesium ion
> key pos 0.161811,0.628388 size 0.115014,0.0147094
> key pos 0.267308,0.693187 size 0.12493,0.0097386
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking
> Models/20242905_epac2_sur1_whole_dock/SUR1_7s5v_rec.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20242905_epac2_sur1_whole_dock/SUR1_7s5v_rec.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for SUR1_7s5v_rec.pdb #3
---
Chain | Description
E | No description available
> close #1
> key pos 0.192442,0.249965 size 0.102744,0.0116025
> select : 860
9 atoms, 8 bonds, 1 residue, 1 model selected
> 882
Unknown command: 882
> 877
Unknown command: 877
> 864
Unknown command: 864
> 998
Unknown command: 998
> 873
Unknown command: 873
> 867
Unknown command: 867
> 875
Unknown command: 875
> 878
Unknown command: 878
> 826
Unknown command: 826
> 881
Unknown command: 881
> 997
Unknown command: 997
> 999
Unknown command: 999
> 1000
Unknown command: 1000
> 611
Unknown command: 611
> 876
Unknown command: 876
> 1001
Unknown command: 1001
> 599
Unknown command: 599
> 603
Unknown command: 603
> 879
Unknown command: 879
> 615
Unknown command: 615
> 822
Unknown command: 822
> 869
Unknown command: 869
> 614
Unknown command: 614
> 817
Unknown command: 817
> 861
Unknown command: 861
> 880
Unknown command: 880
> 1004
Unknown command: 1004
> 619
Unknown command: 619
> 600
Unknown command: 600
> 604
Unknown command: 604
> 865
Unknown command: 865
> 607
Unknown command: 607
> 608
Unknown command: 608
> 620
Unknown command: 620
> 791
Unknown command: 791
> 862
Unknown command: 862
> 601
Unknown command: 601
> 730
Unknown command: 730
> 1002
Unknown command: 1002
> 1003
Unknown command: 1003
> 786
Unknown command: 786
> 816
Unknown command: 816
> 828
Unknown command: 828
> 870
Unknown command: 870
> 871
Unknown command: 871
> 610
Unknown command: 610
> 776
Unknown command: 776
> 778
Unknown command: 778
> 790
Unknown command: 790
> 827
Unknown command: 827
> 863
Unknown command: 863
> 874
Unknown command: 874
> 767
Unknown command: 767
> 772
Unknown command: 772
> 781
Unknown command: 781
> 866
Unknown command: 866
> 602
Unknown command: 602
> 605
Unknown command: 605
> 621
Unknown command: 621
> 820
Unknown command: 820
> 829
Unknown command: 829
> 793
Unknown command: 793
> 612
Unknown command: 612
> 617
Unknown command: 617
> 689
Unknown command: 689
> 725
Unknown command: 725
> 780
Unknown command: 780
> 618
Unknown command: 618
> 774
Unknown command: 774
> 785
Unknown command: 785
> 796
Unknown command: 796
> 846
Unknown command: 846
> 872
Unknown command: 872
> 943
Unknown command: 943
> 944
Unknown command: 944
> 616
Unknown command: 616
> 676
Unknown command: 676
> 703
Unknown command: 703
> 766
Unknown command: 766
> 769
Unknown command: 769
> 770
Unknown command: 770
> 794
Unknown command: 794
> 795
Unknown command: 795
> 797
Unknown command: 797
> 825
Unknown command: 825
> 609
Unknown command: 609
> 677
Unknown command: 677
> 691
Unknown command: 691
> 708
Unknown command: 708
> 732
Unknown command: 732
> 801
Unknown command: 801
> 804
Unknown command: 804
> 847
Unknown command: 847
> 849
Unknown command: 849
> 937
Unknown command: 937
> 938
Unknown command: 938
> 942
Unknown command: 942
> 606
Unknown command: 606
> 613
Unknown command: 613
> 683
Unknown command: 683
> 684
Unknown command: 684
> 706
Unknown command: 706
> 715
Unknown command: 715
> 716
Unknown command: 716
> 717
Unknown command: 717
> 721
Unknown command: 721
> 728
Unknown command: 728
> 729
Unknown command: 729
> 733
Unknown command: 733
> 734
Unknown command: 734
> 735
Unknown command: 735
> 736
Unknown command: 736
> 737
Unknown command: 737
> 738
Unknown command: 738
> 741
Unknown command: 741
> 768
Unknown command: 768
> 798
Unknown command: 798
> 831
Unknown command: 831
> 835
Unknown command: 835
> 889
Unknown command: 889
> 919
Unknown command: 919
> 934
Unknown command: 934
> 936
Unknown command: 936
> 940
Unknown command: 940
> 681
Unknown command: 681
> 686
Unknown command: 686
> 690
Unknown command: 690
> 692
Unknown command: 692
> 696
Unknown command: 696
> 701
Unknown command: 701
> 722
Unknown command: 722
> 739
Unknown command: 739
> 740
Unknown command: 740
> 775
Unknown command: 775
> 779
Unknown command: 779
> 789
Unknown command: 789
> 800
Unknown command: 800
> 809
Unknown command: 809
> 811
Unknown command: 811
> 813
Unknown command: 813
> 814
Unknown command: 814
> 834
Unknown command: 834
> 855
Unknown command: 855
> 890
Unknown command: 890
> 892
Unknown command: 892
> 896
Unknown command: 896
> 898
Unknown command: 898
> 899
Unknown command: 899
> 904
Unknown command: 904
> 905
Unknown command: 905
> 910
Unknown command: 910
> 915
Unknown command: 915
> 916
Unknown command: 916
> 918
Unknown command: 918
> 920
Unknown command: 920
> 922
Unknown command: 922
> 924
Unknown command: 924
> 926
Unknown command: 926
> 927
Unknown command: 927
> 931
Unknown command: 931
> 935
Unknown command: 935
> 941
Unknown command: 941
> select :599-677, 681, 683-684, 686, 689-692, 696, 701, 703, 706, 708, 715,
> 716, 717, 721, 722, 725, 728-730, 732-741, 766-770, 772, 774-776, 778-781,
> 785-786, 778-781, 785-786, 789, 790, 791, 793, 794-798, 800-801, 804, 809,
> 811, 813-814, 816-817, 820, 822, 825-829, 831, 834-835, 846-847, 849, 855,
> 860-882, 889-890, 892, 896, 898-899, 904, 905, 910, 915-916, 918-919, 920,
> 922, 924, 926-927, 931, 934, 935-944, 997-1004
1725 atoms, 1702 bonds, 3 pseudobonds, 165 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> show surfaces
> key pos 0.242145,0.799727 size 0.14032,0.0397935
> close #2
> ui mousemode right translate
> color #fff9e2ff
> color #fff9e1ff
> color #fffae0ff
> color #ffffd7ff
> color #fdffc7ff
> color #fdffc5ff
> color #fdffc4ff
[Repeated 1 time(s)]
> color #fdffc5ff
> color #fdffc8ff
> color #fbffcaff
> color #f9ffcbff
> color #f3ffceff
> color #f1ffd0ff
> color #f1ffd1ff
[Repeated 1 time(s)]
> color #f0ffd3ff
> color #eeffd6ff
> color #ebffd7ff
> color #ebffd8ff
> color #ecffd9ff
> color #ecffdbff
> color #edffe0ff
> color #ecffe4ff
> color #ebffe4ff
> color #e7ffe4ff
> color #e3ffe4ff
> color #e3ffe3ff
[Repeated 1 time(s)]
> color #e4ffe3ff
> color #f5ffe8ff
> color #fff2deff
> color #ffd5c7ff
> color #ffd4c6ff
> color #ffd3c6ff
> color #ffd2c5ff
> color #ffcec4ff
> color #ffc0bbff
> color #ffbcb8ff
> color #ffbfb8ff
> color #ffc5b9ff
> color #ffc8baff
> color #ffcabaff
> color #ffceb8ff
> color #ffcfb8ff
> color #ffcfb9ff
> color #ffd0b9ff
> color #ffd1baff
> color #ffd1bbff
> color #ffd2bbff
> color #ffd4bcff
> color #ffddbdff
> color #ffe2bcff
> color #ffe3bcff
[Repeated 1 time(s)]
> color #ffe1bbff
> color #ffdab4ff
> color #ffcaa4ff
> color #ffc9a3ff
> color #ffc9a2ff
[Repeated 1 time(s)]
> color #ffc9a3ff
[Repeated 1 time(s)]
> color #ffc9a4ff
> color #ffc8a5ff
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_noninteracting_residues.pdb"
> close #3
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_interacting_residues.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_noninteracting_residues.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/SUR1_interacting_residues.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/SUR1_noninteracting_residues.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for SUR1_interacting_residues.pdb #1
---
Chain | Description
E | No description available
Chain information for SUR1_noninteracting_residues.pdb #2
---
Chain | Description
E | No description available
> show surfaces
> hide #!1 models
> show #!1 models
> close #1
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/Frequency
> Models/SUR1_interacting_residue_surface.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking Models/Frequency
Models/SUR1_interacting_residue_surface.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for SUR1_interacting_residue_surface.pdb #1
---
Chain | Description
E | No description available
> show surfaces
> select : 860, 882, 877, 864, 998
60 atoms, 57 bonds, 5 residues, 1 model selected
> color (#!1 & sel) red
> select : 873, 867, 875, 878, 826, 881, 997, 999, 1000
108 atoms, 102 bonds, 9 residues, 1 model selected
> color (#!1 & sel) orange
> select : 611, 876, 1001, 599, 603, 879, 615, 822, 869, 614, 817, 861, 880,
> 1004
150 atoms, 141 bonds, 14 residues, 1 model selected
> color (#!1 & sel) yellow
> select : 610, 776, 778, 790, 827, 863, 874, 767, 772, 781, 866, 602, 605,
> 621, 820, 829, 793, 612, 617, 689, 725, 780
245 atoms, 232 bonds, 22 residues, 1 model selected
> color (#!1 & sel) lime
> select : 619, 600, 604, 865, 607, 608, 620, 791, 862, 601, 730, 1002, 1003,
> 786, 816, 828, 870, 871
158 atoms, 146 bonds, 18 residues, 1 model selected
> color (#!1 & sel) cyan
> select : 618, 774, 785, 796, 846, 872, 943, 944, 616, 676, 703, 766, 769,
> 770, 794, 795, 797, 825, 609, 677, 691, 708, 732, 801, 804, 847, 849, 937,
> 938, 942, 606, 613, 683, 684, 706, 715, 716, 717, 721, 728, 729, 733-738,
> 741, 768, 798, 831, 835, 889, 919, 934, 936, 940
570 atoms, 540 bonds, 57 residues, 1 model selected
> color (#!1 & sel) blue
> select : 681, 686, 690, 692, 696, 701, 722, 739, 740, 775, 779, 789, 800,
> 809, 811, 813, 814, 834, 855, 890, 892, 896, 898, 899, 904, 905, 910, 915,
> 916, 918, 920, 922, 924, 926, 927, 931, 935, 941, 953, 939, 868
434 atoms, 408 bonds, 40 residues, 1 model selected
> color (#!1 & sel) purple
> color #1 #fffff4ff
> undo
> color #2 #ffe3b0ff
> color #2 #cebea1ff
> color #2 #cebea0ff
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue-white-red :min : :max white:
> key blue:min white: red:max white: white:
> key blue:min white: red:max white: white: white:
> key blue:min white: red:max white: white: white: white:
> key blue:min white: red:max white: white: white: white: white:
> key blue:min white: red:max white: white: white: white: white: white:
> key blue:min white: red:max white: white: white: white: white:
Fetching url
https://www.colourlovers.com/api/palettes?keywords=custom&format=json&numResults=100
failed:
HTTP Error 500: Internal Server Error
> ui tool show "Color Key"
> key blue:min white: red:max white: white: white: white: #ff2600:
> key blue:min white: red:max white: white: white: #ff9300: #ff2600:
> key blue:min white: red:max white: white: #fffb00: #ff9300: #ff2600:
> key blue:min white: red:max white: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min white: red:max #00fdff: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min white: #0433ff:max #00fdff: #00f900: #fffb00: #ff9300: #ff2600:
> key blue:min #942192: #0433ff:max #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:min #942192: #0433ff:max #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2: #942192: #0433ff:max #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192: #0433ff:max #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:max #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2 #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2- #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff: #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6 #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6- #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-1 #00f900: #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900: #fffb00: #ff9300:
> #ff2600:
> key colorTreatment distinct
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:1 #fffb00: #ff9300:
> #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11 #fffb00:
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11- #fffb00:
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-5 #fffb00:
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11- #fffb00:
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-1 #fffb00:
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-16 #fffb00:
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 "#00f900:11-16\\\" #fffb00:
> #ff9300: #ff2600:
[Repeated 5 time(s)]
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:1
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-2
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300: #ff2600:
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300: #ff2600:2
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300: #ff2600:25
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300: #ff2600:25-
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300: #ff2600:25-3
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300: #ff2600:25-30
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:2 #ff2600:25-30
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21 #ff2600:25-30
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21- #ff2600:25-30
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21-2 #ff2600:25-30
> key #fffad2:0 #942192:1 #0433ff:2-5 #00fdff:6-10 #00f900:11-15 #fffb00:16-20
> #ff9300:21-24 #ff2600:25-30
> ui mousemode right translate
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right translate
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right translate
> ui mousemode left 'color key'
> ui mousemode left rotate
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right translate
> ui mousemode left 'color key'
> ui mousemode left rotate
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right translate
> ui mousemode left 'color key'
> key pos 0.0459614,0.103429 size 0.695769,0.0438045
> key pos 0.0573605,0.0977318 size 0.908522,0.0476685
> key pos 0.0465385,0.228494 size 0.933026,0.042251
> ui mousemode left rotate
> ui mousemode right 'color key'
> ui mousemode right translate
> select clear
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/AmyDeLury/Desktop/movie1.mp4
Movie saved to /Users/AmyDeLury/Desktop/movie1.mp4
> hide #3#!1-2 target m
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.00.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.00.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for model.000.00.pdb
---
Chain | Description
4.2/A | No description available
4.1/E | No description available
> interfaces #4.2#!4.1 & ~solvent
1 buried areas: #4.2/A #4.1/E 1377
Alignment identifier is 4.1/E
Alignment identifier is 4.2/A
> select ~sel & ##selected
12084 atoms, 12309 bonds, 3 pseudobonds, 1237 residues, 3 models selected
> delete atoms (#4.2#!4.1 & sel)
> delete bonds (#4.2#!4.1 & sel)
> show #!4.1-2 surfaces
> mlp #!4.1-2
Map values for surface "model.000.00.pdb_A SES surface": minimum -21.29, mean
-5.576, maximum 19.15
Map values for surface "model.000.00.pdb_E SES surface": minimum -23.41, mean
-3.292, maximum 21.61
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!4.1-2
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Coulombic values for model.000.00.pdb_E SES surface
#4.1.2: minimum, -8.55, mean 3.20, maximum 16.51
Coulombic values for model.000.00.pdb_A SES surface #4.2.2: minimum, -19.26,
mean -1.83, maximum 8.27
To also show corresponding color key, enter the above coulombic command and
add key true
> color #!4.1-2 byhetero
> color #!4.1-2 bychain
> color #4.1 #00fdffff
> color #4.2 #ff2600ff
> interfaces #!4.1-2 & ~solvent
1 buried areas: #4.1/E #4.2/A 1178
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/Interacting_Residues_Only/model000.pdb"
> style #!4.1-2 ball
Changed 537 atom styles
> hide #!4.1-2 surfaces
> style #!4.1-2 sphere
Changed 537 atom styles
> style #!4.1-2 ball
Changed 537 atom styles
> nucleotides #!4.1-2 atoms
> style nucleic & #!4.1-2 stick
Changed 0 atom styles
> show #!4.1-2 cartoons
> show #!4.1-2 surfaces
> save /Users/AmyDeLury/Desktop/image3.png supersample 3
> close #4
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.01.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.01.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for model.000.01.pdb
---
Chain | Description
4.2/A | No description available
4.1/E | No description available
> interfaces #4.2#!4.1 & ~solvent
1 buried areas: #4.2/A #4.1/E 974
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.02.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.03.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.04.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.05.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.06.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.07.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.08.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.09.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.10.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.11.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.12.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.13.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.14.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.15.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.16.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.17.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.18.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.19.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.20.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.21.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.22.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.23.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.24.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.25.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.26.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.27.pdb"
> "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/model.000.28.pdb" "/Users/AmyDeLury/Library/CloudStorage/Box-
> Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
> Models/20240719_Shibisaki_model/Balanced Models/model.000.29.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.02.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.03.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.04.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.05.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.06.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.07.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.08.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.09.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.10.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.11.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.12.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.13.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.14.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.15.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.16.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.17.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.18.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.19.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.20.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.21.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.22.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.23.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.24.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.25.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.26.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.27.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.28.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced Models/model.000.29.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for model.000.02.pdb
---
Chain | Description
5.2/A | No description available
5.1/E | No description available
Chain information for model.000.03.pdb
---
Chain | Description
6.2/A | No description available
6.1/E | No description available
Chain information for model.000.04.pdb
---
Chain | Description
7.2/A | No description available
7.1/E | No description available
Chain information for model.000.05.pdb
---
Chain | Description
8.2/A | No description available
8.1/E | No description available
Chain information for model.000.06.pdb
---
Chain | Description
9.2/A | No description available
9.1/E | No description available
Chain information for model.000.07.pdb
---
Chain | Description
10.2/A | No description available
10.1/E | No description available
Chain information for model.000.08.pdb
---
Chain | Description
11.2/A | No description available
11.1/E | No description available
Chain information for model.000.09.pdb
---
Chain | Description
12.2/A | No description available
12.1/E | No description available
Chain information for model.000.10.pdb
---
Chain | Description
13.2/A | No description available
13.1/E | No description available
Chain information for model.000.11.pdb
---
Chain | Description
14.2/A | No description available
14.1/E | No description available
Chain information for model.000.12.pdb
---
Chain | Description
15.2/A | No description available
15.1/E | No description available
Chain information for model.000.13.pdb
---
Chain | Description
16.2/A | No description available
16.1/E | No description available
Chain information for model.000.14.pdb
---
Chain | Description
17.2/A | No description available
17.1/E | No description available
Chain information for model.000.15.pdb
---
Chain | Description
18.2/A | No description available
18.1/E | No description available
Chain information for model.000.16.pdb
---
Chain | Description
19.2/A | No description available
19.1/E | No description available
Chain information for model.000.17.pdb
---
Chain | Description
20.2/A | No description available
20.1/E | No description available
Chain information for model.000.18.pdb
---
Chain | Description
21.2/A | No description available
21.1/E | No description available
Chain information for model.000.19.pdb
---
Chain | Description
22.2/A | No description available
22.1/E | No description available
Chain information for model.000.20.pdb
---
Chain | Description
23.2/A | No description available
23.1/E | No description available
Chain information for model.000.21.pdb
---
Chain | Description
24.2/A | No description available
24.1/E | No description available
Chain information for model.000.22.pdb
---
Chain | Description
25.2/A | No description available
25.1/E | No description available
Chain information for model.000.23.pdb
---
Chain | Description
26.2/A | No description available
26.1/E | No description available
Chain information for model.000.24.pdb
---
Chain | Description
27.2/A | No description available
27.1/E | No description available
Chain information for model.000.25.pdb
---
Chain | Description
28.2/A | No description available
28.1/E | No description available
Chain information for model.000.26.pdb
---
Chain | Description
29.2/A | No description available
29.1/E | No description available
Chain information for model.000.27.pdb
---
Chain | Description
30.2/A | No description available
30.1/E | No description available
Chain information for model.000.28.pdb
---
Chain | Description
31.2/A | No description available
31.1/E | No description available
Chain information for model.000.29.pdb
---
Chain | Description
32.2/A | No description available
32.1/E | No description available
> color
> #4.2#5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#31.2#32.2#!4.1#!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1#!31.1#!32.1
> byhetero
> color
> #4.2#5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#31.2#32.2#!4.1#!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1#!31.1#!32.1
> bychain
> hide
> #4.2#5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#31.2#32.2#!4-32#!4.1#!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1#!31.1#!32.1
> target m
> show #!4.1 models
> show #4.2 models
Alignment identifier is 4.1/E
Alignment identifier is 4.2/A
> select ~sel & ##selected
12251 atoms, 12465 bonds, 3 pseudobonds, 1253 residues, 3 models selected
> delete atoms (#4.2#!4.1 & sel)
> delete bonds (#4.2#!4.1 & sel)
> show #!4.1-2 surfaces
> color #4.1 #00fdffff
> color #4.2 #ff2600ff
> color #4 cyan
> color #5.1 #00fdffff
> show
> #!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1#!31.1#!32.1
> target m
> color
> #4#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1#15.1#16.1#17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1#28.1#29.1#30.1#31.1#32.1#!5-32
> cyan
> hide
> #!5.1#!6.1#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1#!31.1#!32.1
> target m
> color #4.2 #ff2600ff
> hide #!6 models
> hide #!7 models
> show #!32.1 models
> hide #!32.1 models
> hide
> #7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#31.2#!7-32#!7.1#!8.1#!9.1#!10.1#!11.1#!12.1#!13.1#!14.1#!15.1#!16.1#!17.1#!18.1#!19.1#!20.1#!21.1#!22.1#!23.1#!24.1#!25.1#!26.1#!27.1#!28.1#!29.1#!30.1#!31.1#!32.1
> target m
> hide #!4-5#!4.1-2 target m
> show #5.2 models
> show #6.2 models
> show #7.2 models
> show #8.2 models
> show #9.2 models
> show #10.2 models
> show #11.2 models
> show #12.2 models
> show #13.2 models
> show #14.2 models
> show #16.2 models
> show #15.2 models
> show #17.2 models
> show #18.2 models
> show #19.2 models
> show #21.2 models
> show #20.2 models
> show #22.2 models
> show #23.2 models
> show #25.2 models
> show #24.2 models
> show #26.2 models
> show #27.2 models
> show #28.2 models
> show #29.2 models
> show #30.2 models
> show #31.2 models
> show #32.2 models
> color
> #5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#31.2#32.2#!5-32
> red
> show
> #5.2#6.2#7.2#8.2#9.2#10.2#11.2#12.2#13.2#14.2#15.2#16.2#17.2#18.2#19.2#20.2#21.2#22.2#23.2#24.2#25.2#26.2#27.2#28.2#29.2#30.2#31.2#32.2
> surfaces
> hide
> #!5-32#!4.2#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2#!31.1-2#!32.1-2
> target m
> show #!4.1 models
> rainbow #!4.1
> undo
> hide #!4.1 models
> color #4.1 #00fdffff
> show #!4.1 models
> show #!4.2 models
> interfaces #!4.1-2 & ~solvent
1 buried areas: #4.2/A #4.1/E 941
> save /Users/AmyDeLury/Desktop/image1.png supersample 3
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/Interacting_Residues_Only/model000.01.pdb" models #4
> close #4
> show #!5.1 models
> show #!5.2 models
> show
> #!5-32#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2#!31.1-2#!32.1-2
> target m
> show
> #!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2#!31.1-2#!32.1-2
> surfaces
> hide target m
> show #!5.1 models
> show #!5.2 models
> show #!6.1 models
> show #!6.2 models
> hide #!6.2 models
> hide #!6.1 models
> hide #!5 models
> hide #!5.1 models
> hide #!5.2 models
> hide #!6 models
> show
> #!5-32#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2#!31.1-2#!32.1-2
> target m
> show
> #!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2#!31.1-2#!32.1-2
> surfaces
> hide
> #!5-32#!5.1-2#!6.1-2#!7.1-2#!8.1-2#!9.1-2#!10.1-2#!11.1-2#!12.1-2#!13.1-2#!14.1-2#!15.1-2#!16.1-2#!17.1-2#!18.1-2#!19.1-2#!20.1-2#!21.1-2#!22.1-2#!23.1-2#!24.1-2#!25.1-2#!26.1-2#!27.1-2#!28.1-2#!29.1-2#!30.1-2#!31.1-2#!32.1-2
> target m
> show #!5.1 models
> show #!5.2 models
> interfaces #!5.1-2 & ~solvent
1 buried areas: #5.2/A #5.1/E 1491
> select ~sel
377969 atoms, 384201 bonds, 137 pseudobonds, 38615 residues, 116 models
selected
> select clear
> select ~sel & ##selected
12101 atoms, 12331 bonds, 3 pseudobonds, 1237 residues, 3 models selected
> delete atoms (#!5.1-2 & sel)
> delete bonds (#!5.1-2 & sel)
> interfaces #!5.1-2 & ~solvent
1 buried areas: #5.2/A #5.1/E 1382
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/Interacting_Residues_Only/model000.02.pdb" models #5
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> close #5
> undo
Undo failed, probably because structures have been modified.
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/Interacting_Residues_Only/model000.02.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced
Models/Interacting_Residues_Only/model000.02.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 VAL E 608 LEU E 615
1 4
Start residue of secondary structure not found: HELIX 2 2 ARG E 999 LYS E 1003
1 5
Chain information for model000.02.pdb
---
Chain | Description
4.2/A | No description available
4.1/E | No description available
> color #4.1 #00fdffff
> color #4.2 #ff2600ff
> show #!4.1-2 surfaces
> interfaces #!4.1-2 & ~solvent
1 buried areas: #4.2/A #4.1/E 1382
> save /Users/AmyDeLury/Desktop/image2.png supersample 3
> close #4
> show #!6.1 models
> show #!6.2 models
> interfaces #!6.1-2 & ~solvent
1 buried areas: #6.2/A #6.1/E 1601
> select ~sel & ##selected
12036 atoms, 12265 bonds, 3 pseudobonds, 1231 residues, 3 models selected
> delete atoms (#!6.1-2 & sel)
> delete bonds (#!6.1-2 & sel)
> interfaces #!6.1-2 & ~solvent
1 buried areas: #6.2/A #6.1/E 1547
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/Interacting_Residues_Only/model000.03.pdb" models #6
> save /Users/AmyDeLury/Desktop/image3.png supersample 3
> close #6
> show #!7.1 models
> show #!7.2 models
> interfaces #!7.1-2 & ~solvent
1 buried areas: #7.2/A #7.1/E 1939
> select ~sel & ##selected
11904 atoms, 12128 bonds, 3 pseudobonds, 1215 residues, 3 models selected
> delete atoms (#!7.1-2 & sel)
> delete bonds (#!7.1-2 & sel)
> interfaces #!7.1-2 & ~solvent
1 buried areas: #7.1/E #7.2/A 1863
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/Interacting_Residues_Only/model000.04pdb.pdb" models #7
> close #7
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/Interacting_Residues_Only/model000.04pdb.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20240719_Shibisaki_model/Balanced
Models/Interacting_Residues_Only/model000.04pdb.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Start residue of secondary structure not found: HELIX 1 1 PHE E 614 LEU E 615
1 2
Start residue of secondary structure not found: HELIX 2 2 LEU E 725 LEU E 725
1 1
Start residue of secondary structure not found: SHEET 1 1 1 TYR E 772 TYR E
772 0
Chain information for model000.04pdb.pdb
---
Chain | Description
4.2/A | No description available
4.1/E | No description available
> color #4 cyan
> hide #!4.1 models
> color #4.2#!4 red
> show #!4.1 models
> show #!4.1-2 surfaces
> interfaces #!4.1-2 & ~solvent
1 buried areas: #4.1/E #4.2/A 1863
> save /Users/AmyDeLury/Desktop/image4.png supersample 3
> close #4
> show #!8.1 models
> show #!8.2 models
> interfaces #!8.1-2 & ~solvent
1 buried areas: #8.2/A #8.1/E 1457
> select ~sel & ##selected
12100 atoms, 12327 bonds, 3 pseudobonds, 1240 residues, 3 models selected
> delete atoms (#!8.1-2 & sel)
> delete bonds (#!8.1-2 & sel)
> interfaces #!8.1-2 & ~solvent
1 buried areas: #8.2/A #8.1/E 1374
> save "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking Models/20240719_Shibisaki_model/Balanced
> Models/Interacting_Residues_Only/model000.05.pdb" models #8
> save /Users/AmyDeLury/Desktop/image5.png supersample 3
> close #8
> show #!9.1 models
> show #!9.2 models
> close
> #9-32#9.1-2#10.1-2#11.1-2#12.1-2#13.1-2#14.1-2#15.1-2#16.1-2#17.1-2#18.1-2#19.1-2#20.1-2#21.1-2#22.1-2#23.1-2#24.1-2#25.1-2#26.1-2#27.1-2#28.1-2#29.1-2#30.1-2#31.1-2#32.1-2
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> open "/Users/AmyDeLury/Library/CloudStorage/Box-Box/Klein Lab/Klein Lab
> Data/Epac2-SUR1 Project/Docking
> Models/20242905_epac2_sur1_whole_dock/EPAC2_AF_lig.pdb"
Summary of feedback from opening /Users/AmyDeLury/Library/CloudStorage/Box-
Box/Klein Lab/Klein Lab Data/Epac2-SUR1 Project/Docking
Models/20242905_epac2_sur1_whole_dock/EPAC2_AF_lig.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK original generated coordinate pdb file
Chain information for EPAC2_AF_lig.pdb #4
---
Chain | Description
A | No description available
> view
> select : 353
30 atoms, 28 bonds, 3 residues, 3 models selected
> color (#4 & sel) red
> show sel & #4 surfaces
> select
35035 atoms, 35591 bonds, 54 pseudobonds, 3640 residues, 5 models selected
> hide sel & #!4 surfaces
> show sel & #!4 surfaces
> select : 353
30 atoms, 28 bonds, 3 residues, 3 models selected
> select : 353, 181, 184, 351, 423, 190, 354, 369, 183, 187, 374, 398, 457,
> 186, 359, 182, 193, 352, 360, 364, 366, 424, 173, 361, 427, 428, 446, 172,
> 180, 227, 228, 456, 161, 175, 176, 178, 370, 372, 376, 417, 151, 165, 171,
> 174, 177, 198, 355, 362, 419, 453, 179, 188, 226, 283, 284, 338, 367, 444,
> 845, 294, 412, 413, 420, 429, 849, 164, 189, 194, 197, 201, 277, 310, 363,
> 373, 378, 383, 415, 458, 152, 185, 199, 204, 223, 276, 290, 386, 389, 409,
> 442, 772, 883, 978, 1, 220, 229, 239, 278, 311, 335, 399, 405, 406, 407,
> 416, 431, 451, 452, 770, 774, 890, 975, 977, 9, 12, 29, 169, 170, 191, 275,
> 293, 296, 302, 306, 314, 317, 337, 371, 379, 408, 422, 430, 433, 440, 485,
> 853, 856, 880, 884, 933, 979, 1010, 1011, 5, 6, 147, 148, 196, 219, 224,
> 225, 230, 272, 295, 303, 333, 336, 356, 365, 387 388, 404, 410, 421, 441,
> 455, 461, 486, 488, 491, 495, 517, 519, 524, 769, 775, 799, 803, 817, 842,
> 886, 887, 889, 892, 894, 897, 902, 929, 932, 936, 942, 944, 972, 974, 2, 8,
> 22, 36, 40, 66, 144, 153, 160, 166, 167, 200, 208, 216, 217, 281, 285, 291,
> 298, 299, 307, 309, 334, 340, 368, 375, 377, 382, 394, 411, 414, 437, 439,
> 466, 480, 482, 484, 487, 492, 496, 497, 514, 521, 528, 545, 548, 551, 555,
> 557, 562,564, 565, 568, 604, 615, 693, 725, 733, 839, 846, 906, 928, 939,
> 941, 943, 1009, 11, 14, 20, 24, 32, 33, 37, 48, 61, 62, 64, 65, 67, 68, 75,
> 76, 78, 79, 85, 91, 94, 134, 137, 139, 140,, 141, 155, 168, 192, 195, 202,
> 205, 231-234, 240, 247, 250, 274, 279, 282, 301, 305, 321, 330, 339, 342,
> 344, 345, 358, 381, 384, 390, 434, 447, 449, 454, 459, 460, 462, 465, 467,
> 468, 472, 473, 476, 477, 478, 481, 483, 489, 490, 493, 494, 498, 499, 501,
> 506, 511, 512, 515, 518, 520, 522, 525, 529, 532, 544, 552, 560, 563, 567,
> 569, 571, 572, 573, 575, 576, 608, 618, 677-680, 707, 708, 710, 720, 722,
> 724, 726, 745-749, 755, 758, 761, 804, 807, 814, 821, 838, 868, 871, 873,
> 877, 879, 903, 904, 917, 938, 945, 947, 949, 952, 956, 959, 966, 967, 968,
> 970, 976, 981, 1000, 1002
Expected a keyword
> select : 353, 181, 184, 351, 423, 190, 354, 369, 183, 187, 374, 398, 457,
> 186, 359, 182, 193, 352, 360, 364, 366, 424, 173, 361, 427, 428, 446, 172,
> 180, 227, 228, 456, 161, 175, 176, 178, 370, 372, 376, 417, 151, 165, 171,
> 174, 177, 198, 355, 362, 419, 453, 179, 188, 226, 283, 284, 338, 367, 444,
> 845, 294, 412, 413, 420, 429, 849, 164, 189, 194, 197, 201, 277, 310, 363,
> 373, 378, 383, 415, 458, 152, 185, 199, 204, 223, 276, 290, 386, 389, 409,
> 442, 772, 883, 978, 1, 220, 229, 239, 278, 311, 335, 399, 405, 406, 407,
> 416, 431, 451, 452, 770, 774, 890, 975, 977, 9, 12, 29, 169, 170, 191, 275,
> 293, 296, 302, 306, 314, 317, 337, 371, 379, 408, 422, 430, 433, 440, 485,
> 853, 856, 880, 884, 933, 979, 1010, 1011, 5, 6, 147, 148, 196, 219, 224,
> 225, 230, 272, 295, 303, 333, 336, 356, 365, 387, 388, 404, 410, 421, 441,
> 455, 461, 486, 488, 491, 495, 517, 519, 524, 769, 775, 799, 803, 817, 842,
> 886, 887, 889, 892, 894, 897, 902, 929, 932, 936, 942, 944, 972, 974, 2, 8,
> 22, 36, 40, 66, 144, 153, 160, 166, 167, 200, 208, 216, 217, 281, 285, 291,
> 298, 299, 307, 309, 334, 340, 368, 375, 377, 382, 394, 411, 414, 437, 439,
> 466, 480, 482, 484, 487, 492, 496, 497, 514, 521, 528, 545, 548, 551, 555,
> 557, 562,564, 565, 568, 604, 615, 693, 725, 733, 839, 846, 906, 928, 939,
> 941, 943, 1009, 11, 14, 20, 24, 32, 33, 37, 48, 61, 62, 64, 65, 67, 68, 75,
> 76, 78, 79, 85, 91, 94, 134, 137, 139, 140,, 141, 155, 168, 192, 195, 202,
> 205, 231-234, 240, 247, 250, 274, 279, 282, 301, 305, 321, 330, 339, 342,
> 344, 345, 358, 381, 384, 390, 434, 447, 449, 454, 459, 460, 462, 465, 467,
> 468, 472, 473, 476, 477, 478, 481, 483, 489, 490, 493, 494, 498, 499, 501,
> 506, 511, 512, 515, 518, 520, 522, 525, 529, 532, 544, 552, 560, 563, 567,
> 569, 571, 572, 573, 575, 576, 608, 618, 677-680, 707, 708, 710, 720, 722,
> 724, 726, 745-749, 755, 758, 761, 804, 807, 814, 821, 838, 868, 871, 873,
> 877, 879, 903, 904, 917, 938, 945, 947, 949, 952, 956, 959, 966, 967, 968,
> 970, 976, 981, 1000, 1002
Expected an objects specifier or a keyword
OpenGL version: 4.1 ATI-5.1.35
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 580~743
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 2 days, 13 hours, 26 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → glGetIntegerv: invalid value |
comment:2 by , 15 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | glGetIntegerv: invalid value → Crash in QTimer event callback |
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Crash in QTimer event callback. Appears the Python callback was probably already released. I think QTimer may not keep a reference to its Python callback which would be a PyQt bug. No Python traceback so don't know what QTimer.