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Opened 67 minutes ago
#20843 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-27.0-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jtp_pts/Desktop/NoonyDocking/out_compound5.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/out_compound5.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.4 0.000 0.000
Ignored bad PDB record found on line 3
REMARK Name = 22134092
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: P_1 and O_2
Ignored bad PDB record found on line 7
REMARK 2 A between atoms: P_1 and O_3
607 messages similar to the above omitted
Opened out_compound5.pdbqt containing 9 structures (216 atoms, 207 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK Name = 2fs.pdb
Ignored bad PDB record found on line 54
REMARK 4 active torsions:
Ignored bad PDB record found on line 55
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 56
REMARK 1 A between atoms: C2_1 and C4_2
Ignored bad PDB record found on line 57
REMARK 2 A between atoms: C12_7 and C10_23
13 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 1 1 1 ILE A 328 ALA A
331 0
Start residue of secondary structure not found: SHEET 2 2 1 LEU A 342 TYR A
345 0
Start residue of secondary structure not found: SHEET 3 3 1 TRP A 352 ASP A
354 0
Start residue of secondary structure not found: SHEET 4 4 1 ALA A 366 VAL A
370 0
Start residue of secondary structure not found: SHEET 5 5 1 LEU A 373 VAL A
377 0
23 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.2 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 16
ENDROOT
Ignored bad PDB record found on line 17
BRANCH 1 18
Ignored bad PDB record found on line 24
BRANCH 13 19
103 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_1xm.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.6 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 20
ENDROOT
Ignored bad PDB record found on line 21
TORSDOF 0
Ignored bad PDB record found on line 24
REMARK VINA RESULT: -6.4 2.069 2.563
31 messages similar to the above omitted
Opened 4n1b_1xm.pdbqt containing 9 structures (144 atoms, 153 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.2 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 16
ENDROOT
Ignored bad PDB record found on line 17
BRANCH 1 18
Ignored bad PDB record found on line 24
BRANCH 13 19
103 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.2 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 16
ENDROOT
Ignored bad PDB record found on line 17
BRANCH 1 18
Ignored bad PDB record found on line 24
BRANCH 13 19
103 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.2 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 16
ENDROOT
Ignored bad PDB record found on line 17
BRANCH 1 18
Ignored bad PDB record found on line 24
BRANCH 13 19
103 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> rmsd #1 #2
Missing required "to" argument
> rmsd 2fs
Missing or invalid "atoms" argument: invalid atoms specifier
> rmsd #1 #2
Missing required "to" argument
> rmsd #1 #2
Missing required "to" argument
> rmsd #1 to #2
Number of atoms from first atom spec (32) differs from number in second (288)
> rmsd #1 to #2.4
RMSD between 32 atom pairs is 1.112
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 18
ENDROOT
Ignored bad PDB record found on line 19
TORSDOF 0
Opened 1xm.pdbqt containing 1 structures (16 atoms, 17 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/5wiy_1xm.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/5wiy_1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.5 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 20
ENDROOT
Ignored bad PDB record found on line 21
TORSDOF 0
Ignored bad PDB record found on line 24
REMARK VINA RESULT: -6.5 1.922 1.957
31 messages similar to the above omitted
Opened 5wiy_1xm.pdbqt containing 9 structures (144 atoms, 153 bonds)
> delete atoms #1#2.9#!2
> delete bonds #1#2.9#!2
> close #2
> open /Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm
'/Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm' has no suffix
> open /Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.9 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 20
ENDROOT
Ignored bad PDB record found on line 21
TORSDOF 0
Ignored bad PDB record found on line 24
REMARK VINA RESULT: -4.9 1.963 3.484
31 messages similar to the above omitted
Opened 5wiy2_1xm.pdbqt containing 9 structures (144 atoms, 153 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 18
ENDROOT
Ignored bad PDB record found on line 19
TORSDOF 0
Opened 1xm.pdbqt containing 1 structures (16 atoms, 17 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 18
ENDROOT
Ignored bad PDB record found on line 19
TORSDOF 0
Opened 1xm.pdbqt containing 1 structures (16 atoms, 17 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.9 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 20
ENDROOT
Ignored bad PDB record found on line 21
TORSDOF 0
Ignored bad PDB record found on line 24
REMARK VINA RESULT: -4.9 1.963 3.484
31 messages similar to the above omitted
Opened 5wiy2_1xm.pdbqt containing 9 structures (144 atoms, 153 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 18
ENDROOT
Ignored bad PDB record found on line 19
TORSDOF 0
Opened 1xm.pdbqt containing 1 structures (16 atoms, 17 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.9 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 20
ENDROOT
Ignored bad PDB record found on line 21
TORSDOF 0
Ignored bad PDB record found on line 24
REMARK VINA RESULT: -4.9 2.050 3.549
31 messages similar to the above omitted
Opened 5wiy2_1xm.pdbqt containing 9 structures (144 atoms, 153 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 18
ENDROOT
Ignored bad PDB record found on line 19
TORSDOF 0
Opened 1xm.pdbqt containing 1 structures (16 atoms, 17 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/log_5wiy2_2xm.txt
Unrecognized file suffix '.txt'
> open /Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/5wiy2_1xm.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.9 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 20
ENDROOT
Ignored bad PDB record found on line 21
TORSDOF 0
Ignored bad PDB record found on line 24
REMARK VINA RESULT: -4.9 2.055 3.553
75 messages similar to the above omitted
Opened 5wiy2_1xm.pdbqt containing 20 structures (320 atoms, 340 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b.pdbqt
Chain information for 4n1b.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Opened 4n1b.pdbqt containing 1 structures (2704 atoms, 2757 bonds)
> select /A:381
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /A:527
16 atoms, 14 bonds, 2 residues, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> style sel ball
Changed 16 atom styles
> style sel stick
Changed 16 atom styles
> show sel atoms
> select /A:527
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:528
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:381@HD22
1 atom, 1 residue, 1 model selected
> select add /A:528@HE22
2 atoms, 2 residues, 1 model selected
> distance /A:381@HD22 /A:528@HE22
Distance between /A ASN 381 HD22 and GLN 528 HE22: 30.964Å
> ~distance /A:381@HD22 /A:528@HE22
> ui tool show "Volume Viewer"
> volume #1 region all
No volumes specified
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.3 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 16
ENDROOT
Ignored bad PDB record found on line 17
BRANCH 1 18
Ignored bad PDB record found on line 24
BRANCH 13 19
103 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> rmsd #1 to #2.4
RMSD between 32 atom pairs is 7.036
> rmsd #1 to #2.5
RMSD between 32 atom pairs is 1.170
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.3 0.000 0.000
Ignored bad PDB record found on line 3
ROOT
Ignored bad PDB record found on line 16
ENDROOT
Ignored bad PDB record found on line 17
BRANCH 1 18
Ignored bad PDB record found on line 24
BRANCH 13 19
103 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinA.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinA.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK Name = 31553
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: O_4 and C_15
Ignored bad PDB record found on line 7
REMARK 2 A between atoms: O_5 and C_20
301 messages similar to the above omitted
Opened 4n1b_silybinA.pdbqt containing 9 structures (360 atoms, 396 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinB.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinB.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.9 0.000 0.000
Ignored bad PDB record found on line 3
REMARK Name = 1548994
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: O_4 and C_15
Ignored bad PDB record found on line 7
REMARK 2 A between atoms: O_5 and C_20
301 messages similar to the above omitted
Opened 4n1b_silybinB.pdbqt containing 9 structures (360 atoms, 396 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound1.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.0 0.000 0.000
Ignored bad PDB record found on line 3
REMARK Name = 6328920
Ignored bad PDB record found on line 4
REMARK 6 active torsions:
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: O_1 and C_5
184 messages similar to the above omitted
Opened 4n1b_compound1.pdbqt containing 9 structures (81 atoms, 72 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound2.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound2.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.6 0.000 0.000
Ignored bad PDB record found on line 3
REMARK Name = 70227
Ignored bad PDB record found on line 4
REMARK 8 active torsions:
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: N_1 and C_3
166 messages similar to the above omitted
Opened 4n1b_compound2.pdbqt containing 9 structures (90 atoms, 81 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound3.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound3.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.1 0.000 0.000
Ignored bad PDB record found on line 3
REMARK Name = 20467
Ignored bad PDB record found on line 4
REMARK 0 active torsions:
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 8
ROOT
58 messages similar to the above omitted
Opened 4n1b_compound3.pdbqt containing 9 structures (72 atoms, 72 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/compound4_out.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/compound4_out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -3.658 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -3.658
Ignored bad PDB record found on line 4
REMARK INTER: -3.658
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
103 messages similar to the above omitted
Opened compound4_out.pdbqt containing 9 structures (54 atoms, 54 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/compound4_out.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/compound4_out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -3.658 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -3.658
Ignored bad PDB record found on line 4
REMARK INTER: -3.658
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
103 messages similar to the above omitted
Opened compound4_out.pdbqt containing 9 structures (54 atoms, 54 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound1.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -3.966 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.073
Ignored bad PDB record found on line 4
REMARK INTER: -4.894
Ignored bad PDB record found on line 5
REMARK INTRA: -0.180
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.180
220 messages similar to the above omitted
Opened 4n1b_compound1.pdbqt containing 9 structures (81 atoms, 72 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.319 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.043
Ignored bad PDB record found on line 4
REMARK INTER: -12.732
Ignored bad PDB record found on line 5
REMARK INTRA: 0.688
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.688
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.932 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -9.148
Ignored bad PDB record found on line 4
REMARK INTER: -7.319
Ignored bad PDB record found on line 5
REMARK INTRA: -1.830
Ignored bad PDB record found on line 6
REMARK UNBOUND: -1.830
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.932 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -9.148
Ignored bad PDB record found on line 4
REMARK INTER: -7.319
Ignored bad PDB record found on line 5
REMARK INTRA: -1.830
Ignored bad PDB record found on line 6
REMARK UNBOUND: -1.830
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.932 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -9.147
Ignored bad PDB record found on line 4
REMARK INTER: -7.319
Ignored bad PDB record found on line 5
REMARK INTRA: -1.828
Ignored bad PDB record found on line 6
REMARK UNBOUND: -1.828
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.050
Ignored bad PDB record found on line 4
REMARK INTER: -12.737
Ignored bad PDB record found on line 5
REMARK INTRA: 0.687
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.687
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.050
Ignored bad PDB record found on line 4
REMARK INTER: -12.737
Ignored bad PDB record found on line 5
REMARK INTRA: 0.687
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.687
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.049
Ignored bad PDB record found on line 4
REMARK INTER: -12.737
Ignored bad PDB record found on line 5
REMARK INTRA: 0.688
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.688
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.324 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.057
Ignored bad PDB record found on line 4
REMARK INTER: -12.739
Ignored bad PDB record found on line 5
REMARK INTRA: 0.682
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.682
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.935 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -9.153
Ignored bad PDB record found on line 4
REMARK INTER: -7.322
Ignored bad PDB record found on line 5
REMARK INTRA: -1.831
Ignored bad PDB record found on line 6
REMARK UNBOUND: -1.831
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> select add #2
288 atoms, 324 bonds, 9 residues, 10 models selected
> delete sel
> select add #3
288 atoms, 324 bonds, 9 residues, 11 models selected
> delete sel
[Repeated 1 time(s)]
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.307 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.036
Ignored bad PDB record found on line 4
REMARK INTER: -12.717
Ignored bad PDB record found on line 5
REMARK INTRA: 0.681
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.681
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> RMSD #1 to #4.5
Unknown command: RMSD #1 to #4.5
> rmsd #1 to #4.5
RMSD between 32 atom pairs is 1.232
> hide #4.5 models
> show #4.4 models
> show #4.5 models
> hide #4.5 models
> hide #4.4 models
> view clip false
[Repeated 1 time(s)]
> show #4.3 models
> show #4.4 models
> hide #4.3 models
> hide #4.4 models
> show #4.5 models
> show #4.6 models
> show #4.8 models
> show #4.7 models
> show #4.9 models
> close #4.9
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdb
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 1 1 ILE A 328 ALA A 331 0
Start residue of secondary structure not found: SHEET 2 2 1 LEU A 342 TYR A
345 0
Start residue of secondary structure not found: SHEET 3 3 1 TRP A 352 ASP A
354 0
Start residue of secondary structure not found: SHEET 4 4 1 ALA A 366 VAL A
370 0
Start residue of secondary structure not found: SHEET 5 5 1 LEU A 373 VAL A
377 0
23 messages similar to the above omitted
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.048
Ignored bad PDB record found on line 4
REMARK INTER: -12.737
Ignored bad PDB record found on line 5
REMARK INTRA: 0.688
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.688
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.048
Ignored bad PDB record found on line 4
REMARK INTER: -12.737
Ignored bad PDB record found on line 5
REMARK INTRA: 0.688
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.688
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> rmsd #1 to #2.5
RMSD between 32 atom pairs is 1.186
> rmsd #1 to #2.5
RMSD between 32 atom pairs is 1.186
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinA.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinA.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.820 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -13.228
Ignored bad PDB record found on line 4
REMARK INTER: -12.171
Ignored bad PDB record found on line 5
REMARK INTRA: -1.057
Ignored bad PDB record found on line 6
REMARK UNBOUND: -1.057
337 messages similar to the above omitted
Opened 4n1b_silybinA.pdbqt containing 9 structures (360 atoms, 396 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinB.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinB.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.904 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.486
Ignored bad PDB record found on line 4
REMARK INTER: -12.288
Ignored bad PDB record found on line 5
REMARK INTRA: -0.198
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.198
337 messages similar to the above omitted
Opened 4n1b_silybinB.pdbqt containing 9 structures (360 atoms, 396 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound1.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -3.973 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.083
Ignored bad PDB record found on line 4
REMARK INTER: -4.902
Ignored bad PDB record found on line 5
REMARK INTRA: -0.181
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.181
220 messages similar to the above omitted
Opened 4n1b_compound1.pdbqt containing 9 structures (81 atoms, 72 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound2.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound2.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.649 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.428
Ignored bad PDB record found on line 4
REMARK INTER: -5.193
Ignored bad PDB record found on line 5
REMARK INTRA: -0.235
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.235
202 messages similar to the above omitted
Opened 4n1b_compound2.pdbqt containing 9 structures (90 atoms, 81 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound3.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound3.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.134 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -4.134
Ignored bad PDB record found on line 4
REMARK INTER: -4.134
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
94 messages similar to the above omitted
Opened 4n1b_compound3.pdbqt containing 9 structures (72 atoms, 72 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound4.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound4.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -3.667 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -3.667
Ignored bad PDB record found on line 4
REMARK INTER: -3.667
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
103 messages similar to the above omitted
Opened 4n1b_compound4.pdbqt containing 9 structures (54 atoms, 54 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound5.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound5.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.684 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -14.468
Ignored bad PDB record found on line 4
REMARK INTER: -12.330
Ignored bad PDB record found on line 5
REMARK INTRA: -2.138
Ignored bad PDB record found on line 6
REMARK UNBOUND: -2.138
643 messages similar to the above omitted
Opened 4n1b_compound5.pdbqt containing 9 structures (216 atoms, 207 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound6.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound6.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.456 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.891
Ignored bad PDB record found on line 4
REMARK INTER: -5.775
Ignored bad PDB record found on line 5
REMARK INTRA: -0.116
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.116
148 messages similar to the above omitted
Opened 4n1b_compound6.pdbqt containing 9 structures (90 atoms, 90 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound7.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound7.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.137 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -10.600
Ignored bad PDB record found on line 4
REMARK INTER: -9.641
Ignored bad PDB record found on line 5
REMARK INTRA: -0.958
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.958
517 messages similar to the above omitted
Opened 4n1b_compound7.pdbqt containing 9 structures (171 atoms, 162 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound1.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -3.973 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.083
Ignored bad PDB record found on line 4
REMARK INTER: -4.902
Ignored bad PDB record found on line 5
REMARK INTRA: -0.181
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.181
220 messages similar to the above omitted
Opened 4n1b_compound1.pdbqt containing 9 structures (81 atoms, 72 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound2.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound2.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.649 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.428
Ignored bad PDB record found on line 4
REMARK INTER: -5.193
Ignored bad PDB record found on line 5
REMARK INTRA: -0.235
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.235
202 messages similar to the above omitted
Opened 4n1b_compound2.pdbqt containing 9 structures (90 atoms, 81 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound3.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound3.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.134 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -4.134
Ignored bad PDB record found on line 4
REMARK INTER: -4.134
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
94 messages similar to the above omitted
Opened 4n1b_compound3.pdbqt containing 9 structures (72 atoms, 72 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound4.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound4.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -3.667 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -3.667
Ignored bad PDB record found on line 4
REMARK INTER: -3.667
Ignored bad PDB record found on line 5
REMARK INTRA: 0.000
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.000
103 messages similar to the above omitted
Opened 4n1b_compound4.pdbqt containing 9 structures (54 atoms, 54 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound5.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound5.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.684 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -14.468
Ignored bad PDB record found on line 4
REMARK INTER: -12.330
Ignored bad PDB record found on line 5
REMARK INTRA: -2.138
Ignored bad PDB record found on line 6
REMARK UNBOUND: -2.138
643 messages similar to the above omitted
Opened 4n1b_compound5.pdbqt containing 9 structures (216 atoms, 207 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound6.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound6.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.456 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.891
Ignored bad PDB record found on line 4
REMARK INTER: -5.775
Ignored bad PDB record found on line 5
REMARK INTRA: -0.116
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.116
148 messages similar to the above omitted
Opened 4n1b_compound6.pdbqt containing 9 structures (90 atoms, 90 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound7.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound7.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.137 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -10.600
Ignored bad PDB record found on line 4
REMARK INTER: -9.641
Ignored bad PDB record found on line 5
REMARK INTRA: -0.958
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.958
517 messages similar to the above omitted
Opened 4n1b_compound7.pdbqt containing 9 structures (171 atoms, 162 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound7.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound7.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.137 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -10.600
Ignored bad PDB record found on line 4
REMARK INTER: -9.641
Ignored bad PDB record found on line 5
REMARK INTRA: -0.958
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.958
517 messages similar to the above omitted
Opened 4n1b_compound7.pdbqt containing 9 structures (171 atoms, 162 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound6.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound6.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.456 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.891
Ignored bad PDB record found on line 4
REMARK INTER: -5.775
Ignored bad PDB record found on line 5
REMARK INTRA: -0.116
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.116
148 messages similar to the above omitted
Opened 4n1b_compound6.pdbqt containing 9 structures (90 atoms, 90 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound8.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_compound8.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.976 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.971
Ignored bad PDB record found on line 4
REMARK INTER: -10.067
Ignored bad PDB record found on line 5
REMARK INTRA: -2.904
Ignored bad PDB record found on line 6
REMARK UNBOUND: -2.904
580 messages similar to the above omitted
Opened 4n1b_compound8.pdbqt containing 9 structures (189 atoms, 180 bonds)
> close
> set bgColor white
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b.pdbqt
Chain information for 4n1b.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Opened 4n1b.pdbqt containing 1 structures (2704 atoms, 2757 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinA.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_silybinA.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.820 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -13.228
Ignored bad PDB record found on line 4
REMARK INTER: -12.171
Ignored bad PDB record found on line 5
REMARK INTRA: -1.057
Ignored bad PDB record found on line 6
REMARK UNBOUND: -1.057
337 messages similar to the above omitted
Opened 4n1b_silybinA.pdbqt containing 9 structures (360 atoms, 396 bonds)
> hide H
> select #2
360 atoms, 396 bonds, 9 residues, 10 models selected
> select zone #2 5
Selected 219 atoms
> show sel
> style sel stick
Changed 219 atom styles
> ui tool show Matchmaker
> matchmaker #2.1 to #1
No matrix compatible with both reference structure and all match structures
> ui tool show H-Bonds
> hbonds reveal true
337 hydrogen bonds found
> close session
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b.pdbqt
Chain information for 4n1b.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Opened 4n1b.pdbqt containing 1 structures (2704 atoms, 2757 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.048
Ignored bad PDB record found on line 4
REMARK INTER: -12.737
Ignored bad PDB record found on line 5
REMARK INTRA: 0.688
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.688
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> hide H
> show #1 cartoons
> select #2
288 atoms, 324 bonds, 9 residues, 10 models selected
> Plaintext
Unknown command: Plaintext
> select #2 :<5
511 atoms, 537 bonds, 31 residues, 11 models selected
> show sel atoms
> style sel stick
Changed 511 atom styles
> transparency #1 cartoon 50
Missing or invalid "percent" argument: Expected a number
> transparency #1 50
> transparency #1 10
> transparency #1 50
> ui tool show H-Bonds
> select #2
288 atoms, 324 bonds, 9 residues, 10 models selected
> ui tool show H-Bonds
> hbonds reveal true
333 hydrogen bonds found
> hbonds sel restrict cross
7 hydrogen bonds found
> close session
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b.pdbqt
Chain information for 4n1b.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Opened 4n1b.pdbqt containing 1 structures (2704 atoms, 2757 bonds)
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
> hide H
> select #2
32 atoms, 36 bonds, 1 residue, 1 model selected
> select #2 :<5
189 atoms, 184 bonds, 17 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 189 atom styles
> transparency #1 cartoon 50
Missing or invalid "percent" argument: Expected a number
> transparency #1 50
> select #2
32 atoms, 36 bonds, 1 residue, 1 model selected
> hbonds sel restrict cross
1 hydrogen bonds found
> contacts sel restrict cross
50 contacts
> undo
[Repeated 1 time(s)]
> close pseudobonds
Expected a models specifier or a keyword
> hbonds delete
> contacts delete
> select #2
32 atoms, 36 bonds, 1 residue, 1 model selected
> hbonds sel restrict cross relax true color blue radius 0.1
1 hydrogen bonds found
> contacts sel restrict cross color orange radius 0.05
50 contacts
> color #1 white
> color #2 black
> color #2 #0433ffff
> color #2 #aa7942ff
> color #2 #00fdffff
> color #2 #942192ff
> color #2 #ff2600ff
> color #2 #00fdffff
> label sel attribute name
> label delete
> label :334,382415,701509,556,602,577 text "{res_name} {res_num}" color black
> height 1.5
> label :334,382415,701509,556,602,577 color black height 1.5
> labeldelete
Unknown command: labeldelete
> label delete
> lighting soft
> lighting soft shadows true
> graphics silhouettes true color black width 1
> hbonds sel restrict cross relax true color blue radius 0.3
1 hydrogen bonds found
> graphics quality 3
> save /Users/jtp_pts/Desktop/NoonyDocking/test.png width 3000 height 3000
> transparentBackground true
> label :415,483,525 color black height 1.5
> label remove
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label delete
> label :415,483,525 color black height 1
> select #1 & #2:<4.0
113 atoms, 106 bonds, 12 residues, 1 model selected
> info selection level residue
residue id #1/A:334 name TYR index 8
residue id #1/A:364 name GLY index 38
residue id #1/A:382 name ASN index 56
residue id #1/A:414 name ASN index 88
residue id #1/A:415 name ARG index 89
residue id #1/A:462 name GLY index 136
residue id #1/A:509 name GLY index 183
residue id #1/A:556 name ALA index 230
residue id #1/A:572 name TYR index 246
residue id #1/A:577 name PHE index 251
residue id #1/A:602 name SER index 276
residue id #1/A:603 name GLY index 277
> label :8,38,56,88,89,136,183,230,246,251,276,277 text "{name} {number}"
> color black height 1.5
> label :8,38,56,88,89,136,183,230,246,251,276,277 color black height 1.5
[Repeated 3 time(s)]
> label :415,483,525,530 color black height 1
> label :8,38 color black height 1
> label :577 color black height 1
> close session
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop
mw.dragEnterEvent(event)
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop
mw.dragEnterEvent(event)
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
See log for complete Python traceback.
> close
> open /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
Summary of feedback from opening /Users/jtp_pts/Desktop/NoonyDocking/2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 1
ROOT
Ignored bad PDB record found on line 14
ENDROOT
Ignored bad PDB record found on line 15
BRANCH 1 18
Ignored bad PDB record found on line 22
BRANCH 13 19
Ignored bad PDB record found on line 26
ENDBRANCH 13 19
6 messages similar to the above omitted
Opened 2fs.pdbqt containing 1 structures (32 atoms, 36 bonds)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop
mw.dragEnterEvent(event)
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
See log for complete Python traceback.
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
Summary of feedback from opening
/Users/jtp_pts/Desktop/NoonyDocking/4n1b_2fs.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.323 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -12.048
Ignored bad PDB record found on line 4
REMARK INTER: -12.737
Ignored bad PDB record found on line 5
REMARK INTRA: 0.688
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.688
139 messages similar to the above omitted
Opened 4n1b_2fs.pdbqt containing 9 structures (288 atoms, 324 bonds)
> hide #2.1 models
> show #2.5 models
> rmsd #1 and 2.5
Expected a keyword
> rmsd #1 and 2.5
Expected a keyword
> rmsd #1 and 2.5
Expected a keyword
> rmsd #1 and #2.5
Expected a keyword
> rmsd #1 to #2.5
RMSD between 32 atom pairs is 1.186
> close session
> open /Users/jtp_pts/Desktop/NoonyDocking/4n1b.pdbqt
Chain information for 4n1b.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
Opened 4n1b.pdbqt containing 1 structures (2704 atoms, 2757 bonds)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop
mw.dragEnterEvent(event)
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop
mw.dragEnterEvent(event)
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
AttributeError: 'QKeyEvent' object has no attribute 'mimeData'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 824, in dragEnterEvent
md = event.mimeData()
^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 91.7
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15Y002JYTH/A
Chip: Apple M2
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 16 GB
System Firmware Version: 20457.0.125.0.2
OS Loader Version: 20457.0.125.0.2
Software:
System Software Overview:
System Version: macOS 27.0 (26A5388g)
Kernel Version: Darwin 27.0.0
Time since boot: 21 hours, 49 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Smart M70C:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
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