id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15755	Crash in QTimer event callback	chimerax-bug-report@…	Tom Goddard	"{{{
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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===== 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

}}}
"	defect	closed	normal		Graphics		can't reproduce						all	ChimeraX