AllMetal3D: wrapped C/C++ object of type QLabel has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/model2_chimerax_corrected.pdb

Chain information for model2_chimerax_corrected.pdb #1  
---  
Chain | Description  
A | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for model2_chimerax_corrected.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> close session

> open C:\Users\model2_chimerax_corrected.pdb format pdb

Chain information for model2_chimerax_corrected.pdb #1  
---  
Chain | Description  
A | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for model2_chimerax_corrected.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> isolde sim start
> /A:55-56,59,62-67,69,84,89,109,112-121,125-126,131-132,184,186-187,189-191,193-194,197,217-233,236,245,249,253,256,305-321,369,372-379,400-404,438-439,447,479-492,508

Sim termination reason: None  
ISOLDE: stopped sim  
Deleted the following atoms from residue HEM A508: FE  

> isolde sim start /A:508

ISOLDE: started sim  

> ui mousemode right "isolde tug residue"

> ui mousemode right "isolde tug atom"

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

[Repeated 3 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> ui mousemode right select

> select /A:447@SG

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:508@FE

1 atom, 1 residue, 1 model selected  

> select /A:447@SG

1 atom, 1 residue, 1 model selected  

> select /A:447@SG /A:508@FE

2 atoms, 2 residues, 1 model selected  

> save C:/Users/m0del2_chimeraX_corrected.pdb

> close session

> open C:/Users/model4_chimerax_corrected.pdb

Chain information for model4_chimerax_corrected.pdb #1  
---  
Chain | Description  
A | No description available  
  
Drag select of 8 atoms, 14 residues, 4 bonds  
Drag select of 4 residues  

> select clear

Drag select of 11 residues  

> select clear

[Repeated 1 time(s)]

> ui mousemode right translate

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1 to IUPAC-IUB
standards.  
Chain information for model4_chimerax_corrected.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> isolde sim start
> /A:59,64-66,109,113-118,120,125-126,131-132,186,220-232,305-306,308-317,321,373-379,400,480-488,508

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start
> /A:56-67,106-134,183-189,217-235,302-324,370-382,397-403,477-489,508

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde sim start /A

Sim termination reason: None  
ISOLDE: stopped sim  
Deleted the following atoms from residue HEM A508: FE  

> isolde sim start /A:508

ISOLDE: started sim  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

[Repeated 5 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select /A:447@SG /A:508@FE

2 atoms, 2 residues, 1 model selected  

> isolde sim start /A:447,508

ISOLDE: started sim  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save C:/Users/model4_chimerax_corrected.pdb

> close session

> open C:/Users/m1_correctviachimerac.pdb

Chain information for m1_correctviachimerac.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select /A:447@SG /A:508@FE

1 atom, 1 residue, 1 model selected  
Must have exactly two atoms selected!  

> select /A:447@SG /B:508@FE

1 atom, 1 residue, 1 model selected  
Must have exactly two atoms selected!  

> select /A:447@SG /B:1@FE

2 atoms, 1 pseudobond, 2 residues, 2 models selected  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for m1_correctviachimerac.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> isolde sim start
> /A:109-129,131-134,220,222-233,236,245-246,249-250,252-253,256-257,302,305-306,309,379,483-485

Sim termination reason: None  
ISOLDE: stopped sim  

> undo

[Repeated 2 time(s)]

> close session

> open C:\Users\m1_correctviachimerac.pdb format pdb

Chain information for m1_correctviachimerac.pdb #1  
---  
Chain | Description  
A | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for m1_correctviachimerac.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> isolde sim start
> /A:109-134,219-234,236-237,242,245-257,298,301-310,312-313,317,379,398,400,482-485,487/B

Sim termination reason: None  
ISOLDE: stopped sim  
Deleted the following atoms from residue HEM B1: FE  

> isolde sim start /B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select /A:447@SG /B:1@FE

2 atoms, 2 residues, 1 model selected  

> isolde sim start /A:447/B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save C:/Users/model1_chimeraX.pdb

> close session

> open C:/Users/model3_cofactor.pdb

Summary of feedback from opening C:/Users/model3_cofactor.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2025-03-21T21:00:05Z  
  
Chain information for model3_cofactor.pdb #1  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 79 residues in model #1 to IUPAC-IUB
standards.  
Chain information for model3_cofactor.pdb  
---  
Chain | Description  
1.2/? | No description available  
  

> isolde sim start
> /*:109-129,131-134,222-234,236-237,245-246,249-250,253,305,309,379,484

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde sim start
> /*:109-129,131-134,222-234,236-237,245-246,249-250,253,305,309,379,484

Sim termination reason: None  
ISOLDE: stopped sim  
Deleted the following atoms from residue ALA 500: HC1, HN, OC2, OC1, HC2, HC  
Deleted the following atoms from residue HEM A1: H15, H21, H4, H24, H12, H3,
H28, H5, H23, H7, FE, H2, H29, H19, H18, H20, H25, H17, H26, H8, H14, H16,
H22, H11, H13, H30, H1, H10, H9, H6, H27  

> isolde sim start /A

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> ui mousemode right select

> select /?:447@HG

1 atom, 1 residue, 1 model selected  

> select /?:447@HG

1 atom, 1 residue, 1 model selected  

> delete /?:447@HG

> select /A:447@SG /A:1@FE

1 atom, 1 residue, 1 model selected  

> select /?:447@SG /A:1@FE

2 atoms, 2 residues, 1 model selected  

> isolde sim start /*:447/A

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "C:/Users/model3_chimerax_corrected .pdb"

> close session

> open C:/Users/johna/Downloads/model_0_aligned_with_heme_1chain.pdb

Summary of feedback from opening
C:/Users/johna/Downloads/model_0_aligned_with_heme_1chain.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2025-03-18T21:17:27Z  
  
Chain information for model_0_aligned_with_heme_1chain.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 84 residues in model #1 to IUPAC-IUB
standards.  
Chain information for model_0_aligned_with_heme_1chain.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> isolde sim start
> /A:59,64-66,89,109-118,120,125-126,131-132,134,220,223-233,306,308-314,317,321,373-380,400,402,439,480-487/Z

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde sim start /A-Z

Sim termination reason: None  
ISOLDE: stopped sim  
Fetching CCD CSO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CSO/CSO.cif  
Fetching CCD CSS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/CSS/CSS.cif  
Fetching CCD SC2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/SC2/SC2.cif  
Deleted the following atoms from residue CYS A116: HN, HB1  
Deleted the following atoms from residue HEM Z508: H10, H24, H25, H16, H23,
H4, H18, H7, H1, H9, H19, FE, H21, H26, H8, H14, H6, H22, H12, H15, H20, H11,
H2, H5, H13, H17, H3  
Fetching CCD NMM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/NMM/NMM.cif  
Fetching CCD AAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/AAG/AAG.cif  
Deleted the following atoms from residue ARG A153: 1HH2, HG1, HH2, 1HH1, HD1,
2HH2, HN, HB1, 2HH1  

> isolde sim start /A:153

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> close session

> open C:/Users/johna/Downloads/complex0.pdb

Chain information for complex0.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 85 residues in model #1 to IUPAC-IUB
standards.  
Chain information for complex0.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> isolde sim start /A-B

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde sim start
> /A:109-134,219-237,245-247,249-250,252-254,256-257,302,305-306,309-310,379,398,445,483-485/B

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to complex0.pdb #1.2  
---  
notes | No usable SEQRES records for complex0.pdb (#1.2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 500  
Chain-final residues that are not actual C termini:  
538 hydrogen bonds  
4113 hydrogens added  
  
Deleted the following atoms from residue HEM B1: HAD1, HBC2, HMC2, FE, HMD3,
HMA2, HAD2, HAA1, HBB1, HBC1, HMD2, HMC3, HMA1, HBA2, HMB3, HMC1, HMB2, HBC3,
HBB2, HBA1, HBD1, HAA2, HMB1, HMD1, HMA3, HBB3, HBD2  

> isolde sim start /B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select /A:447@SG /B:1@FE

2 atoms, 2 residues, 1 model selected  

> delete /A:447@HG

> isolde sim start /A:447/B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "C:/Users/model0_chimerax_corrected .pdb"

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to complex0.pdb #1.2  
---  
notes | No usable SEQRES records for complex0.pdb (#1.2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 500  
Chain-final residues that are not actual C termini:  
513 hydrogen bonds  
0 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HEM+CYS (net charge +0) with am1-bcc
method  
HEM+CYS: number of electrons (413) + formal charge (+0) is odd; cannot compute
charges for radical species using AM1-BCC method  

> select Fe

1 atom, 1 residue, 1 model selected  

> ui tool show "Add Charges"

Closest equivalent command: addcharge sel standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HEM+CYS (net charge +0) with am1-bcc
method  
HEM+CYS: number of electrons (413) + formal charge (+0) is odd; cannot compute
charges for radical species using AM1-BCC method  

> ui tool show "Add Charges"

Closest equivalent command: addcharge sel standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HEM+CYS (net charge -1) with gasteiger
method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -i
C:\Users\johna\AppData\Local\Temp\tmpp09ugldo\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmpp09ugldo\ante.out.mol2 -fo mol2 -c gas
-nc -1 -j 5 -s 2 -dr n  
(HEM+CYS) ``  
(HEM+CYS) `Welcome to antechamber 20.0: molecular input file processor.`  
(HEM+CYS) ``  
(HEM+CYS) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmpp09ugldo\ante.in.mol2); atoms read (95),
bonds read (102).`  
(HEM+CYS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HEM+CYS) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/bondtype"
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HEM+CYS) `bash.exe: warning: could not find /tmp, please create!`  
(HEM+CYS) `Warning: For atom (ID: 66, Name: Fe1) the best APS is not zero.`  
(HEM+CYS) ` Bonds involving this atom are frozen.`  
(HEM+CYS) ``  
(HEM+CYS) ``  
(HEM+CYS) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype"
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HEM+CYS) `bash.exe: warning: could not find /tmp, please create!`  
(HEM+CYS) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype"
-i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d "C:/Program Files/ChimeraX
1.9/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF"`  
(HEM+CYS) `bash.exe: warning: could not find /tmp, please create!`  
(HEM+CYS) `/usr/bin/antechamber: Fatal Error!`  
(HEM+CYS) `No Gasteiger parameter for atom (ID: 65, Name: Fe1, Type: DU).`  
Failure running ANTECHAMBER for residue HEM+CYS  
Check reply log for details  

> toolshed show

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/model4_chimerax_corrected_nowater.pdbqt

Chain information for model4_chimerax_corrected_nowater.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened model4_chimerax_corrected_nowater.pdbqt containing 1 structures (4099
atoms, 4207 bonds)  
Computing secondary structure  

> ui tool show "Add Charges"

None of the selected residues are in the structures being assigned charges  

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/m0del2_chimeraX_corrected.pdbqt

Chain information for m0del2_chimeraX_corrected.pdb #3  
---  
Chain | Description  
A | No description available  
  
Opened m0del2_chimeraX_corrected.pdbqt containing 1 structures (4099 atoms,
4207 bonds)  
Computing secondary structure  

> close session

> open
> "//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/model0_chimerax_corrected
> .pdb"

> open
> "\\\wsl.localhost\Ubuntu\home\johnsimp\cyp_alpha_corrected\model0_chimerax_corrected
> .pdb" format pdb

[Repeated 1 time(s)]

> open
> "//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/model0_chimerax_corrected
> .pdb"

Chain information for model0_chimerax_corrected .pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Add Charges"

Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HEM[FE] (net charge +2) with am1-bcc
method  
Assigning partial charges to residue HEM[non-FE] (net charge -4) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmpr_tt6tsc\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmpr_tt6tsc\ante.out.mol2 -fo mol2 -c bcc
-nc -4 -j 5 -s 2 -dr n  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Welcome to antechamber 20.0: molecular input file processor.`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmpr_tt6tsc\ante.in.mol2); atoms read (72),
bonds read (76).`  
(HEM[non-FE]) `Info: Determining atomic numbers from atomic symbols which are
case sensitive.`  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p
gaff`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) `Info: Total number of electrons: 298; net charge: -4`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc"
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i
ANTECHAMBER_AM1BCC_PRE.AC`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
Charges for residue HEM[non-FE] determined  

> close session

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -8.464 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -8.464  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -8.464  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
5 messages similar to the above omitted  
  
Opened out_model4_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h.pdbqt
containing 1 structures (22 atoms, 23 bonds)  

> ui tool show ViewDockX

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/model4_chimerax_corrected_cleaned.pdbqt

Chain information for model4_chimerax_corrected_cleaned.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened model4_chimerax_corrected_cleaned.pdbqt containing 1 structures (5040
atoms, 5148 bonds)  
Computing secondary structure  

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -3.523 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -3.523  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -3.523  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
65 messages similar to the above omitted  
  
Opened out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt
containing 7 structures (154 atoms, 161 bonds)  

> viewdockx #3.1-7

> hide #3.1-7 models

> show #3.1 models

> hide #3.1 models

> show #3.2 models

> hide #3.2 models

> show #3.3 models

> hide #3.3 models

> show #3.1 models

> hide #3.1 models

> show #3.7 models

> hide #3.7 models

> show #3.1 models

> close session

> open
> //wsl.localhost/Ubuntu/home/johnsimp/compounds_dock_cypa/orca_xyz_cembrenes/lactone/lactone_cembreneB_7_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/compounds_dock_cypa/orca_xyz_cembrenes/lactone/lactone_cembreneB_7_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK 0 active torsions:  
  
Ignored bad PDB record found on line 2  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 3  
ROOT  
  
Ignored bad PDB record found on line 26  
ENDROOT  
  
Ignored bad PDB record found on line 27  
TORSDOF 0  
  
Opened lactone_cembreneB_7_h.pdbqt containing 1 structures (22 atoms, 23
bonds)  

> open
> //wsl.localhost/Ubuntu/home/johnsimp/compounds_dock_cypa/orca_xyz_cembrenes/67isolactone_cembreneB_0_h_h_h_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/compounds_dock_cypa/orca_xyz_cembrenes/67isolactone_cembreneB_0_h_h_h_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK 0 active torsions:  
  
Ignored bad PDB record found on line 2  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 3  
ROOT  
  
Ignored bad PDB record found on line 26  
ENDROOT  
  
Ignored bad PDB record found on line 27  
TORSDOF 0  
  
Opened 67isolactone_cembreneB_0_h_h_h_h.pdbqt containing 1 structures (22
atoms, 23 bonds)  

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/model1_chimeraX_cleaned.pdbqt

Chain information for model1_chimeraX_cleaned.pdb #3  
---  
Chain | Description  
A | No description available  
  
Opened model1_chimeraX_cleaned.pdbqt containing 1 structures (5039 atoms, 5147
bonds)  
Computing secondary structure  

> close session

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_diol_cembreneB_1_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_diol_cembreneB_1_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.509 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -5.233  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -5.182  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -0.051  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -0.197  
  
52 messages similar to the above omitted  
  
Opened out_model4_chimerax_corrected_cleaned_diol_cembreneB_1_h.pdbqt
containing 3 structures (72 atoms, 72 bonds)  

> viewdockx #1.1-3

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/model4_chimerax_corrected_cleaned.pdbqt

Chain information for model4_chimerax_corrected_cleaned.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened model4_chimerax_corrected_cleaned.pdbqt containing 1 structures (5040
atoms, 5148 bonds)  
Computing secondary structure  

> hide #1.1-3 models

> show #1.1 models

> ui tool show "Build Structure"

> ui tool show "Bond Editor"

> ui mousemode right select

> ui tool show "Build Structure"

> select #1.1/?:1@@serial_number=20

1 atom, 1 residue, 1 model selected  

> select #1.1/?:1@@serial_number=20

1 atom, 1 residue, 1 model selected  

> select #1.1/?:1@@serial_number=20

1 atom, 1 residue, 1 model selected  
Drag select of 1 atoms  
You must select exactly one atom to modify.  

> select #1.1/?:1@@serial_number=2

1 atom, 1 residue, 1 model selected  

> select #1.1/?:1@@serial_number=2

1 atom, 1 residue, 1 model selected  

> ui tool show "Change Substituents"

> select clear

> select #1.1/?:1@@serial_number=17

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> open
> //wsl.localhost/Ubuntu/home/johnsimp/compounds_dock_cypa/orca_xyz_cembrenes/7hydroxy_cembreneB_1.xyz

opened 7hydroxy_cembreneB_1.xyz as an XYZ coordinate file  

> select clear

> select #2/A:295

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

> close session

> open
> \\\wsl.localhost\Ubuntu\home\johnsimp\compounds_dock_cypa\orca_xyz_cembrenes\7hydroxy_cembreneB_1.xyz
> format xyz

opened 7hydroxy_cembreneB_1.xyz as an XYZ coordinate file  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 7hydroxy_cembreneB_1 #1  
---  
notes | Chain-initial residues that are actual N termini:   
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
0 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNK (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmpkz1que4n\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmpkz1que4n\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(UNK) ``  
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNK) ``  
(UNK) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmpkz1que4n\ante.in.mol2); atoms read (53),
bonds read (53).`  
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) `Info: Total number of electrons: 160; net charge: 0`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
Charges for residue UNK determined  
Dock prep finished  
Drag select of 2 atoms, 1 bonds  

> select clear

Drag select of 1 atoms, 3 bonds  

> select clear

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 7hydroxy_cembreneB_1 #1  
---  
notes | Chain-initial residues that are actual N termini:   
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
0 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNK (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmp2v9vltap\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmp2v9vltap\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(UNK) ``  
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNK) ``  
(UNK) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmp2v9vltap\ante.in.mol2); atoms read (53),
bonds read (53).`  
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) `Info: Total number of electrons: 160; net charge: 0`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
Charges for residue UNK determined  
Dock prep finished  

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -3.523 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -3.523  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -3.523  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
65 messages similar to the above omitted  
  
Opened out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt
containing 7 structures (154 atoms, 161 bonds)  

> viewdockx #2.1-7

Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]

> close session

> open
> \\\wsl.localhost\Ubuntu\home\johnsimp\cyp_alpha_corrected\out_model4_chimerax_corrected_cleaned_diol_cembreneB_1_h.pdbqt
> format pdbqt

Summary of feedback from opening
\\\wsl.localhost\Ubuntu\home\johnsimp\cyp_alpha_corrected\out_model4_chimerax_corrected_cleaned_diol_cembreneB_1_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.509 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -5.233  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -5.182  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -0.051  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -0.197  
  
52 messages similar to the above omitted  
  
Opened out_model4_chimerax_corrected_cleaned_diol_cembreneB_1_h.pdbqt
containing 3 structures (72 atoms, 72 bonds)  

> viewdockx #1.1-3

> select clear

> select #1.1/?:1@@serial_number=20

1 atom, 1 residue, 1 model selected  

> select H

6 atoms, 3 residues, 3 models selected  

> select clear

> ui tool show "Add Hydrogens"

> addh #1.1-3

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Chain-initial residues that are actual N termini:   
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
2 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
90 hydrogens added  
  

> hide #1.1-3 models

> show #1.1 models

> close session

> open
> \\\wsl.localhost\Ubuntu\home\johnsimp\cyp_alpha_corrected\out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt
> format pdbqt

Summary of feedback from opening
\\\wsl.localhost\Ubuntu\home\johnsimp\cyp_alpha_corrected\out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -3.523 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -3.523  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -3.523  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
65 messages similar to the above omitted  
  
Opened out_model4_chimerax_corrected_cleaned_lactone_cembreneB_7_h_h.pdbqt
containing 7 structures (154 atoms, 161 bonds)  

> viewdockx #1.1-7

> ui tool show "Add Hydrogens"

> addh #1.1-7

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Chain-initial residues that are actual N termini:   
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
196 hydrogens added  
  

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/model4_chimerax_corrected_cleaned.pdbqt

Chain information for model4_chimerax_corrected_cleaned.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened model4_chimerax_corrected_cleaned.pdbqt containing 1 structures (5040
atoms, 5148 bonds)  
Computing secondary structure  

> hide #1.1-7 models

> show #1.1 models

> select clear

Drag select of 2 atoms, 3 bonds  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."  

[Repeated 287 time(s)]Drag select of 15 atoms, 19 bonds  

> select clear

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h_h_h_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model4_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h_h_h_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -8.472 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -8.472  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -8.472  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
5 messages similar to the above omitted  
  
Opened
out_model4_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h_h_h_h.pdbqt
containing 1 structures (22 atoms, 23 bonds)  
Must select a number of stars next to the 'Close' button  
[Repeated 1 time(s)]Drag select of 2 residues  

> ui tool show "Add Hydrogens"

> addh #2-3#1.1-7

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for model4_chimerax_corrected_cleaned.pdb (#2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini:
model4_chimerax_corrected_cleaned.pdb #2/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
model4_chimerax_corrected_cleaned.pdb #2/A ALA 500  
Chain-final residues that are not actual C termini:  
543 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
3664 hydrogens added  
  
Drag select of 8 atoms, 9 bonds  

> select clear

> hide #1.1 models

> ui tool show "Add Charges"

Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Drag select of 1 bonds  

> show #1.1 models

> hide #1.1 models

> select clear

[Repeated 1 time(s)]

> select #2/A:447@HG

1 atom, 1 residue, 1 model selected  

> select #2/A:447@HG

1 atom, 1 residue, 1 model selected  

> select clear

> undo

[Repeated 1 time(s)]

> save
> "//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/model4_lactone
> .pdb"

Computing secondary structure  
Drag select of 2 atoms, 2 bonds  

> save "C:/Users/johna/Downloads/model4_lasctone .pdb"

Drag select of 5 residues  

> select clear

> select #2/A:508@FE

1 atom, 1 residue, 1 model selected  

> ui tool show "Add Charges"

Closest equivalent command: addcharge sel standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HEM[FE] (net charge -1) with am1-bcc
method  
Assigning partial charges to residue HEM[non-FE] (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmpjbl4om1s\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmpjbl4om1s\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Welcome to antechamber 20.0: molecular input file processor.`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmpjbl4om1s\ante.in.mol2); atoms read (76),
bonds read (80).`  
(HEM[non-FE]) `Info: Determining atomic numbers from atomic symbols which are
case sensitive.`  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p
gaff`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) `Info: Total number of electrons: 298; net charge: 0`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc"
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i
ANTECHAMBER_AM1BCC_PRE.AC`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
Charges for residue HEM[non-FE] determined  
Drag select of 1 atoms, 1 bonds  

> select clear

Drag select of 2 atoms, 6 bonds  
Drag select of 2 atoms, 3 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms, 1 bonds  

> select clear

[Repeated 5 time(s)]Drag select of 2 atoms, 4 bonds  

> close session

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-
> energy-conformer-UFF_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-
energy-conformer-UFF_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.851 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.851  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -9.851  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
35 messages similar to the above omitted  
  
Opened out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-energy-
conformer-UFF_h.pdbqt containing 4 structures (88 atoms, 92 bonds)  

> viewdockx #1.1-4

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/m0del2_chimeraX_corrected_cleaned.pdbqt

Chain information for m0del2_chimeraX_corrected_cleaned.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened m0del2_chimeraX_corrected_cleaned.pdbqt containing 1 structures (5041
atoms, 5149 bonds)  
Computing secondary structure  

> hide #1.1-4 models

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> hide #1.2 models

> show #1.1 models

> ui tool show "Add Charges"

> addh #2#1.1-4

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for m0del2_chimeraX_corrected_cleaned.pdb (#2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini:
m0del2_chimeraX_corrected_cleaned.pdb #2/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
m0del2_chimeraX_corrected_cleaned.pdb #2/A ALA 500  
Chain-final residues that are not actual C termini:  
554 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
3747 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  

> select #2/A:313

16 atoms, 15 bonds, 1 residue, 1 model selected  
Assigning partial charges to residue UNK (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmpfsd97suy\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmpfsd97suy\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(UNK) ``  
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNK) ``  
(UNK) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmpfsd97suy\ante.in.mol2); atoms read (50),
bonds read (51).`  
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) `Info: Total number of electrons: 164; net charge: 0`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
Charges for residue UNK determined  
Assigning partial charges to residue HEM[FE] (net charge -1) with am1-bcc
method  
Assigning partial charges to residue HEM[non-FE] (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmpmjlriyif\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmpmjlriyif\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Welcome to antechamber 20.0: molecular input file processor.`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmpmjlriyif\ante.in.mol2); atoms read (76),
bonds read (80).`  
(HEM[non-FE]) `Info: Determining atomic numbers from atomic symbols which are
case sensitive.`  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p
gaff`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) `Info: Total number of electrons: 298; net charge: 0`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc"
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i
ANTECHAMBER_AM1BCC_PRE.AC`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
Charges for residue HEM[non-FE] determined  
Drag select of 1 residues  

> close session

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/m0del2_chimeraX_corrected_cleaned.pdbqt

Chain information for m0del2_chimeraX_corrected_cleaned.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
Opened m0del2_chimeraX_corrected_cleaned.pdbqt containing 1 structures (5041
atoms, 5149 bonds)  

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-
> energy-conformer-UFF_h_h.pdbqt
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-
> energy-conformer-UFF_h.pdbqt
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-
> energy-conformer-MMFF_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-
energy-conformer-UFF_h_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.230 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.230  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -9.230  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
55 messages similar to the above omitted  
  
Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-
energy-conformer-UFF_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.849 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.849  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -9.849  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
45 messages similar to the above omitted  
  
Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-
energy-conformer-MMFF_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.566 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.566  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -9.566  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
45 messages similar to the above omitted  
  
Opened out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-energy-
conformer-UFF_h_h.pdbqt containing 6 structures (132 atoms, 138 bonds)  
Opened out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-energy-
conformer-UFF_h.pdbqt containing 5 structures (110 atoms, 115 bonds)  
Opened out_m0del2_chimeraX_corrected_cleaned_lactone_B_minimum-energy-
conformer-MMFF_h.pdbqt containing 5 structures (110 atoms, 115 bonds)  

> viewdockx #2.1-6

> viewdockx #3.1-5

> viewdockx #4.1-5

Drag select of 6 residues  

> hide #3.1-5 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> hide #4.1-5 models

> show #4.1 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> hide #2.2-6 models

> show #2.3 models

> hide #2.3 models

> show #2.1 models

> select clear

> hide #4.1 models

> show #4.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> hide #4.1 models

> select clear

> hide #3.1 models

> show #3.2 models

> hide #3.2 models

> show #3.1 models

Drag select of 1 residues, 1 bonds  

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_closed_lactone_epoxide_minimum-
> energy-conformer-UFF_h_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_m0del2_chimeraX_corrected_cleaned_closed_lactone_epoxide_minimum-
energy-conformer-UFF_h_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.226 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.496  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -9.496  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
112 messages similar to the above omitted  
  
Opened out_m0del2_chimeraX_corrected_cleaned_closed_lactone_epoxide_minimum-
energy-conformer-UFF_h_h.pdbqt containing 9 structures (216 atoms, 234 bonds)  

> viewdockx #5.1-9

> hide #5.1-9 models

> show #5.1 models

> select clear

> hide #5.1 models

> show #5.2 models

> hide #5.2 models

> show #5.1 models

> hide #5.1 models

> open
> //wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model0_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h.pdbqt

Summary of feedback from opening
//wsl.localhost/Ubuntu/home/johnsimp/cyp_alpha_corrected/out_model0_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -8.534 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -8.534  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -8.534  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: 0.000  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: 0.000  
  
45 messages similar to the above omitted  
  
Opened out_model0_chimerax_corrected_cleaned_67isolactone_cembreneB_0_h.pdbqt
containing 5 structures (110 atoms, 115 bonds)  

> viewdockx #6.1-5

> select clear

[Repeated 1 time(s)]

> ui tool show "Add Charges"

> addh #1#2.1-6#3.1-5#4.1-5#5.1-9#6.1-5

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for m0del2_chimeraX_corrected_cleaned.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini:
m0del2_chimeraX_corrected_cleaned.pdb #1/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
m0del2_chimeraX_corrected_cleaned.pdb #1/A ALA 500  
Chain-final residues that are not actual C termini:  
554 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
4484 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNK (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmps0z5lef9\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmps0z5lef9\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(UNK) ``  
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNK) ``  
(UNK) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmps0z5lef9\ante.in.mol2); atoms read (50),
bonds read (51).`  
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) `Info: Total number of electrons: 164; net charge: 0`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
Charges for residue UNK determined  
Assigning partial charges to residue HEM[FE] (net charge +0) with am1-bcc
method  
Assigning partial charges to residue HEM[non-FE] (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmpo_ebxu16\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmpo_ebxu16\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Welcome to antechamber 20.0: molecular input file processor.`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmpo_ebxu16\ante.in.mol2); atoms read (76),
bonds read (80).`  
(HEM[non-FE]) `Info: Determining atomic numbers from atomic symbols which are
case sensitive.`  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p
gaff`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) `Info: Total number of electrons: 298; net charge: 0`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc"
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i
ANTECHAMBER_AM1BCC_PRE.AC`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
Charges for residue HEM[non-FE] determined  
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmpj7da0w_d\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmpj7da0w_d\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmpj7da0w_d\ante.in.mol2); atoms read (53),
bonds read (55).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 174; net charge: 0`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
Charges for residue UNL determined  
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmp2iyv3hrs\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmp2iyv3hrs\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmp2iyv3hrs\ante.in.mol2); atoms read (50),
bonds read (51).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 164; net charge: 0`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
Charges for residue UNL determined  

> select clear

> select #1/A:225

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

> select #1/A:141

25 atoms, 24 bonds, 1 residue, 1 model selected  

> select ::name="HEM"

77 atoms, 80 bonds, 1 residue, 1 model selected  

> ui tool show "Add Charges"

Closest equivalent command: addcharge #1 % sel standardizeResidues
5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HEM[FE] (net charge +1) with am1-bcc
method  
Assigning partial charges to residue HEM[non-FE] (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johna\AppData\Local\Temp\tmp0_t241e1\ante.in.mol2 -fi mol2 -o
C:\Users\johna\AppData\Local\Temp\tmp0_t241e1\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Welcome to antechamber 20.0: molecular input file processor.`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Info: Finished reading file
(C:\Users\johna\AppData\Local\Temp\tmp0_t241e1\ante.in.mol2); atoms read (76),
bonds read (80).`  
(HEM[non-FE]) `Info: Determining atomic numbers from atomic symbols which are
case sensitive.`  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p
gaff`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) `Info: Total number of electrons: 298; net charge: 0`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/am1bcc"
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.9/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
(HEM[non-FE]) `Running: "C:/Program Files/ChimeraX
1.9/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i
ANTECHAMBER_AM1BCC_PRE.AC`  
(HEM[non-FE]) `bash.exe: warning: could not find /tmp, please create!`  
(HEM[non-FE]) ``  
Charges for residue HEM[non-FE] determined  

> select #1/A:141

25 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:508@FE

1 atom, 1 residue, 1 model selected  

> select clear

> ui tool show ISOLDE

Please select exactly one .mol2 and one .frcmod file!  

> select #1/A:300

19 atoms, 18 bonds, 1 residue, 1 model selected  
Drag select of 1 residues, 1 atoms, 1 bonds  

> select #1/A:300

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

> select #1/A:300

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

> select ions

1 atom, 1 residue, 1 model selected  

> toolshed show

Downloading bundle ChimeraX_AllMetal3D-0.8-py3-none-any.whl  
Installed ChimeraX-AllMetal3D (0.8)  

> ui tool show AllMetal3D/Water3D

Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  

> select clear

> ui tool show AllMetal3D/Water3D

Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  
No residues selected  

> select ::name="HEM"

77 atoms, 80 bonds, 1 residue, 1 model selected  

> ui tool show AllMetal3D/Water3D

Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  
Drag select of 4 atoms, 4 residues, 4 bonds  

> close session

Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\johna\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\allmetal3d\tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 24.3.1.240216
OpenGL renderer: AMD Radeon (TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: HP
Model: HP ENVY x360 2-in-1 Laptop 15-ey0xxx
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 33,621,536,768
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5625U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AllMetal3D: 0.8
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-Clipper: 0.24.0
    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: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    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-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LAMMPS: 0.9.2
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    fsspec: 2025.3.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    gradio_client: 0.11.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    huggingface-hub: 0.29.3
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
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    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
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    platformdirs: 4.3.6
    platformdirs: 4.2.2
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    pyelftools: 0.31
    Pygments: 2.18.0
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    PyOpenGL-accelerate: 3.1.7
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    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
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    pytz: 2024.2
    pywin32: 306
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    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
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    Send2Trash: 1.8.3
    SEQCROW: 1.8.18
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    soupsieve: 2.6
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
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    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
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    tifffile: 2024.7.24
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    typing_extensions: 4.12.2
    tzdata: 2024.2
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    wcwidth: 0.2.13
    webcolors: 24.6.0
    websockets: 11.0.3
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    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    zipp: 3.19.2