mmCIF fetch: URL can't contain control characters

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1PPi fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 1PPi fetched from pdbe_bio  
---  
warning | Missing or incorrect sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 1PPi bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/1ppi-assembly-1.cif.gz  
Fetching CCD BGC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/BGC/BGC.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif  
Fetching CCD DAF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/DAF/DAF.cif  
Fetching CCD GLC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/GLC/GLC.cif  
  
1PPi bioassembly 1 title:  
The active center of A mammalian α-amylase. The structure of the complex of A
pancreatic α-amylase with A carbohydrate inhibitor refined to 2.2 angstroms
resolution [more info...]  
  
Chain information for 1PPi bioassembly 1 #1  
---  
Chain | Description  
A | ALPHA-AMYLASE  
  
Non-standard residues in 1PPi bioassembly 1 #1  
---  
BGC — (BGC)  
CA — (CA)  
CL — (CL)  
DAF — (DAF)  
GLC — (GLC)  
  
Opened 1 biological assemblies for 1PPi  
Computing secondary structure  

> hide #1.1 models

> open Q9Y2B4 fromDatabase pdbe_bio format mmcif

PDB identifiers are 4 characters, got "Q9Y2B4"  

> Q9Y2B4

Unknown command: Q9Y2B4  

> close session

> open C:/Users/laure/Downloads/AF-Q9Y2B4-F1-model_v4.pdb

AF-Q9Y2B4-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for TP53-target gene 5 protein (Q9Y2B4)
[more info...]  
  
Chain information for AF-Q9Y2B4-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | TP53-target gene 5 protein | T53G5_HUMAN 1-290  
  
Computing secondary structure  

> close session

[Repeated 1 time(s)]

> open 3DM0 fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 3DM0 fetched from pdbe_bio  
---  
warning | Missing or incorrect sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 3DM0 bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/3dm0-assembly-1.cif.gz  
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif  
  
3DM0 bioassembly 1 title:  
Maltose Binding Protein fusion with RACK1 from A. thaliana [more info...]  
  
Chain information for 3DM0 bioassembly 1 #1  
---  
Chain | Description  
A | Maltose-binding periplasmic protein fused with RACK1  
  
Non-standard residues in 3DM0 bioassembly 1 #1  
---  
EDO — (EDO)  
GLC — (GLC)  
  
Computing secondary structure  
Opened 1 biological assemblies for 3DM0  

> 3DM0

Unknown command: 3DM0  

> select ::name="EDO"

4 atoms, 3 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select ::name="GLC"

23 atoms, 24 bonds, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select :4-b

1185 atoms, 1057 bonds, 171 residues, 1 model selected  

> select clear

> select ::name="HOH"

273 atoms, 273 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide atoms

> close session

[Repeated 1 time(s)]

> open 6E2Q fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6E2Q fetched from pdbe_bio  
---  
warnings | Missing or incorrect sequence information. Inferred polymer connectivity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 6E2Q bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6e2q-assembly-1.cif.gz  
Fetching compressed 6E2Q bioassembly 2 from
https://www.ebi.ac.uk/pdbe/static/entry/download/6e2q-assembly-2.cif.gz  
Fetching compressed 6E2Q bioassembly 3 from
https://www.ebi.ac.uk/pdbe/static/entry/download/6e2q-assembly-3.cif.gz  
Fetching compressed 6E2Q bioassembly 4 from
https://www.ebi.ac.uk/pdbe/static/entry/download/6e2q-assembly-4.cif.gz  
  
6E2Q bioassembly 1 title:  
Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor [more
info...]  
  
Chain information for 6E2Q bioassembly 1 #1.1  
---  
Chain | Description  
A | Tyrosine-protein kinase JAK2  
F | Erythropoietin receptor  
  
6E2Q bioassembly 1 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  
6E2Q bioassembly 2 title:  
Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor [more
info...]  
  
Chain information for 6E2Q bioassembly 2 #1.2  
---  
Chain | Description  
B | Tyrosine-protein kinase JAK2  
G | Erythropoietin receptor  
  
6E2Q bioassembly 2 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  
6E2Q bioassembly 3 title:  
Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor [more
info...]  
  
Chain information for 6E2Q bioassembly 3 #1.3  
---  
Chain | Description  
C | Tyrosine-protein kinase JAK2  
E | Erythropoietin receptor  
  
6E2Q bioassembly 3 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  
6E2Q bioassembly 4 title:  
Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor [more
info...]  
  
Chain information for 6E2Q bioassembly 4 #1.4  
---  
Chain | Description  
D | Tyrosine-protein kinase JAK2  
H | Erythropoietin receptor  
  
6E2Q bioassembly 4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  
Computing secondary structure  
[Repeated 3 time(s)]Opened 4 biological assemblies for 6E2Q  

> select protein

16454 atoms, 16884 bonds, 32 pseudobonds, 2037 residues, 8 models selected  

> select clear

> hide #!1.2 models

> hide #!1.3 models

> hide #!1.4 models

> delete atoms #1.1#!1

> delete bonds #1.1#!1

> undo

> select #1.4/D

3493 atoms, 3578 bonds, 14 pseudobonds, 431 residues, 2 models selected  

> select add #1.3/C

7198 atoms, 7373 bonds, 22 pseudobonds, 894 residues, 4 models selected  

> select add #1.3/C

7198 atoms, 7373 bonds, 22 pseudobonds, 894 residues, 4 models selected  

> delete atoms (#!1.4 & sel)

> delete bonds (#!1.4 & sel)

> close session

> open 1YV8 fromDatabase pdb format mmcif

Summary of feedback from opening 1YV8 fetched from pdb  
---  
warnings | Atom HA has no neighbors to form bonds with according to residue template for THR /A:1  
Atom HA has no neighbors to form bonds with according to residue template for
THR /A:1  
Atom HA has no neighbors to form bonds with according to residue template for
THR /A:1  
Atom HA has no neighbors to form bonds with according to residue template for
THR /A:1  
Atom HA has no neighbors to form bonds with according to residue template for
THR /A:1  
15 messages similar to the above omitted  
note | Fetching compressed mmCIF 1yv8 from http://files.rcsb.org/download/1yv8.cif  
  
1yv8 title:  
Solution structure of crambin in acetone/water mixed solvent [more info...]  
  
Chain information for 1yv8  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | Crambin | CRAM_CRAAB 1-46  
  

> close #1.1-20

> hide #1 models

> select add #1

1 model selected  

> show #1 models

> undo

> show #1 models

> select subtract #1

Nothing selected  

> undo

[Repeated 3 time(s)]

> select add #1

1 model selected  

> show target m

> open 1YV8 fromDatabase pdb format mmcif

Summary of feedback from opening 1YV8 fetched from pdb  
---  
warnings | Atom HA has no neighbors to form bonds with according to residue template for THR /A:1  
Atom HA has no neighbors to form bonds with according to residue template for
THR /A:1  
Atom HA has no neighbors to form bonds with according to residue template for
THR /A:1  
Atom HA has no neighbors to form bonds with according to residue template for
THR /A:1  
Atom HA has no neighbors to form bonds with according to residue template for
THR /A:1  
15 messages similar to the above omitted  
  
1yv8 title:  
Solution structure of crambin in acetone/water mixed solvent [more info...]  
  
Chain information for 1yv8  
---  
Chain | Description | UniProt  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | Crambin | CRAM_CRAAB 1-46  
  

> select add #2

12820 atoms, 12960 bonds, 920 residues, 22 models selected  

> select subtract #1

12820 atoms, 12960 bonds, 920 residues, 21 models selected  

> select add #1

12820 atoms, 12960 bonds, 920 residues, 22 models selected  

> close #1

> close #2.2-20

> select clear

> hide atoms

> show atoms

> style ball

Changed 641 atom styles  

> style sphere

Changed 641 atom styles  

> style sphere

Changed 641 atom styles  

> style stick

Changed 641 atom styles  

> style ball

Changed 641 atom styles  

> style sphere

Changed 641 atom styles  

> style ball

Changed 641 atom styles  

> style sphere

Changed 641 atom styles  

> style ball

Changed 641 atom styles  

> style sphere

Changed 641 atom styles  

> style stick

Changed 641 atom styles  

> style ball

Changed 641 atom styles  

> style sphere

Changed 641 atom styles  

> style sphere

Changed 641 atom styles  

> style ball

Changed 641 atom styles  

> close session

> open 3DPL fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 3DPL fetched from pdbe_bio  
---  
warning | Missing or incorrect sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 3DPL bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/3dpl-assembly-1.cif.gz  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
3DPL bioassembly 1 title:  
Structural Insights into NEDD8 Activation of Cullin-RING Ligases:
Conformational Control of Conjugation. [more info...]  
  
Chain information for 3DPL bioassembly 1 #1  
---  
Chain | Description  
A | Cullin-5  
B | RING-box protein 1  
  
Non-standard residues in 3DPL bioassembly 1 #1  
---  
ZN — (ZN)  
  
Opened 1 biological assemblies for 3DPL  
Computing secondary structure  

> select add #1.1

4 pseudobonds, 1 model selected  

> close #1.1

> select add #1.2

14 pseudobonds, 1 model selected  

> close #1.2

Fetching compressed P00720 UniProt info from
https://www.uniprot.org/uniprot/P00720.xml  

> sequence align P00720,#1/A

Alignment identifier is 1  
Associated 3DPL bioassembly 1 chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 45YQ6N5UKHNFRZ8M  
Webservices job finished: 45YQ6N5UKHNFRZ8M  

> close session

> open 3BPL fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 3BPL fetched from pdbe_bio  
---  
warning | Missing or incorrect sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 3BPL bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/3bpl-assembly-1.cif.gz  
Fetching CCD FUC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/FUC/FUC.cif  
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
  
3BPL bioassembly 1 title:  
Crystal structure of the IL4-IL4R-Common γ ternary complex [more info...]  
  
Chain information for 3BPL bioassembly 1 #1  
---  
Chain | Description  
A | Interleukin-4  
B | Interleukin-4 receptor alpha chain  
C | Cytokine receptor common gamma chain  
  
Non-standard residues in 3BPL bioassembly 1 #1  
---  
FUC — (FUC)  
NAG — (NAG)  
  
Computing secondary structure  
Opened 1 biological assemblies for 3BPL  

> select ::name="FUC"::name="HOH"::name="NAG"

245 atoms, 111 bonds, 145 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show cartoons

> hide cartoons

> show cartoons

> show atoms

> hide atoms

> close session

> open P00751 fromDatabase alphafold format mmcif

Summary of feedback from opening P00751 fetched from alphafold  
---  
notes | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold P00751 from
https://alphafold.ebi.ac.uk/files/AF-P00751-F1-model_v3.cif  
  
Chain information for AlphaFold P00751 #1  
---  
Chain | Description | UniProt  
A | Complement factor B | CFAB_HUMAN 1-764  
  
Color AlphaFold P00751 by residue attribute pLDDT_score  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select :1-25

175 atoms, 177 bonds, 25 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save C:/Users/laure/Downloads/alphafold_seq.pdb relModel #1

> close session

> open C:/Users/laure/Downloads/alphafold_seq.pdb

Summary of feedback from opening C:/Users/laure/Downloads/alphafold_seq.pdb  
---  
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence.  
  
Chain information for alphafold_seq.pdb #1  
---  
Chain | Description  
A | No description available  
  

> show target m

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> close session

Enter a PDB ID in the entry field  

> open 5XPE fromDatabase pdb format mmcif

Summary of feedback from opening 5XPE fetched from pdb  
---  
warnings | Atom D1 is not in the residue template for MET /A:1  
Atom D is not in the residue template for ASN /A:2  
Atom D is not in the residue template for ILE /A:3  
Atom D is not in the residue template for PHE /A:4  
Atom D is not in the residue template for GLU /A:5  
Atom D is not in the residue template for MET /A:6  
3 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
notes | Fetching compressed mmCIF 5xpe from http://files.rcsb.org/download/5xpe.cif  
Fetching CCD DOD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/DOD/DOD.cif  
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif  
  
5xpe title:  
Neutron structure of the T26H mutant of T4 lysozyme [more info...]  
  
Chain information for 5xpe #1  
---  
Chain | Description | UniProt  
A | Endolysin | D9IEF7_BPT4 1-164  
  
Non-standard residues in 5xpe #1  
---  
CL — chloride ion  
NA — sodium ion  
  
372 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select ::name="CL"::name="DOD"::name="NA"

204 atoms, 114 bonds, 3 pseudobonds, 90 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> sequence align P00720,#1/A

Alignment identifier is 1  
Associated 5xpe chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 8IZKDP5E29TH9CGG  
Webservices job finished: 8IZKDP5E29TH9CGG  

> select clear

> select /A:12

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

> select /A:12

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

> select /A:12

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

> select /A:12

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

> select /A:12

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

> ui tool show Rotamers

[Repeated 1 time(s)]

> swapaa interactive sel ARG rotLib Dunbrack

/A GLY 12: phi 73.3, psi -173.7 trans  
Changed 600 bond radii  

> swapaa #!1/A:12 ARG criteria 1 rotLib Dunbrack

Using Dunbrack library  
5xpe #!1/A GLY 12: phi 73.3, psi -173.7 trans  
Applying ARG rotamer (chi angles: -67.2 179.5 -179.6 176.7) to 5xpe #!1/A ARG
12  

> select /A:12

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:26

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select /A:26

17 atoms, 17 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

[Repeated 1 time(s)]

> swapaa interactive sel THR rotLib Dunbrack

/A HIS 26: phi -127.5, psi 168.4 trans  
Changed 12 bond radii  

> swapaa #!1/A:26 THR criteria 1 rotLib Dunbrack

Using Dunbrack library  
5xpe #!1/A HIS 26: phi -127.5, psi 168.4 trans  
Applying THR rotamer (chi angles: 65.0) to 5xpe #!1/A THR 26  

> select /A:54

14 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel THR rotLib Dunbrack

/A THR 54: phi -93.1, psi -26.8 trans  
Changed 12 bond radii  

> swapaa #!1/A:54 THR criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
5xpe #!1/A THR 54: phi -93.1, psi -26.8 trans  
Applying THR rotamer (chi angles: 61.0) to 5xpe #!1/A THR 54  

> swapaa interactive sel THR rotLib Dunbrack

/A THR 54: phi -93.1, psi -26.8 trans  
Changed 12 bond radii  

> select /A:39

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:12

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:12

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:50

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:26

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:26

9 atoms, 8 bonds, 1 residue, 1 model selected  

> close session

> open 3RZE fromDatabase pdb format mmcif

Summary of feedback from opening 3RZE fetched from pdb  
---  
notes | Fetching compressed mmCIF 3rze from http://files.rcsb.org/download/3rze.cif  
Fetching CCD 5EH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/5EH/5EH.cif  
Fetching CCD D7V from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/D7V/D7V.cif  
Fetching CCD OLC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/OLC/OLC.cif  
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif  
  
3rze title:  
Structure of the human histamine H1 receptor in complex with doxepin [more
info...]  
  
Chain information for 3rze #1  
---  
Chain | Description | UniProt  
A | Histamine H1 receptor, Lysozyme chimera | HRH1_HUMAN 20-221 405-487, LYS_BPT4 1002-1161  
  
Non-standard residues in 3rze #1  
---  
5EH — (3E)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine  
D7V — (3Z)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
PO4 — phosphate ion  
  
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select ::name="5EH"::name="D7V"::name="HOH"::name="OLC"::name="PO4"

74 atoms, 72 bonds, 8 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> hide #1.1.1 models

> show #!1.1 models

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> show atoms

[Repeated 1 time(s)]

> hide atoms

> style ball

Changed 3481 atom styles  

> style ball

Changed 3481 atom styles  

> show cartoons

> show surfaces

> hide surfaces

> show surfaces

> hide surfaces

> close session

> open 3BPL format mmcif fromDatabase pdbe_bio

Summary of feedback from opening 3BPL fetched from pdbe_bio  
---  
warning | Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
3BPL bioassembly 1 title:  
Crystal structure of the IL4-IL4R-Common γ ternary complex [more info...]  
  
Chain information for 3BPL bioassembly 1 #1  
---  
Chain | Description  
A | Interleukin-4  
B | Interleukin-4 receptor alpha chain  
C | Cytokine receptor common gamma chain  
  
Non-standard residues in 3BPL bioassembly 1 #1  
---  
FUC — (FUC)  
NAG — (NAG)  
  
Computing secondary structure  
Opened 1 biological assemblies for 3BPL  

> close session

> open 3DM0 fromDatabase pdb format mmcif

Summary of feedback from opening 3DM0 fetched from pdb  
---  
note | Fetching compressed mmCIF 3dm0 from http://files.rcsb.org/download/3dm0.cif  
  
3dm0 title:  
Maltose Binding Protein fusion with RACK1 from A. thaliana [more info...]  
  
Chain information for 3dm0 #1  
---  
Chain | Description | UniProt  
A | Maltose-binding periplasmic protein fused with RACK1 | MALE_ECOLI 1-361, GBLP_ARATH 1004-1327  
  
Non-standard residues in 3dm0 #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)  
  

> select ::name="EDO"::name="GLC"::name="HOH"

300 atoms, 27 bonds, 276 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> close session

> open C:/Users/laure/Downloads/3dm0.pdb1.gz

3dm0.pdb1.gz title:  
Maltose binding protein fusion with RACK1 from A. Thaliana [more info...]  
  
Chain information for 3dm0.pdb1.gz #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 3dm0.pdb1.gz #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
GLC — α-D-glucopyranose (α-D-glucose; D-glucose; glucose)  
  

> select ::name="EDO"::name="GLC"::name="HOH"

300 atoms, 27 bonds, 276 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #1.1

1 pseudobond, 2 models selected  

> select subtract #1.1

Nothing selected  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> log metadata #1

Metadata for 3dm0.pdb1.gz #1  
---  
Title | Maltose binding protein fusion with RACK1 from A. Thaliana  
Citation | Structure of A signal transduction regulator, RACK1, fromarabidopsis thaliana. PMID: 18715992  
Experimental method | X-ray diffraction  
  
> select :P0AEX9

Nothing selected  

> select protein

5122 atoms, 5241 bonds, 1 pseudobond, 675 residues, 2 models selected  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> delete atoms #!1

> delete bonds #!1

> open C:/Users/laure/Downloads/3dm0.pdb1.gz

3dm0.pdb1.gz title:  
Maltose binding protein fusion with RACK1 from A. Thaliana [more info...]  
  
Chain information for 3dm0.pdb1.gz #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 3dm0.pdb1.gz #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
GLC — α-D-glucopyranose (α-D-glucose; D-glucose; glucose)  
  

> select ::name="EDO"::name="GLC"::name="HOH"

300 atoms, 27 bonds, 276 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select /A:1271

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 224 residues  

> select clear

Drag select of 72 atoms, 309 residues, 67 bonds  

> select clear

> close session

> open "PDB 3BIK" fromDatabase pdb format mmcif

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 197, in fetch  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 168, in provider_open  
models, status = collated_open(session, database_name, ident,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\mmcif\\__init__.py", line 109, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "src\\\mmcif.pyx", line 462, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\fetch.py", line 99, in fetch_file  
retrieve_url(url, filename, uncompress=uncompress,
transmit_compressed=transmit_compressed,  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\fetch.py", line 192, in retrieve_url  
with urlopen(request, timeout=timeout, context=ssl_context) as response:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 216, in
urlopen  
return opener.open(url, data, timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 519, in
open  
response = self._open(req, data)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 536, in
_open  
result = self._call_chain(self.handle_open, protocol, protocol +  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 496, in
_call_chain  
result = func(*args)  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 1377, in
http_open  
return self.do_open(http.client.HTTPConnection, req)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 1348, in
do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1286, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1297, in
_send_request  
self.putrequest(method, url, **skips)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1131, in
putrequest  
self._validate_path(url)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1231, in
_validate_path  
raise InvalidURL(f"URL can't contain control characters. {url!r} "  
http.client.InvalidURL: URL can't contain control characters.
'/download/pdb_pdb 3bik.cif' (found at least ' ')  
  
http.client.InvalidURL: URL can't contain control characters.
'/download/pdb_pdb 3bik.cif' (found at least ' ')  
  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1231, in
_validate_path  
raise InvalidURL(f"URL can't contain control characters. {url!r} "  
  
See log for complete Python traceback.  
  

> open "PDB 3BIK" fromDatabase pdb format mmcif

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 197, in fetch  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 168, in provider_open  
models, status = collated_open(session, database_name, ident,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\mmcif\\__init__.py", line 109, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "src\\\mmcif.pyx", line 462, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\fetch.py", line 99, in fetch_file  
retrieve_url(url, filename, uncompress=uncompress,
transmit_compressed=transmit_compressed,  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\fetch.py", line 192, in retrieve_url  
with urlopen(request, timeout=timeout, context=ssl_context) as response:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 216, in
urlopen  
return opener.open(url, data, timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 519, in
open  
response = self._open(req, data)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 536, in
_open  
result = self._call_chain(self.handle_open, protocol, protocol +  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 496, in
_call_chain  
result = func(*args)  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 1377, in
http_open  
return self.do_open(http.client.HTTPConnection, req)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\urllib\request.py", line 1348, in
do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1286, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1297, in
_send_request  
self.putrequest(method, url, **skips)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1131, in
putrequest  
self._validate_path(url)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1231, in
_validate_path  
raise InvalidURL(f"URL can't contain control characters. {url!r} "  
http.client.InvalidURL: URL can't contain control characters.
'/download/pdb_pdb 3bik.cif' (found at least ' ')  
  
http.client.InvalidURL: URL can't contain control characters.
'/download/pdb_pdb 3bik.cif' (found at least ' ')  
  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\http\client.py", line 1231, in
_validate_path  
raise InvalidURL(f"URL can't contain control characters. {url!r} "  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 573.22
OpenGL renderer: NVIDIA RTX A5500 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: LENOVO
Model: 21DC0031US
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 68,369,113,088
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i9-12900H
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2025.6.15
    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: 1.10
    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-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: 1.45.2
    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
    comtypes: 1.4.10
    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
    nvidia-cuda-cupti-cu12: 12.9.79
    nvidia-cuda-nvcc-cu12: 12.9.86
    nvidia-cuda-nvrtc-cu12: 12.9.86
    nvidia-cuda-runtime-cu12: 12.9.79
    nvidia-cufft-cu12: 11.4.1.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    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
    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: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    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: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[Eric Pettersen]

Reproducible with the command given in the report (open "PDB 3BIK" fromDatabase pdb format mmcif).