PICKLUSTER: list index out of range

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.3-arm64-arm-64bit
ChimeraX Version: 1.10rc202506130232 (2025-06-13 02:32:35 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/zhangmi/Downloads/AlphaFold3/Method B/S113-WT-MBD3.cxs"

Log from Tue Jun 17 19:02:56 2025UCSF ChimeraX version: 1.10rc202506130232
(2025-06-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/zhangmi/Downloads/AlphaFold3/Method
> B/GRAMMresults-97730-GATAD2A-WT/receptor-ligand_model1.pdb"

Summary of feedback from opening /Users/zhangmi/Downloads/AlphaFold3/Method
B/GRAMMresults-97730-GATAD2A-WT/receptor-ligand_model1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Docking models Generated by GRAMM  
  
Chain information for receptor-ligand_model1.pdb #1  
---  
Chain | Description  
A | No description available  
C | No description available  
  
Computing secondary structure  

> select /A

4765 atoms, 4846 bonds, 633 residues, 1 model selected  

> select clear

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Cluster information for receptor-ligand_model1.pdb['A', 'C']  
---  
Cluster | Residues  
1 | [['A', 'ASP', 22], ['A', 'GLU', 25], ['A', 'SER', 26], ['A', 'LYS', 27], ['A', 'ILE', 29], ['A', 'LYS', 30], ['A', 'MET', 31], ['A', 'GLU', 32], ['A', 'ARG', 33], ['A', 'GLY', 34], ['A', 'LEU', 376], ['A', 'PRO', 377], ['A', 'SER', 378], ['A', 'ALA', 379], ['A', 'ALA', 380], ['A', 'ASN', 381], ['A', 'ASN', 382], ['A', 'GLU', 383], ['A', 'TYR', 386], ['A', 'LEU', 390], ['A', 'GLU', 392], ['A', 'VAL', 393], ['A', 'VAL', 394], ['A', 'ASN', 396], ['A', 'LEU', 397], ['A', 'THR', 400], ['A', 'GLN', 401], ['A', 'MET', 404], ['A', 'SER', 405], ['A', 'ALA', 406], ['A', 'ALA', 407], ['A', 'THR', 408], ['A', 'VAL', 409], ['A', 'LEU', 410], ['A', 'SER', 411], ['A', 'ARG', 412], ['A', 'GLU', 413], ['A', 'PRO', 414], ['A', 'TYR', 415], ['A', 'MET', 416], ['A', 'CYS', 417], ['A', 'ALA', 418], ['A', 'LYS', 421], ['A', 'ASP', 423], ['A', 'PHE', 424], ['A', 'THR', 425], ['A', 'CYS', 426], ['A', 'ARG', 427], ['A', 'TRP', 428], ['A', 'GLU', 430], ['A', 'SER', 433], ['A', 'GLY', 434], ['A', 'ALA', 435], ['A', 'ILE', 436], ['A', 'TYR', 616], ['C', 'MET', 1], ['C', 'GLU', 2], ['C', 'ARG', 3], ['C', 'LYS', 4], ['C', 'TRP', 6], ['C', 'GLU', 19], ['C', 'ARG', 22], ['C', 'ARG', 23], ['C', 'ARG', 31], ['C', 'ASP', 32], ['C', 'PHE', 34], ['C', 'SER', 39], ['C', 'GLY', 40], ['C', 'LYS', 41], ['C', 'LYS', 42], ['C', 'ARG', 44], ['C', 'SER', 45], ['C', 'LYS', 46], ['C', 'PRO', 47], ['C', 'GLN', 48], ['C', 'ARG', 51], ['C', 'PRO', 93], ['C', 'LEU', 95], ['C', 'TRP', 139], ['C', 'LEU', 143], ['C', 'LEU', 146], ['C', 'ASN', 147], ['C', 'ALA', 148], ['C', 'PHE', 149], ['C', 'ILE', 151], ['C', 'ALA', 152], ['C', 'GLU', 153], ['C', 'VAL', 156], ['C', 'THR', 158], ['C', 'MET', 159], ['C', 'ASP', 160], ['C', 'GLU', 175], ['C', 'LEU', 178], ['C', 'SER', 179], ['C', 'ALA', 182], ['C', 'SER', 183], ['C', 'GLN', 228], ['C', 'GLU', 229], ['C', 'LEU', 231], ['C', 'VAL', 232], ['C', 'GLN', 234], ['C', 'VAL', 235], ['C', 'ARG', 236], ['C', 'ARG', 238], ['C', 'LEU', 239]]  
2 | [['A', 'ARG', 213], ['A', 'MET', 214], ['A', 'PRO', 215], ['A', 'GLY', 216], ['A', 'SER', 217], ['A', 'VAL', 218], ['C', 'THR', 189], ['C', 'MET', 190], ['C', 'PRO', 191], ['C', 'THR', 193], ['C', 'GLY', 194], ['C', 'GLN', 195], ['C', 'LEU', 196], ['C', 'TRP', 207], ['C', 'ASN', 209], ['C', 'THR', 211], ['C', 'GLN', 212]]  
3 | [['A', 'ALA', 37], ['A', 'SER', 38], ['A', 'ASP', 39], ['A', 'LEU', 40], ['C', 'GLU', 7], ['C', 'CYS', 8], ['C', 'PRO', 9], ['C', 'ALA', 10], ['C', 'MET', 69], ['C', 'MET', 71]]  
4 | [['A', 'SER', 608], ['A', 'ALA', 609], ['A', 'VAL', 610], ['A', 'ASP', 611], ['A', 'GLN', 613], ['A', 'ARG', 614], ['C', 'GLU', 241], ['C', 'ALA', 242], ['C', 'LEU', 243], ['C', 'MET', 244], ['C', 'ALA', 245], ['C', 'ASP', 246], ['C', 'MET', 247], ['C', 'LEU', 248], ['C', 'ALA', 249], ['C', 'GLU', 252]]  
5 | [['A', 'ARG', 563], ['A', 'THR', 564], ['A', 'GLY', 565], ['A', 'ARG', 566], ['C', 'GLU', 289], ['C', 'HIS', 290], ['C', 'VAL', 291]]  
6 | [['A', 'SER', 239], ['A', 'SER', 240], ['A', 'GLN', 241], ['C', 'GLU', 223], ['C', 'ARG', 226], ['C', 'LYS', 227], ['C', 'GLU', 230]]  
7 | [['A', 'ARG', 143], ['C', 'LEU', 26]]  
8 | [['A', 'VAL', 294], ['A', 'ALA', 295], ['A', 'ASN', 296], ['A', 'VAL', 297], ['A', 'PRO', 298], ['A', 'ASN', 299], ['C', 'GLY', 258], ['C', 'GLU', 259], ['C', 'ALA', 260], ['C', 'PRO', 261], ['C', 'LEU', 262], ['C', 'ASP', 263], ['C', 'LYS', 264], ['C', 'CYS', 266]]  
9 | [['A', 'ARG', 403], ['C', 'HIS', 118]]  
10 | [['A', 'THR', 121], ['A', 'VAL', 123], ['C', 'VAL', 89], ['C', 'LYS', 90]]  
11 | [['A', 'LEU', 36], ['C', 'LYS', 68]]  
12 | [['A', 'PRO', 311], ['C', 'GLU', 281]]  
13 | [['A', 'ASP', 84], ['C', 'ARG', 82]]  
14 | [['A', 'LEU', 350], ['A', 'LYS', 354], ['C', 'GLU', 275], ['C', 'GLU', 277]]  
  
No interface found for A:C  
Calculation of interface was successful  
Interactions in clusters in receptor-ligand_model1.pdb['A', 'C']  
---  
Cluster | Interactions  
1 | [[['A', 'ASP', 22], ['C', 'ARG', 23]], [['A', 'ASP', 22], ['C', 'MET', 1]], [['A', 'GLU', 25], ['C', 'MET', 1]], [['A', 'SER', 26], ['C', 'GLU', 2]], [['A', 'SER', 26], ['C', 'MET', 1]], [['A', 'LYS', 27], ['C', 'MET', 1]], [['A', 'LYS', 27], ['C', 'GLU', 2]], [['A', 'ILE', 29], ['C', 'LYS', 4]], [['A', 'ILE', 29], ['C', 'MET', 1]], [['A', 'ILE', 29], ['C', 'GLU', 2]], [['A', 'LYS', 30], ['C', 'GLU', 2]], [['A', 'LYS', 30], ['C', 'LYS', 4]], [['A', 'LYS', 30], ['C', 'ARG', 3]], [['A', 'MET', 31], ['C', 'LYS', 4]], [['A', 'MET', 31], ['C', 'GLU', 2]], [['A', 'GLU', 32], ['C', 'LYS', 4]], [['A', 'ARG', 33], ['C', 'TRP', 6]], [['A', 'ARG', 33], ['C', 'LYS', 4]], [['A', 'ARG', 33], ['C', 'ARG', 31]], [['A', 'ARG', 33], ['C', 'GLU', 19]], [['A', 'GLY', 34], ['C', 'TRP', 6]], [['A', 'GLY', 34], ['C', 'LYS', 4]], [['A', 'LEU', 376], ['C', 'LEU', 239]], [['A', 'PRO', 377], ['C', 'LEU', 239]], [['A', 'SER', 378], ['C', 'LEU', 239]], [['A', 'SER', 378], ['C', 'ARG', 238]], [['A', 'SER', 378], ['C', 'VAL', 235]], [['A', 'ALA', 379], ['C', 'VAL', 235]], [['A', 'ALA', 379], ['C', 'ARG', 238]], [['A', 'ALA', 380], ['C', 'VAL', 235]], [['A', 'ALA', 380], ['C', 'ARG', 238]], [['A', 'ALA', 380], ['C', 'GLN', 234]], [['A', 'ALA', 380], ['C', 'LEU', 231]], [['A', 'ALA', 380], ['C', 'ARG', 236]], [['A', 'ALA', 380], ['C', 'LEU', 239]], [['A', 'ASN', 381], ['C', 'VAL', 235]], [['A', 'ASN', 381], ['C', 'VAL', 232]], [['A', 'ASN', 381], ['C', 'LEU', 231]], [['A', 'ASN', 381], ['C', 'ARG', 236]], [['A', 'ASN', 382], ['C', 'VAL', 235]], [['A', 'ASN', 382], ['C', 'LEU', 231]], [['A', 'GLU', 383], ['C', 'GLN', 228]], [['A', 'GLU', 383], ['C', 'VAL', 232]], [['A', 'GLU', 383], ['C', 'GLU', 229]], [['A', 'GLU', 383], ['C', 'LEU', 231]], [['A', 'TYR', 386], ['C', 'MET', 159]], [['A', 'TYR', 386], ['C', 'ASP', 160]], [['A', 'TYR', 386], ['C', 'GLN', 228]], [['A', 'LEU', 390], ['C', 'MET', 159]], [['A', 'LEU', 390], ['C', 'LEU', 178]], [['A', 'LEU', 390], ['C', 'ALA', 182]], [['A', 'GLU', 392], ['C', 'PHE', 149]], [['A', 'GLU', 392], ['C', 'ALA', 148]], [['A', 'GLU', 392], ['C', 'VAL', 156]], [['A', 'VAL', 393], ['C', 'LEU', 178]], [['A', 'VAL', 393], ['C', 'SER', 179]], [['A', 'VAL', 393], ['C', 'THR', 158]], [['A', 'VAL', 393], ['C', 'GLU', 175]], [['A', 'VAL', 394], ['C', 'ALA', 182]], [['A', 'ASN', 396], ['C', 'ALA', 148]], [['A', 'ASN', 396], ['C', 'PHE', 149]], [['A', 'ASN', 396], ['C', 'ASN', 147]], [['A', 'LEU', 397], ['C', 'LEU', 143]], [['A', 'LEU', 397], ['C', 'SER', 179]], [['A', 'LEU', 397], ['C', 'TRP', 139]], [['A', 'LEU', 397], ['C', 'SER', 183]], [['A', 'THR', 400], ['C', 'LEU', 146]], [['A', 'THR', 400], ['C', 'LEU', 143]], [['A', 'GLN', 401], ['C', 'LEU', 143]], [['A', 'GLN', 401], ['C', 'TRP', 139]], [['A', 'MET', 404], ['C', 'ARG', 51]], [['A', 'MET', 404], ['C', 'PRO', 47]], [['A', 'SER', 405], ['C', 'LEU', 95]], [['A', 'ALA', 406], ['C', 'PRO', 93]], [['A', 'ALA', 406], ['C', 'LEU', 146]], [['A', 'ALA', 406], ['C', 'LEU', 95]], [['A', 'ALA', 407], ['C', 'LEU', 95]], [['A', 'ALA', 407], ['C', 'PRO', 93]], [['A', 'THR', 408], ['C', 'PRO', 47]], [['A', 'THR', 408], ['C', 'LYS', 46]], [['A', 'VAL', 409], ['C', 'PRO', 47]], [['A', 'VAL', 409], ['C', 'LEU', 146]], [['A', 'VAL', 409], ['C', 'ASN', 147]], [['A', 'LEU', 410], ['C', 'PHE', 149]], [['A', 'SER', 411], ['C', 'PRO', 47]], [['A', 'SER', 411], ['C', 'SER', 45]], [['A', 'ARG', 412], ['C', 'SER', 45]], [['A', 'ARG', 412], ['C', 'ARG', 51]], [['A', 'ARG', 412], ['C', 'GLU', 153]], [['A', 'ARG', 412], ['C', 'GLN', 48]], [['A', 'ARG', 412], ['C', 'PRO', 47]], [['A', 'GLU', 413], ['C', 'ARG', 22]], [['A', 'GLU', 413], ['C', 'ARG', 44]], [['A', 'GLU', 413], ['C', 'GLU', 153]], [['A', 'GLU', 413], ['C', 'ASP', 32]], [['A', 'GLU', 413], ['C', 'SER', 45]], [['A', 'PRO', 414], ['C', 'GLU', 153]], [['A', 'PRO', 414], ['C', 'ARG', 44]], [['A', 'TYR', 415], ['C', 'GLN', 48]], [['A', 'TYR', 415], ['C', 'ARG', 44]], [['A', 'TYR', 415], ['C', 'ILE', 151]], [['A', 'TYR', 415], ['C', 'GLU', 153]], [['A', 'TYR', 415], ['C', 'ARG', 51]], [['A', 'MET', 416], ['C', 'ARG', 44]], [['A', 'MET', 416], ['C', 'ASP', 32]], [['A', 'MET', 416], ['C', 'PHE', 34]], [['A', 'CYS', 417], ['C', 'ARG', 44]], [['A', 'ALA', 418], ['C', 'LYS', 42]], [['A', 'ALA', 418], ['C', 'ARG', 3]], [['A', 'LYS', 421], ['C', 'ARG', 3]], [['A', 'LYS', 421], ['C', 'LYS', 42]], [['A', 'ASP', 423], ['C', 'ALA', 152]], [['A', 'ASP', 423], ['C', 'ILE', 151]], [['A', 'PHE', 424], ['C', 'ALA', 152]], [['A', 'THR', 425], ['C', 'ILE', 151]], [['A', 'THR', 425], ['C', 'ALA', 152]], [['A', 'CYS', 426], ['C', 'ILE', 151]], [['A', 'ARG', 427], ['C', 'ILE', 151]], [['A', 'TRP', 428], ['C', 'ILE', 151]], [['A', 'TRP', 428], ['C', 'ARG', 44]], [['A', 'TRP', 428], ['C', 'ALA', 152]], [['A', 'GLU', 430], ['C', 'LYS', 41]], [['A', 'SER', 433], ['C', 'LYS', 41]], [['A', 'SER', 433], ['C', 'GLY', 40]], [['A', 'SER', 433], ['C', 'SER', 39]], [['A', 'SER', 433], ['C', 'LYS', 42]], [['A', 'GLY', 434], ['C', 'LYS', 41]], [['A', 'GLY', 434], ['C', 'LYS', 42]], [['A', 'ALA', 435], ['C', 'LYS', 41]], [['A', 'ALA', 435], ['C', 'LYS', 42]], [['A', 'ILE', 436], ['C', 'ARG', 44]], [['A', 'ILE', 436], ['C', 'GLN', 48]], [['A', 'ILE', 436], ['C', 'LYS', 42]], [['A', 'TYR', 616], ['C', 'ARG', 238]]]  
2 | [[['A', 'ARG', 213], ['C', 'LEU', 196]], [['A', 'ARG', 213], ['C', 'TRP', 207]], [['A', 'MET', 214], ['C', 'ASN', 209]], [['A', 'MET', 214], ['C', 'LEU', 196]], [['A', 'MET', 214], ['C', 'GLN', 212]], [['A', 'MET', 214], ['C', 'GLY', 194]], [['A', 'MET', 214], ['C', 'GLN', 195]], [['A', 'MET', 214], ['C', 'THR', 193]], [['A', 'MET', 214], ['C', 'THR', 211]], [['A', 'PRO', 215], ['C', 'GLN', 212]], [['A', 'PRO', 215], ['C', 'PRO', 191]], [['A', 'PRO', 215], ['C', 'MET', 190]], [['A', 'PRO', 215], ['C', 'THR', 193]], [['A', 'PRO', 215], ['C', 'THR', 211]], [['A', 'PRO', 215], ['C', 'ASN', 209]], [['A', 'GLY', 216], ['C', 'PRO', 191]], [['A', 'GLY', 216], ['C', 'MET', 190]], [['A', 'GLY', 216], ['C', 'THR', 193]], [['A', 'GLY', 216], ['C', 'GLN', 212]], [['A', 'SER', 217], ['C', 'PRO', 191]], [['A', 'SER', 217], ['C', 'MET', 190]], [['A', 'SER', 217], ['C', 'THR', 189]], [['A', 'VAL', 218], ['C', 'THR', 189]], [['A', 'VAL', 218], ['C', 'MET', 190]], [['A', 'VAL', 218], ['C', 'PRO', 191]]]  
3 | [[['A', 'ALA', 37], ['C', 'PRO', 9]], [['A', 'ALA', 37], ['C', 'GLU', 7]], [['A', 'ALA', 37], ['C', 'CYS', 8]], [['A', 'SER', 38], ['C', 'PRO', 9]], [['A', 'ASP', 39], ['C', 'PRO', 9]], [['A', 'LEU', 40], ['C', 'MET', 71]], [['A', 'LEU', 40], ['C', 'ALA', 10]], [['A', 'LEU', 40], ['C', 'MET', 69]], [['A', 'LEU', 40], ['C', 'PRO', 9]]]  
4 | [[['A', 'SER', 608], ['C', 'LEU', 248]], [['A', 'ALA', 609], ['C', 'MET', 244]], [['A', 'ALA', 609], ['C', 'ALA', 245]], [['A', 'ALA', 609], ['C', 'GLU', 241]], [['A', 'ALA', 609], ['C', 'LEU', 248]], [['A', 'VAL', 610], ['C', 'ALA', 245]], [['A', 'VAL', 610], ['C', 'LEU', 248]], [['A', 'VAL', 610], ['C', 'MET', 247]], [['A', 'VAL', 610], ['C', 'ASP', 246]], [['A', 'VAL', 610], ['C', 'MET', 244]], [['A', 'VAL', 610], ['C', 'ALA', 249]], [['A', 'VAL', 610], ['C', 'GLU', 241]], [['A', 'ASP', 611], ['C', 'GLU', 252]], [['A', 'ASP', 611], ['C', 'ALA', 245]], [['A', 'ASP', 611], ['C', 'LEU', 248]], [['A', 'GLN', 613], ['C', 'ALA', 242]], [['A', 'GLN', 613], ['C', 'ALA', 245]], [['A', 'GLN', 613], ['C', 'ASP', 246]], [['A', 'GLN', 613], ['C', 'GLU', 241]], [['A', 'GLN', 613], ['C', 'LEU', 243]], [['A', 'ARG', 614], ['C', 'GLU', 252]]]  
5 | [[['A', 'ARG', 563], ['C', 'VAL', 291]], [['A', 'THR', 564], ['C', 'VAL', 291]], [['A', 'THR', 564], ['C', 'HIS', 290]], [['A', 'THR', 564], ['C', 'GLU', 289]], [['A', 'GLY', 565], ['C', 'VAL', 291]], [['A', 'ARG', 566], ['C', 'HIS', 290]]]  
6 | [[['A', 'SER', 239], ['C', 'GLU', 223]], [['A', 'SER', 239], ['C', 'ARG', 226]], [['A', 'SER', 240], ['C', 'GLU', 223]], [['A', 'SER', 240], ['C', 'LYS', 227]], [['A', 'GLN', 241], ['C', 'GLU', 230]]]  
7 | [[['A', 'ARG', 143], ['C', 'LEU', 26]]]  
8 | [[['A', 'VAL', 294], ['C', 'LYS', 264]], [['A', 'VAL', 294], ['C', 'CYS', 266]], [['A', 'ALA', 295], ['C', 'LYS', 264]], [['A', 'ASN', 296], ['C', 'PRO', 261]], [['A', 'ASN', 296], ['C', 'LEU', 262]], [['A', 'ASN', 296], ['C', 'LYS', 264]], [['A', 'ASN', 296], ['C', 'ASP', 263]], [['A', 'VAL', 297], ['C', 'LEU', 262]], [['A', 'PRO', 298], ['C', 'GLU', 259]], [['A', 'PRO', 298], ['C', 'PRO', 261]], [['A', 'PRO', 298], ['C', 'ALA', 260]], [['A', 'PRO', 298], ['C', 'GLY', 258]], [['A', 'ASN', 299], ['C', 'GLY', 258]]]  
9 | [[['A', 'ARG', 403], ['C', 'HIS', 118]]]  
10 | [[['A', 'THR', 121], ['C', 'VAL', 89]], [['A', 'THR', 121], ['C', 'LYS', 90]], [['A', 'VAL', 123], ['C', 'LYS', 90]]]  
11 | [[['A', 'LEU', 36], ['C', 'LYS', 68]]]  
12 | [[['A', 'PRO', 311], ['C', 'GLU', 281]]]  
13 | [[['A', 'ASP', 84], ['C', 'ARG', 82]]]  
14 | [[['A', 'LEU', 350], ['C', 'GLU', 277]], [['A', 'LEU', 350], ['C', 'GLU', 275]], [['A', 'LYS', 354], ['C', 'GLU', 277]]]  
  

> save "/Users/zhangmi/Downloads/AlphaFold3/Method B/S113-WT-MBD3.cxs"

——— End of log from Tue Jun 17 19:02:56 2025 ———

> view name session-start

opened ChimeraX session  

> select /A

4765 atoms, 4846 bonds, 633 residues, 1 model selected  

> select sequence ss

114 atoms, 105 bonds, 19 residues, 1 model selected  

> select clear

> select /A:113

6 atoms, 5 bonds, 1 residue, 1 model selected  

> label sel text Ser113

> label height 5

[Repeated 1 time(s)]

> color sel #79ff4cff

[Repeated 1 time(s)]

> color sel #81ff2bff

> color sel #ff824fff

[Repeated 1 time(s)]

> color sel #ff8250ff

> color sel #ff8150ff

> color sel #ff8151ff

> color sel #ff8438ff

[Repeated 1 time(s)]

> color sel #ff5733ff

> color sel #ff5633ff

> color sel #ff5533ff

[Repeated 2 time(s)]

> color sel #ff5533fd

> color sel #ff5533fb

> color sel #ff5533ed

> color sel #ff5533eb

> color sel #ff5533e9

> color sel #ff5533e6

> color sel #ff5533e3

> color sel #ff5533e0

> color sel #ff5533db

> color sel #ff5533d8

> color sel #ff5533d5

> color sel #ff5533cf

> color sel #ff5533ca

> color sel #ff5533c5

> color sel #ff5533bf

> color sel #ff5533bc

> color sel #ff5533ba

> color sel #ff5533b7

> color sel #ff5533b5

> color sel #ff5533b3

> color sel #ff5533b0

> color sel #ff5533af

> color sel #ff5533ae

[Repeated 1 time(s)]

> color sel #ff5533ad

> color sel #ff5533ac

> color sel #ff5533aa

> color sel #ff5533a8

> color sel #ff5533a6

> color sel #ff5533a4

> color sel #ff5533a3

> color sel #ff5533a1

> color sel #ff5533a0

> color sel #ff55339f

[Repeated 1 time(s)]

> color sel #ff55339e

[Repeated 1 time(s)]

> color sel #ff55339d

[Repeated 1 time(s)]

> color sel #ff55339e

[Repeated 1 time(s)]

> color sel #ff55339f

> color sel #ff5533a1

> color sel #ff5533a3

> color sel #ff5533a6

> color sel #ff5533a8

> color sel #ff5533aa

[Repeated 1 time(s)]

> color sel #ff5533ab

> color sel #ff5533ac

[Repeated 1 time(s)]

> color sel #ff5533ad

> color sel #ff5533ae

[Repeated 1 time(s)]

> color sel #ff5533af

[Repeated 1 time(s)]

> color sel #ff5533b0

[Repeated 1 time(s)]

> color sel #ff5533b1

> color sel #ff5533b2

> color sel #ff5533b3

[Repeated 1 time(s)]

> color sel #ff5533b4

> color sel #ff5533b5

[Repeated 1 time(s)]

> color sel #ff5533b6

[Repeated 2 time(s)]

> color sel #ff5533b7

> color sel #ff5533b8

> color sel #ff5533b9

> color sel #ff5533ba

> color sel #ff5533bb

> color sel #ff5533bc

> color sel #ff5533bd

> color sel #ff5533be

> color sel #ff5533bf

> color sel #ff5533c0

> color sel #ff5533c1

> color sel #ff5533c3

> color sel #ff5533c4

> color sel #ff5533c5

> color sel #ff5533c7

> color sel #ff5533ca

> color sel #ff5533cb

> color sel #ff5533cd

> color sel #ff5533d0

> color sel #ff5533d3

> color sel #ff5533d5

> color sel #ff5533d8

> color sel #ff5533db

> color sel #ff5533dd

> color sel #ff5533df

> color sel #ff5533e1

> color sel #ff5533e3

> color sel #ff5533e5

> color sel #ff5533e6

> color sel #ff5533e8

> color sel #ff5533e9

> color sel #ff5533ea

> color sel #ff5533eb

> color sel #ff5533ed

> color sel #ff5533ef

> color sel #ff5533f1

> color sel #ff5533f4

> color sel #ff5533f6

> color sel #ff5533f7

[Repeated 1 time(s)]

> color sel #ff5533f8

[Repeated 1 time(s)]

> color sel #ff5533f9

[Repeated 1 time(s)]

> color sel #ff5533fa

> color sel #ff5533fb

[Repeated 1 time(s)]

> color sel #ff5533fc

> color sel #ff5533fd

> color sel #ff5533ff

> color sel #ff5533ef

> color sel #ff5533e8

> color sel #ff5533e4

> color sel #ff5533e3

> color sel #ff5533e2

> color sel #ff5533e1

> color sel #ff5533dc

> color sel #ff5533d5

> color sel #ff5533cd

> color sel #ff5533c5

> color sel #ff5533bf

> color sel #ff5533bc

[Repeated 1 time(s)]

> color sel #ff5533bb

> color sel #ff5533ba

[Repeated 1 time(s)]

> color sel #ff5533b8

> color sel #ff5533b4

> select clear

> select /C

2300 atoms, 2344 bonds, 291 residues, 1 model selected  

> show sel surfaces

> color (#!1 & sel) black

> color (#!1 & sel) #404040ff

> color (#!1 & sel) #808080ff

> color (#!1 & sel) #bfbfbfff

> color (#!1 & sel) #808080ff

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1458, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/zhangmi/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/PICKLUSTER/__init__.py", line 50, in start_tool  
return tool.PICKLUSTER(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/zhangmi/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/PICKLUSTER/tool.py",
line 63, in __init__  
for chain in model.chains:  
^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute 'chains'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'PseudobondGroup' object has no attribute 'chains'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool PICKLUSTER
in bundle ChimeraX-PICKLUSTER:  
'PseudobondGroup' object has no attribute 'chains'  
  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  
Drag select of receptor-ligand_model1.pdb_C SES surface, 126 of 412620
triangles, 3 residues  

> style sel stick

Changed 29 atom styles  
Drag select of receptor-ligand_model1.pdb_C SES surface, 4973 of 412620
triangles, 21 residues, 7 pseudobonds  

> style sel stick

Changed 161 atom styles  

> select clear

[Repeated 1 time(s)]Drag select of receptor-ligand_model1.pdb_C SES surface,
228 of 412620 triangles, 14 residues  

> style sel stick

Changed 104 atom styles  

> select clear

Drag select of 7 residues  

> style sel stick

Changed 59 atom styles  

> style sel stick

Changed 59 atom styles  

> show sel cartoons

> show sel atoms

> hide sel atoms

Drag select of receptor-ligand_model1.pdb_C SES surface, 108 of 412620
triangles, 4 residues  

> show sel atoms

> select clear

Drag select of receptor-ligand_model1.pdb_C SES surface, 143 of 412620
triangles, 9 atoms, 4 residues, 7 bonds  

> hide sel atoms

> show sel atoms

> show sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> select clear

Drag select of receptor-ligand_model1.pdb_C SES surface, 92 of 412620
triangles, 14 atoms, 4 residues, 11 bonds  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> label height 5

[Repeated 1 time(s)]

> select clear

> color yellow

> undo

> set bgColor white

> select /A

4765 atoms, 4846 bonds, 633 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> show sel cartoons

> color (#!1 & sel) #92614eff

> color (#!1 & sel) #92614dff

> color (#!1 & sel) #927c3eff

> color (#!1 & sel) #2a4292ff

> color (#!1 & sel) #506292ff

> color (#!1 & sel) #922b20ff

[Repeated 3 time(s)]

> color (#!1 & sel) #923814ff

> color (#!1 & sel) #924614ff

> color (#!1 & sel) #923c1aff

> color (#!1 & sel) #923b1aff

> color (#!1 & sel) #922b20ff

> select clear

> transparency 30

> cartoon

> style ball

Changed 7065 atom styles  

> style stick

Changed 7065 atom styles  

> label #1-2 text "{0.name} {0.number}{0.insertion_code}"

> ~label #1-2 residues

> close

> open "/Users/zhangmi/Downloads/AlphaFold3/Method B/receptor-
> ligand_model1.pdb_A_S113D.pdb"

Summary of feedback from opening /Users/zhangmi/Downloads/AlphaFold3/Method
B/receptor-ligand_model1.pdb_A_S113D.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK THIS MUTANT(MUTABIND-A_1-S113D) STRUCTURE IS PRODUCED BY 100-STEP
ENERGY MINIMIZATION  
  
Ignored bad PDB record found on line 2  
REMARK DATE: 06/09/2025 05:02:12 PM CREATED BY SERVER: MUTABIND2  
  
Ignored bad PDB record found on line 3  
REMARK REFERENCE: PLEASE CITE ***  
  
Chain information for receptor-ligand_model1.pdb_A_S113D.pdb #1  
---  
Chain | Description  
A | No description available  
C | No description available  
  
Computing secondary structure  

> select /A

9671 atoms, 9752 bonds, 633 residues, 1 model selected  

> select sequence ss

187 atoms, 179 bonds, 17 residues, 1 model selected  

> select sequence ss

187 atoms, 179 bonds, 17 residues, 1 model selected  

> select clear

> select /A:113

12 atoms, 11 bonds, 1 residue, 1 model selected  

> close

> open /Users/zhangmi/Downloads/AlphaFold3/BATF-
> MOTIF_GATAD2A-WT/fold_s113_wt_batf_motif/fold_s113_wt_batf_motif_model_0.cif

Chain information for fold_s113_wt_batf_motif_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> ui tool show PICKLUSTER

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.10-rc2025.06.16.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 479, in thread_safe  
func(*args, **kw)  
File "/Users/zhangmi/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/PICKLUSTER/tool.py",
line 498, in handle_scheme  
chain1 = query["chain1"][0].split(':')[1]  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/Users/zhangmi/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/PICKLUSTER/tool.py",
line 498, in handle_scheme  
chain1 = query["chain1"][0].split(':')[1]  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,13
      Model Number: MXD13CH/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.81.1
      OS Loader Version: 10151.81.1

Software:

    System Software Overview:

      System Version: macOS 14.3 (23D2057)
      Kernel Version: Darwin 23.3.0
      Time since boot: 4天1小时35分钟

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2880 x 1864 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.4.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202506130232
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 2.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.0
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14