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Opened 10 hours ago
#20407 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-15.7.5-arm64-arm-64bit
ChimeraX Version: 1.11rc202512110057 (2025-12-11 00:57:51 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11rc202512110057 (2025-12-11)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/manellab/Desktop/Sebastian/20260526_cholesterol_trimming.cxs
Log from Tue May 26 06:38:15 2026UCSF ChimeraX version: 1.11rc202512110057
(2025-12-11)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/20260129_allign_100X.cxs format session
Log from Thu Jan 29 22:09:09 2026You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.11rc202512110057 (2025-12-11)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_0.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_1.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_2.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_3.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_4.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_5.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_6.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_7.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_8.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_9.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_10.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_11.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_12.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_13.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_14.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_15.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_16.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_17.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_18.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_19.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_20.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_21.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_22.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_23.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_24.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_25.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_26.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_27.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_28.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_29.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_30.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_31.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_32.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_33.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_34.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_35.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_36.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_37.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_38.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_39.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_40.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_41.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_42.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_43.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_44.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_45.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_46.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_47.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_48.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_49.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_50.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_51.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_52.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_53.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_54.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_55.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_56.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_57.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_58.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_59.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_60.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_61.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_62.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_63.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_64.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_65.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_66.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_67.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_68.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_69.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_70.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_71.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_72.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_73.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_74.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_75.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_76.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_77.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_78.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_79.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_80.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_81.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_82.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_83.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_84.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_85.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_86.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_87.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_88.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_89.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_90.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_91.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_92.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_93.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_94.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_95.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_96.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_97.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_98.cif"
> "/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/100X_cif files/ranked_99.cif"
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_0.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_1.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_2.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_3.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_4.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_5.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_6.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_7.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_8.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_9.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_10.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
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analyse/results/alphaFold3/100X_cif files/ranked_97.cif
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warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_98.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Summary of feedback from opening
/Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
analyse/results/alphaFold3/100X_cif files/ranked_99.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Chain information for ranked_0.cif #1
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Chain information for ranked_60.cif #61
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Chain information for ranked_61.cif #62
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Chain information for ranked_62.cif #63
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Chain information for ranked_63.cif #64
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Chain information for ranked_64.cif #65
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Chain information for ranked_65.cif #66
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Chain information for ranked_66.cif #67
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Chain information for ranked_67.cif #68
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Chain information for ranked_69.cif #70
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Chain information for ranked_91.cif #92
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Chain information for ranked_92.cif #93
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Chain information for ranked_93.cif #94
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Chain information for ranked_95.cif #96
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Chain information for ranked_96.cif #97
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Chain information for ranked_97.cif #98
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Chain information for ranked_98.cif #99
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Color ranked_98.cif by residue attribute pLDDT_score
Chain information for ranked_99.cif #100
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Chain | Description
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Color ranked_99.cif by residue attribute pLDDT_score
Computing secondary structure
[Repeated 99 time(s)]
> mmaker #2-100 to #1 pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranked_0.cif, chain A (#1) with ranked_1.cif, chain A (#2),
sequence alignment score = 1253.9
RMSD between 200 pruned atom pairs is 0.340 angstroms; (across all 243 pairs:
3.469)
Matchmaker ranked_0.cif, chain A (#1) with ranked_2.cif, chain A (#3),
sequence alignment score = 1253.9
RMSD between 216 pruned atom pairs is 0.396 angstroms; (across all 243 pairs:
2.308)
Matchmaker ranked_0.cif, chain A (#1) with ranked_3.cif, chain A (#4),
sequence alignment score = 1253.9
RMSD between 207 pruned atom pairs is 0.405 angstroms; (across all 243 pairs:
4.713)
Matchmaker ranked_0.cif, chain A (#1) with ranked_4.cif, chain A (#5),
sequence alignment score = 1253.9
RMSD between 207 pruned atom pairs is 0.453 angstroms; (across all 243 pairs:
4.004)
Matchmaker ranked_0.cif, chain A (#1) with ranked_5.cif, chain A (#6),
sequence alignment score = 1253.9
RMSD between 201 pruned atom pairs is 0.372 angstroms; (across all 243 pairs:
6.660)
Matchmaker ranked_0.cif, chain A (#1) with ranked_6.cif, chain A (#7),
sequence alignment score = 1253.9
RMSD between 194 pruned atom pairs is 0.338 angstroms; (across all 243 pairs:
18.236)
Matchmaker ranked_0.cif, chain A (#1) with ranked_7.cif, chain A (#8),
sequence alignment score = 1253.9
RMSD between 192 pruned atom pairs is 0.221 angstroms; (across all 243 pairs:
8.027)
Matchmaker ranked_0.cif, chain A (#1) with ranked_8.cif, chain A (#9),
sequence alignment score = 1253.9
RMSD between 197 pruned atom pairs is 0.449 angstroms; (across all 243 pairs:
7.168)
Matchmaker ranked_0.cif, chain A (#1) with ranked_9.cif, chain A (#10),
sequence alignment score = 1253.9
RMSD between 207 pruned atom pairs is 0.315 angstroms; (across all 243 pairs:
5.762)
Matchmaker ranked_0.cif, chain A (#1) with ranked_10.cif, chain A (#11),
sequence alignment score = 1236.5
RMSD between 192 pruned atom pairs is 0.340 angstroms; (across all 243 pairs:
4.680)
Matchmaker ranked_0.cif, chain A (#1) with ranked_11.cif, chain A (#12),
sequence alignment score = 1253.9
RMSD between 210 pruned atom pairs is 0.436 angstroms; (across all 243 pairs:
3.395)
Matchmaker ranked_0.cif, chain A (#1) with ranked_12.cif, chain A (#13),
sequence alignment score = 1253.9
RMSD between 209 pruned atom pairs is 0.358 angstroms; (across all 243 pairs:
4.980)
Matchmaker ranked_0.cif, chain A (#1) with ranked_13.cif, chain A (#14),
sequence alignment score = 1250.3
RMSD between 207 pruned atom pairs is 0.480 angstroms; (across all 243 pairs:
6.918)
Matchmaker ranked_0.cif, chain A (#1) with ranked_14.cif, chain A (#15),
sequence alignment score = 1243.1
RMSD between 204 pruned atom pairs is 0.492 angstroms; (across all 243 pairs:
3.901)
Matchmaker ranked_0.cif, chain A (#1) with ranked_15.cif, chain A (#16),
sequence alignment score = 1239.5
RMSD between 200 pruned atom pairs is 0.339 angstroms; (across all 243 pairs:
6.936)
Matchmaker ranked_0.cif, chain A (#1) with ranked_16.cif, chain A (#17),
sequence alignment score = 1246.7
RMSD between 191 pruned atom pairs is 0.330 angstroms; (across all 243 pairs:
9.109)
Matchmaker ranked_0.cif, chain A (#1) with ranked_17.cif, chain A (#18),
sequence alignment score = 1246.7
RMSD between 215 pruned atom pairs is 0.551 angstroms; (across all 243 pairs:
1.602)
Matchmaker ranked_0.cif, chain A (#1) with ranked_18.cif, chain A (#19),
sequence alignment score = 1253.9
RMSD between 198 pruned atom pairs is 0.418 angstroms; (across all 243 pairs:
6.799)
Matchmaker ranked_0.cif, chain A (#1) with ranked_19.cif, chain A (#20),
sequence alignment score = 1253.9
RMSD between 195 pruned atom pairs is 0.439 angstroms; (across all 243 pairs:
4.846)
Matchmaker ranked_0.cif, chain A (#1) with ranked_20.cif, chain A (#21),
sequence alignment score = 1253.9
RMSD between 201 pruned atom pairs is 0.314 angstroms; (across all 243 pairs:
5.704)
Matchmaker ranked_0.cif, chain A (#1) with ranked_21.cif, chain A (#22),
sequence alignment score = 1240.1
RMSD between 201 pruned atom pairs is 0.483 angstroms; (across all 243 pairs:
11.606)
Matchmaker ranked_0.cif, chain A (#1) with ranked_22.cif, chain A (#23),
sequence alignment score = 1253.9
RMSD between 189 pruned atom pairs is 0.263 angstroms; (across all 243 pairs:
8.666)
Matchmaker ranked_0.cif, chain A (#1) with ranked_23.cif, chain A (#24),
sequence alignment score = 1250.3
RMSD between 205 pruned atom pairs is 0.357 angstroms; (across all 243 pairs:
6.315)
Matchmaker ranked_0.cif, chain A (#1) with ranked_24.cif, chain A (#25),
sequence alignment score = 1253.9
RMSD between 208 pruned atom pairs is 0.465 angstroms; (across all 243 pairs:
5.459)
Matchmaker ranked_0.cif, chain A (#1) with ranked_25.cif, chain A (#26),
sequence alignment score = 1250.9
RMSD between 195 pruned atom pairs is 0.278 angstroms; (across all 243 pairs:
4.843)
Matchmaker ranked_0.cif, chain A (#1) with ranked_26.cif, chain A (#27),
sequence alignment score = 1241.3
RMSD between 200 pruned atom pairs is 0.317 angstroms; (across all 243 pairs:
5.735)
Matchmaker ranked_0.cif, chain A (#1) with ranked_27.cif, chain A (#28),
sequence alignment score = 1253.9
RMSD between 205 pruned atom pairs is 0.384 angstroms; (across all 243 pairs:
4.524)
Matchmaker ranked_0.cif, chain A (#1) with ranked_28.cif, chain A (#29),
sequence alignment score = 1253.9
RMSD between 214 pruned atom pairs is 0.586 angstroms; (across all 243 pairs:
2.056)
Matchmaker ranked_0.cif, chain A (#1) with ranked_29.cif, chain A (#30),
sequence alignment score = 1246.7
RMSD between 201 pruned atom pairs is 0.359 angstroms; (across all 243 pairs:
8.971)
Matchmaker ranked_0.cif, chain A (#1) with ranked_30.cif, chain A (#31),
sequence alignment score = 1250.3
RMSD between 208 pruned atom pairs is 0.367 angstroms; (across all 243 pairs:
5.840)
Matchmaker ranked_0.cif, chain A (#1) with ranked_31.cif, chain A (#32),
sequence alignment score = 1250.3
RMSD between 195 pruned atom pairs is 0.286 angstroms; (across all 243 pairs:
23.689)
Matchmaker ranked_0.cif, chain A (#1) with ranked_32.cif, chain A (#33),
sequence alignment score = 1253.9
RMSD between 199 pruned atom pairs is 0.443 angstroms; (across all 243 pairs:
5.310)
Matchmaker ranked_0.cif, chain A (#1) with ranked_33.cif, chain A (#34),
sequence alignment score = 1253.9
RMSD between 187 pruned atom pairs is 0.399 angstroms; (across all 243 pairs:
5.151)
Matchmaker ranked_0.cif, chain A (#1) with ranked_34.cif, chain A (#35),
sequence alignment score = 1253.9
RMSD between 202 pruned atom pairs is 0.270 angstroms; (across all 243 pairs:
7.520)
Matchmaker ranked_0.cif, chain A (#1) with ranked_35.cif, chain A (#36),
sequence alignment score = 1253.9
RMSD between 204 pruned atom pairs is 0.365 angstroms; (across all 243 pairs:
4.504)
Matchmaker ranked_0.cif, chain A (#1) with ranked_36.cif, chain A (#37),
sequence alignment score = 1250.9
RMSD between 204 pruned atom pairs is 0.522 angstroms; (across all 243 pairs:
5.087)
Matchmaker ranked_0.cif, chain A (#1) with ranked_37.cif, chain A (#38),
sequence alignment score = 1253.9
RMSD between 209 pruned atom pairs is 0.341 angstroms; (across all 243 pairs:
4.948)
Matchmaker ranked_0.cif, chain A (#1) with ranked_38.cif, chain A (#39),
sequence alignment score = 1250.9
RMSD between 191 pruned atom pairs is 0.444 angstroms; (across all 243 pairs:
7.146)
Matchmaker ranked_0.cif, chain A (#1) with ranked_39.cif, chain A (#40),
sequence alignment score = 1232.3
RMSD between 211 pruned atom pairs is 0.465 angstroms; (across all 243 pairs:
4.548)
Matchmaker ranked_0.cif, chain A (#1) with ranked_40.cif, chain A (#41),
sequence alignment score = 1223.3
RMSD between 207 pruned atom pairs is 0.497 angstroms; (across all 243 pairs:
3.086)
Matchmaker ranked_0.cif, chain A (#1) with ranked_41.cif, chain A (#42),
sequence alignment score = 1253.9
RMSD between 203 pruned atom pairs is 0.474 angstroms; (across all 243 pairs:
5.600)
Matchmaker ranked_0.cif, chain A (#1) with ranked_42.cif, chain A (#43),
sequence alignment score = 1253.9
RMSD between 201 pruned atom pairs is 0.345 angstroms; (across all 243 pairs:
4.205)
Matchmaker ranked_0.cif, chain A (#1) with ranked_43.cif, chain A (#44),
sequence alignment score = 1253.9
RMSD between 205 pruned atom pairs is 0.333 angstroms; (across all 243 pairs:
4.043)
Matchmaker ranked_0.cif, chain A (#1) with ranked_44.cif, chain A (#45),
sequence alignment score = 1253.9
RMSD between 189 pruned atom pairs is 0.363 angstroms; (across all 243 pairs:
7.662)
Matchmaker ranked_0.cif, chain A (#1) with ranked_45.cif, chain A (#46),
sequence alignment score = 1250.3
RMSD between 197 pruned atom pairs is 0.440 angstroms; (across all 243 pairs:
8.028)
Matchmaker ranked_0.cif, chain A (#1) with ranked_46.cif, chain A (#47),
sequence alignment score = 1253.9
RMSD between 198 pruned atom pairs is 0.418 angstroms; (across all 243 pairs:
6.267)
Matchmaker ranked_0.cif, chain A (#1) with ranked_47.cif, chain A (#48),
sequence alignment score = 1253.9
RMSD between 210 pruned atom pairs is 0.449 angstroms; (across all 243 pairs:
3.474)
Matchmaker ranked_0.cif, chain A (#1) with ranked_48.cif, chain A (#49),
sequence alignment score = 1244.9
RMSD between 209 pruned atom pairs is 0.335 angstroms; (across all 243 pairs:
5.237)
Matchmaker ranked_0.cif, chain A (#1) with ranked_49.cif, chain A (#50),
sequence alignment score = 1244.9
RMSD between 206 pruned atom pairs is 0.459 angstroms; (across all 243 pairs:
2.343)
Matchmaker ranked_0.cif, chain A (#1) with ranked_50.cif, chain A (#51),
sequence alignment score = 1244.9
RMSD between 207 pruned atom pairs is 0.419 angstroms; (across all 243 pairs:
6.306)
Matchmaker ranked_0.cif, chain A (#1) with ranked_51.cif, chain A (#52),
sequence alignment score = 1253.9
RMSD between 191 pruned atom pairs is 0.362 angstroms; (across all 243 pairs:
9.515)
Matchmaker ranked_0.cif, chain A (#1) with ranked_52.cif, chain A (#53),
sequence alignment score = 1253.9
RMSD between 219 pruned atom pairs is 0.604 angstroms; (across all 243 pairs:
2.299)
Matchmaker ranked_0.cif, chain A (#1) with ranked_53.cif, chain A (#54),
sequence alignment score = 1250.9
RMSD between 192 pruned atom pairs is 0.519 angstroms; (across all 243 pairs:
9.928)
Matchmaker ranked_0.cif, chain A (#1) with ranked_54.cif, chain A (#55),
sequence alignment score = 1253.9
RMSD between 190 pruned atom pairs is 0.303 angstroms; (across all 243 pairs:
8.549)
Matchmaker ranked_0.cif, chain A (#1) with ranked_55.cif, chain A (#56),
sequence alignment score = 1250.3
RMSD between 207 pruned atom pairs is 0.468 angstroms; (across all 243 pairs:
2.882)
Matchmaker ranked_0.cif, chain A (#1) with ranked_56.cif, chain A (#57),
sequence alignment score = 1253.9
RMSD between 209 pruned atom pairs is 0.261 angstroms; (across all 243 pairs:
6.491)
Matchmaker ranked_0.cif, chain A (#1) with ranked_57.cif, chain A (#58),
sequence alignment score = 1253.9
RMSD between 197 pruned atom pairs is 0.342 angstroms; (across all 243 pairs:
6.730)
Matchmaker ranked_0.cif, chain A (#1) with ranked_58.cif, chain A (#59),
sequence alignment score = 1244.9
RMSD between 203 pruned atom pairs is 0.345 angstroms; (across all 243 pairs:
8.311)
Matchmaker ranked_0.cif, chain A (#1) with ranked_59.cif, chain A (#60),
sequence alignment score = 1223.3
RMSD between 203 pruned atom pairs is 0.547 angstroms; (across all 243 pairs:
4.929)
Matchmaker ranked_0.cif, chain A (#1) with ranked_60.cif, chain A (#61),
sequence alignment score = 1253.9
RMSD between 202 pruned atom pairs is 0.315 angstroms; (across all 243 pairs:
9.699)
Matchmaker ranked_0.cif, chain A (#1) with ranked_61.cif, chain A (#62),
sequence alignment score = 1253.9
RMSD between 208 pruned atom pairs is 0.475 angstroms; (across all 243 pairs:
1.959)
Matchmaker ranked_0.cif, chain A (#1) with ranked_62.cif, chain A (#63),
sequence alignment score = 1253.9
RMSD between 201 pruned atom pairs is 0.326 angstroms; (across all 243 pairs:
4.835)
Matchmaker ranked_0.cif, chain A (#1) with ranked_63.cif, chain A (#64),
sequence alignment score = 1246.7
RMSD between 205 pruned atom pairs is 0.246 angstroms; (across all 243 pairs:
4.791)
Matchmaker ranked_0.cif, chain A (#1) with ranked_64.cif, chain A (#65),
sequence alignment score = 1253.9
RMSD between 177 pruned atom pairs is 0.373 angstroms; (across all 243 pairs:
6.926)
Matchmaker ranked_0.cif, chain A (#1) with ranked_65.cif, chain A (#66),
sequence alignment score = 1253.9
RMSD between 199 pruned atom pairs is 0.358 angstroms; (across all 243 pairs:
5.633)
Matchmaker ranked_0.cif, chain A (#1) with ranked_66.cif, chain A (#67),
sequence alignment score = 1253.9
RMSD between 209 pruned atom pairs is 0.430 angstroms; (across all 243 pairs:
5.732)
Matchmaker ranked_0.cif, chain A (#1) with ranked_67.cif, chain A (#68),
sequence alignment score = 1253.9
RMSD between 200 pruned atom pairs is 0.370 angstroms; (across all 243 pairs:
6.247)
Matchmaker ranked_0.cif, chain A (#1) with ranked_68.cif, chain A (#69),
sequence alignment score = 1243.1
RMSD between 201 pruned atom pairs is 0.429 angstroms; (across all 243 pairs:
4.457)
Matchmaker ranked_0.cif, chain A (#1) with ranked_69.cif, chain A (#70),
sequence alignment score = 1253.9
RMSD between 191 pruned atom pairs is 0.354 angstroms; (across all 243 pairs:
9.604)
Matchmaker ranked_0.cif, chain A (#1) with ranked_70.cif, chain A (#71),
sequence alignment score = 1253.9
RMSD between 206 pruned atom pairs is 0.387 angstroms; (across all 243 pairs:
4.351)
Matchmaker ranked_0.cif, chain A (#1) with ranked_71.cif, chain A (#72),
sequence alignment score = 1253.9
RMSD between 194 pruned atom pairs is 0.317 angstroms; (across all 243 pairs:
7.246)
Matchmaker ranked_0.cif, chain A (#1) with ranked_72.cif, chain A (#73),
sequence alignment score = 1244.9
RMSD between 206 pruned atom pairs is 0.465 angstroms; (across all 243 pairs:
3.754)
Matchmaker ranked_0.cif, chain A (#1) with ranked_73.cif, chain A (#74),
sequence alignment score = 1253.9
RMSD between 204 pruned atom pairs is 0.362 angstroms; (across all 243 pairs:
9.873)
Matchmaker ranked_0.cif, chain A (#1) with ranked_74.cif, chain A (#75),
sequence alignment score = 1250.3
RMSD between 192 pruned atom pairs is 0.385 angstroms; (across all 243 pairs:
6.876)
Matchmaker ranked_0.cif, chain A (#1) with ranked_75.cif, chain A (#76),
sequence alignment score = 1244.9
RMSD between 186 pruned atom pairs is 0.488 angstroms; (across all 243 pairs:
8.223)
Matchmaker ranked_0.cif, chain A (#1) with ranked_76.cif, chain A (#77),
sequence alignment score = 1244.9
RMSD between 215 pruned atom pairs is 0.433 angstroms; (across all 243 pairs:
2.708)
Matchmaker ranked_0.cif, chain A (#1) with ranked_77.cif, chain A (#78),
sequence alignment score = 1253.9
RMSD between 202 pruned atom pairs is 0.250 angstroms; (across all 243 pairs:
3.761)
Matchmaker ranked_0.cif, chain A (#1) with ranked_78.cif, chain A (#79),
sequence alignment score = 1253.9
RMSD between 209 pruned atom pairs is 0.499 angstroms; (across all 243 pairs:
6.068)
Matchmaker ranked_0.cif, chain A (#1) with ranked_79.cif, chain A (#80),
sequence alignment score = 1253.9
RMSD between 205 pruned atom pairs is 0.468 angstroms; (across all 243 pairs:
3.141)
Matchmaker ranked_0.cif, chain A (#1) with ranked_80.cif, chain A (#81),
sequence alignment score = 1253.9
RMSD between 208 pruned atom pairs is 0.374 angstroms; (across all 243 pairs:
13.018)
Matchmaker ranked_0.cif, chain A (#1) with ranked_81.cif, chain A (#82),
sequence alignment score = 1250.9
RMSD between 207 pruned atom pairs is 0.417 angstroms; (across all 243 pairs:
3.496)
Matchmaker ranked_0.cif, chain A (#1) with ranked_82.cif, chain A (#83),
sequence alignment score = 1244.9
RMSD between 213 pruned atom pairs is 0.445 angstroms; (across all 243 pairs:
2.528)
Matchmaker ranked_0.cif, chain A (#1) with ranked_83.cif, chain A (#84),
sequence alignment score = 1250.9
RMSD between 204 pruned atom pairs is 0.411 angstroms; (across all 243 pairs:
4.685)
Matchmaker ranked_0.cif, chain A (#1) with ranked_84.cif, chain A (#85),
sequence alignment score = 1253.9
RMSD between 205 pruned atom pairs is 0.434 angstroms; (across all 243 pairs:
4.327)
Matchmaker ranked_0.cif, chain A (#1) with ranked_85.cif, chain A (#86),
sequence alignment score = 1253.9
RMSD between 202 pruned atom pairs is 0.288 angstroms; (across all 243 pairs:
5.071)
Matchmaker ranked_0.cif, chain A (#1) with ranked_86.cif, chain A (#87),
sequence alignment score = 1250.3
RMSD between 201 pruned atom pairs is 0.478 angstroms; (across all 243 pairs:
4.187)
Matchmaker ranked_0.cif, chain A (#1) with ranked_87.cif, chain A (#88),
sequence alignment score = 1250.3
RMSD between 193 pruned atom pairs is 0.399 angstroms; (across all 243 pairs:
11.423)
Matchmaker ranked_0.cif, chain A (#1) with ranked_88.cif, chain A (#89),
sequence alignment score = 1243.7
RMSD between 202 pruned atom pairs is 0.455 angstroms; (across all 243 pairs:
3.127)
Matchmaker ranked_0.cif, chain A (#1) with ranked_89.cif, chain A (#90),
sequence alignment score = 1250.3
RMSD between 208 pruned atom pairs is 0.421 angstroms; (across all 243 pairs:
3.483)
Matchmaker ranked_0.cif, chain A (#1) with ranked_90.cif, chain A (#91),
sequence alignment score = 1250.9
RMSD between 206 pruned atom pairs is 0.439 angstroms; (across all 243 pairs:
2.759)
Matchmaker ranked_0.cif, chain A (#1) with ranked_91.cif, chain A (#92),
sequence alignment score = 1253.9
RMSD between 198 pruned atom pairs is 0.328 angstroms; (across all 243 pairs:
5.624)
Matchmaker ranked_0.cif, chain A (#1) with ranked_92.cif, chain A (#93),
sequence alignment score = 1253.9
RMSD between 208 pruned atom pairs is 0.375 angstroms; (across all 243 pairs:
6.309)
Matchmaker ranked_0.cif, chain A (#1) with ranked_93.cif, chain A (#94),
sequence alignment score = 1253.9
RMSD between 208 pruned atom pairs is 0.461 angstroms; (across all 243 pairs:
3.298)
Matchmaker ranked_0.cif, chain A (#1) with ranked_94.cif, chain A (#95),
sequence alignment score = 1232.9
RMSD between 191 pruned atom pairs is 0.376 angstroms; (across all 243 pairs:
14.398)
Matchmaker ranked_0.cif, chain A (#1) with ranked_95.cif, chain A (#96),
sequence alignment score = 1250.9
RMSD between 204 pruned atom pairs is 0.337 angstroms; (across all 243 pairs:
8.465)
Matchmaker ranked_0.cif, chain A (#1) with ranked_96.cif, chain A (#97),
sequence alignment score = 1246.7
RMSD between 196 pruned atom pairs is 0.334 angstroms; (across all 243 pairs:
5.661)
Matchmaker ranked_0.cif, chain A (#1) with ranked_97.cif, chain A (#98),
sequence alignment score = 1253.9
RMSD between 203 pruned atom pairs is 0.337 angstroms; (across all 243 pairs:
3.931)
Matchmaker ranked_0.cif, chain A (#1) with ranked_98.cif, chain A (#99),
sequence alignment score = 1250.3
RMSD between 207 pruned atom pairs is 0.350 angstroms; (across all 243 pairs:
4.219)
Matchmaker ranked_0.cif, chain A (#1) with ranked_99.cif, chain A (#100),
sequence alignment score = 1253.9
RMSD between 218 pruned atom pairs is 0.540 angstroms; (across all 243 pairs:
1.519)
> set bgColor white
> zoom 3
> zoom -3
Missing or invalid "factor" argument: Must be greater than 0
> zoom out
Expected a number > 0 or a keyword
> zoom 0.3
> zoom 2
> zoom 2.5
> zoom 2.0
> zoom 0.5
[Repeated 2 time(s)]
> zoom 1.5
> zoom 1
> zoom 1.4
> zoom 0.8
> zoom 0.5
> zoom 1.7
> color lightgray protein
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color lightgray
> log metadata #1
The model has no metadata
> log chains #1
Chain information for ranked_0.cif #1
---
Chain | Description
A | .
> log metadata #2
The model has no metadata
> log chains #2
Chain information for ranked_1.cif #2
---
Chain | Description
A | .
> log metadata #3
The model has no metadata
> log chains #3
Chain information for ranked_2.cif #3
---
Chain | Description
A | .
> log metadata #4
The model has no metadata
> log chains #4
Chain information for ranked_3.cif #4
---
Chain | Description
A | .
> log metadata #5
The model has no metadata
> log chains #5
Chain information for ranked_4.cif #5
---
Chain | Description
A | .
> log metadata #6
The model has no metadata
> log chains #6
Chain information for ranked_5.cif #6
---
Chain | Description
A | .
> log metadata #7
The model has no metadata
> log chains #7
Chain information for ranked_6.cif #7
---
Chain | Description
A | .
> log metadata #8
The model has no metadata
> log chains #8
Chain information for ranked_7.cif #8
---
Chain | Description
A | .
> log metadata #9
The model has no metadata
> log chains #9
Chain information for ranked_8.cif #9
---
Chain | Description
A | .
> log metadata #10
The model has no metadata
> log chains #10
Chain information for ranked_9.cif #10
---
Chain | Description
A | .
> log metadata #11
The model has no metadata
> log chains #11
Chain information for ranked_10.cif #11
---
Chain | Description
A | .
> log metadata #12
The model has no metadata
> log chains #12
Chain information for ranked_11.cif #12
---
Chain | Description
A | .
> log metadata #13
The model has no metadata
> log chains #13
Chain information for ranked_12.cif #13
---
Chain | Description
A | .
> log metadata #14
The model has no metadata
> log chains #14
Chain information for ranked_13.cif #14
---
Chain | Description
A | .
> log metadata #15
The model has no metadata
> log chains #15
Chain information for ranked_14.cif #15
---
Chain | Description
A | .
> log metadata #16
The model has no metadata
> log chains #16
Chain information for ranked_15.cif #16
---
Chain | Description
A | .
> log metadata #17
The model has no metadata
> log chains #17
Chain information for ranked_16.cif #17
---
Chain | Description
A | .
> log metadata #18
The model has no metadata
> log chains #18
Chain information for ranked_17.cif #18
---
Chain | Description
A | .
> log metadata #19
The model has no metadata
> log chains #19
Chain information for ranked_18.cif #19
---
Chain | Description
A | .
> log metadata #20
The model has no metadata
> log chains #20
Chain information for ranked_19.cif #20
---
Chain | Description
A | .
> log metadata #21
The model has no metadata
> log chains #21
Chain information for ranked_20.cif #21
---
Chain | Description
A | .
> log metadata #22
The model has no metadata
> log chains #22
Chain information for ranked_21.cif #22
---
Chain | Description
A | .
> log metadata #23
The model has no metadata
> log chains #23
Chain information for ranked_22.cif #23
---
Chain | Description
A | .
> log metadata #24
The model has no metadata
> log chains #24
Chain information for ranked_23.cif #24
---
Chain | Description
A | .
> log metadata #25
The model has no metadata
> log chains #25
Chain information for ranked_24.cif #25
---
Chain | Description
A | .
> log metadata #26
The model has no metadata
> log chains #26
Chain information for ranked_25.cif #26
---
Chain | Description
A | .
> log metadata #27
The model has no metadata
> log chains #27
Chain information for ranked_26.cif #27
---
Chain | Description
A | .
> log metadata #28
The model has no metadata
> log chains #28
Chain information for ranked_27.cif #28
---
Chain | Description
A | .
> log metadata #29
The model has no metadata
> log chains #29
Chain information for ranked_28.cif #29
---
Chain | Description
A | .
> log metadata #30
The model has no metadata
> log chains #30
Chain information for ranked_29.cif #30
---
Chain | Description
A | .
> log metadata #31
The model has no metadata
> log chains #31
Chain information for ranked_30.cif #31
---
Chain | Description
A | .
> log metadata #32
The model has no metadata
> log chains #32
Chain information for ranked_31.cif #32
---
Chain | Description
A | .
> log metadata #33
The model has no metadata
> log chains #33
Chain information for ranked_32.cif #33
---
Chain | Description
A | .
> log metadata #34
The model has no metadata
> log chains #34
Chain information for ranked_33.cif #34
---
Chain | Description
A | .
> log metadata #35
The model has no metadata
> log chains #35
Chain information for ranked_34.cif #35
---
Chain | Description
A | .
> log metadata #36
The model has no metadata
> log chains #36
Chain information for ranked_35.cif #36
---
Chain | Description
A | .
> log metadata #37
The model has no metadata
> log chains #37
Chain information for ranked_36.cif #37
---
Chain | Description
A | .
> log metadata #38
The model has no metadata
> log chains #38
Chain information for ranked_37.cif #38
---
Chain | Description
A | .
> log metadata #39
The model has no metadata
> log chains #39
Chain information for ranked_38.cif #39
---
Chain | Description
A | .
> log metadata #40
The model has no metadata
> log chains #40
Chain information for ranked_39.cif #40
---
Chain | Description
A | .
> log metadata #41
The model has no metadata
> log chains #41
Chain information for ranked_40.cif #41
---
Chain | Description
A | .
> log metadata #42
The model has no metadata
> log chains #42
Chain information for ranked_41.cif #42
---
Chain | Description
A | .
> log metadata #43
The model has no metadata
> log chains #43
Chain information for ranked_42.cif #43
---
Chain | Description
A | .
> log metadata #44
The model has no metadata
> log chains #44
Chain information for ranked_43.cif #44
---
Chain | Description
A | .
> log metadata #45
The model has no metadata
> log chains #45
Chain information for ranked_44.cif #45
---
Chain | Description
A | .
> log metadata #46
The model has no metadata
> log chains #46
Chain information for ranked_45.cif #46
---
Chain | Description
A | .
> log metadata #47
The model has no metadata
> log chains #47
Chain information for ranked_46.cif #47
---
Chain | Description
A | .
> log metadata #48
The model has no metadata
> log chains #48
Chain information for ranked_47.cif #48
---
Chain | Description
A | .
> log metadata #49
The model has no metadata
> log chains #49
Chain information for ranked_48.cif #49
---
Chain | Description
A | .
> log metadata #50
The model has no metadata
> log chains #50
Chain information for ranked_49.cif #50
---
Chain | Description
A | .
> log metadata #51
The model has no metadata
> log chains #51
Chain information for ranked_50.cif #51
---
Chain | Description
A | .
> log metadata #52
The model has no metadata
> log chains #52
Chain information for ranked_51.cif #52
---
Chain | Description
A | .
> log metadata #53
The model has no metadata
> log chains #53
Chain information for ranked_52.cif #53
---
Chain | Description
A | .
> log metadata #54
The model has no metadata
> log chains #54
Chain information for ranked_53.cif #54
---
Chain | Description
A | .
> log metadata #55
The model has no metadata
> log chains #55
Chain information for ranked_54.cif #55
---
Chain | Description
A | .
> log metadata #56
The model has no metadata
> log chains #56
Chain information for ranked_55.cif #56
---
Chain | Description
A | .
> log metadata #57
The model has no metadata
> log chains #57
Chain information for ranked_56.cif #57
---
Chain | Description
A | .
> log metadata #58
The model has no metadata
> log chains #58
Chain information for ranked_57.cif #58
---
Chain | Description
A | .
> log metadata #59
The model has no metadata
> log chains #59
Chain information for ranked_58.cif #59
---
Chain | Description
A | .
> log metadata #60
The model has no metadata
> log chains #60
Chain information for ranked_59.cif #60
---
Chain | Description
A | .
> log metadata #61
The model has no metadata
> log chains #61
Chain information for ranked_60.cif #61
---
Chain | Description
A | .
> log metadata #62
The model has no metadata
> log chains #62
Chain information for ranked_61.cif #62
---
Chain | Description
A | .
> log metadata #63
The model has no metadata
> log chains #63
Chain information for ranked_62.cif #63
---
Chain | Description
A | .
> log metadata #64
The model has no metadata
> log chains #64
Chain information for ranked_63.cif #64
---
Chain | Description
A | .
> log metadata #65
The model has no metadata
> log chains #65
Chain information for ranked_64.cif #65
---
Chain | Description
A | .
> log metadata #66
The model has no metadata
> log chains #66
Chain information for ranked_65.cif #66
---
Chain | Description
A | .
> log metadata #67
The model has no metadata
> log chains #67
Chain information for ranked_66.cif #67
---
Chain | Description
A | .
> log metadata #68
The model has no metadata
> log chains #68
Chain information for ranked_67.cif #68
---
Chain | Description
A | .
> log metadata #69
The model has no metadata
> log chains #69
Chain information for ranked_68.cif #69
---
Chain | Description
A | .
> log metadata #70
The model has no metadata
> log chains #70
Chain information for ranked_69.cif #70
---
Chain | Description
A | .
> log metadata #71
The model has no metadata
> log chains #71
Chain information for ranked_70.cif #71
---
Chain | Description
A | .
> log metadata #72
The model has no metadata
> log chains #72
Chain information for ranked_71.cif #72
---
Chain | Description
A | .
> log metadata #73
The model has no metadata
> log chains #73
Chain information for ranked_72.cif #73
---
Chain | Description
A | .
> log metadata #74
The model has no metadata
> log chains #74
Chain information for ranked_73.cif #74
---
Chain | Description
A | .
> log metadata #75
The model has no metadata
> log chains #75
Chain information for ranked_74.cif #75
---
Chain | Description
A | .
> log metadata #76
The model has no metadata
> log chains #76
Chain information for ranked_75.cif #76
---
Chain | Description
A | .
> log metadata #77
The model has no metadata
> log chains #77
Chain information for ranked_76.cif #77
---
Chain | Description
A | .
> log metadata #78
The model has no metadata
> log chains #78
Chain information for ranked_77.cif #78
---
Chain | Description
A | .
> log metadata #79
The model has no metadata
> log chains #79
Chain information for ranked_78.cif #79
---
Chain | Description
A | .
> log metadata #80
The model has no metadata
> log chains #80
Chain information for ranked_79.cif #80
---
Chain | Description
A | .
> log metadata #81
The model has no metadata
> log chains #81
Chain information for ranked_80.cif #81
---
Chain | Description
A | .
> log metadata #82
The model has no metadata
> log chains #82
Chain information for ranked_81.cif #82
---
Chain | Description
A | .
> log metadata #83
The model has no metadata
> log chains #83
Chain information for ranked_82.cif #83
---
Chain | Description
A | .
> log metadata #84
The model has no metadata
> log chains #84
Chain information for ranked_83.cif #84
---
Chain | Description
A | .
> log metadata #85
The model has no metadata
> log chains #85
Chain information for ranked_84.cif #85
---
Chain | Description
A | .
> log metadata #86
The model has no metadata
> log chains #86
Chain information for ranked_85.cif #86
---
Chain | Description
A | .
> log metadata #87
The model has no metadata
> log chains #87
Chain information for ranked_86.cif #87
---
Chain | Description
A | .
> log metadata #88
The model has no metadata
> log chains #88
Chain information for ranked_87.cif #88
---
Chain | Description
A | .
> log metadata #89
The model has no metadata
> log chains #89
Chain information for ranked_88.cif #89
---
Chain | Description
A | .
> log metadata #90
The model has no metadata
> log chains #90
Chain information for ranked_89.cif #90
---
Chain | Description
A | .
> log metadata #91
The model has no metadata
> log chains #91
Chain information for ranked_90.cif #91
---
Chain | Description
A | .
> log metadata #92
The model has no metadata
> log chains #92
Chain information for ranked_91.cif #92
---
Chain | Description
A | .
> log metadata #93
The model has no metadata
> log chains #93
Chain information for ranked_92.cif #93
---
Chain | Description
A | .
> log metadata #94
The model has no metadata
> log chains #94
Chain information for ranked_93.cif #94
---
Chain | Description
A | .
> log metadata #95
The model has no metadata
> log chains #95
Chain information for ranked_94.cif #95
---
Chain | Description
A | .
> log metadata #96
The model has no metadata
> log chains #96
Chain information for ranked_95.cif #96
---
Chain | Description
A | .
> log metadata #97
The model has no metadata
> log chains #97
Chain information for ranked_96.cif #97
---
Chain | Description
A | .
> log metadata #98
The model has no metadata
> log chains #98
Chain information for ranked_97.cif #98
---
Chain | Description
A | .
> log metadata #99
The model has no metadata
> log chains #99
Chain information for ranked_98.cif #99
---
Chain | Description
A | .
> log metadata #100
The model has no metadata
> log chains #100
Chain information for ranked_99.cif #100
---
Chain | Description
A | .
> chain B
Unknown command: chain B
> chain
Unknown command: chain
> select clear
> segmentations mouseModes true
> ui mousemode shift wheel 'resize segmentation cursor'
> ui mousemode right 'create segmentations'
> ui mousemode shift right 'erase segmentations'
> ui mousemode shift middle 'move segmentation cursor'
> zoom 1.5
> select: lig
Unknown command: select: lig
> select :
Expected an objects specifier or a keyword
> select : LIG
Nothing selected
> save
> /Users/manellab/Desktop/Sebastian/20260129_from_100X_seeds_LBDWT_CHOL/proteinfold-
> analyse/results/alphaFold3/20260129_allign_100X.cxs
——— End of log from Thu Jan 29 22:09:09 2026 ———
> view name session-start
opened ChimeraX session
> select clear
> color byhetero
> select #1-100
194500 atoms, 198300 bonds, 24400 residues, 100 models selected
> select clear
> color /B blue
> color /B magenta
> color /B green
> select /B
2800 atoms, 3100 bonds, 100 residues, 100 models selected
> color sel byhetero
> select up
194500 atoms, 198300 bonds, 24400 residues, 100 models selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:5-49,76-78,127-137,139-141,145-165,189-213
871 atoms, 880 bonds, 108 residues, 1 model selected
> select #1/A:203
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:203-210
57 atoms, 56 bonds, 8 residues, 1 model selected
> hide /A 212-243
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select /A
191700 atoms, 195200 bonds, 24300 residues, 100 models selected
> hide 212-243
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide cartoons 212-243
Expected ',' or a keyword
> hide/A 212-243
Unknown command: hide/A 212-243
> hide sel cartoons
> show sel cartoons
> hide cartoons 212-243
Expected ',' or a keyword
> hide /cartoon 212-243
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /A 212-243
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select A/212-243
Expected an objects specifier or a keyword
> select /A 212-243
Expected a keyword
> select clear
> select A/
Expected an objects specifier or a keyword
> select /A
191700 atoms, 195200 bonds, 24300 residues, 100 models selected
> select /A 12
Expected a keyword
> select clear
> hide cartoons #1-100
Expected ',' or a keyword
> hide /A
> show /A
> hide /A
> show A/#202
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> A:212-243
Unknown command: A:212-243
> /A:212-243
Unknown command: /A:212-243
> select #1/A:62-67,83-88,92-94,102-104,107-113,116-125,173-178
344 atoms, 344 bonds, 41 residues, 1 model selected
> select #1/A:102
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:102
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:102
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1-100
194500 atoms, 198300 bonds, 24400 residues, 100 models selected
> select #1-100/A:212-243
24000 atoms, 24400 bonds, 3200 residues, 100 models selected
> hide sel cartoons
> select #1-100/A 102
Expected a keyword
> select #1-100/A:102
1100 atoms, 1000 bonds, 100 residues, 100 models selected
> show sel atoms
> ui mousemode right zoom
> save /Users/manellab/Desktop/Sebastian/20260526_cholesterol_trimming.cxs
> select #1/A:91
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:91-117
218 atoms, 219 bonds, 27 residues, 1 model selected
> show sel atoms
> select clear
> color lime
> color /B lime
> color /B lightblue see green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /B light sea green
> select /B
2800 atoms, 3100 bonds, 100 residues, 100 models selected
> color sel byhetero
> select clear
> save /Users/manellab/Desktop/Sebastian/20260526_cholesterol_trimming.cxs
> includeMaps true
——— End of log from Tue May 26 06:38:15 2026 ———
> view name session-start
opened ChimeraX session
> open
> /Users/manellab/Desktop/Sebastian/20260516_LBD_7KC_ribbons_and_ligand.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11-rc2025.12.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 847, in restore
cls = name.class_of(self)
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11-rc2025.12.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 228, in class_of
cls = bundle_info.get_class(class_name, session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11-rc2025.12.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 487, in get_class
return f(class_name)
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11-rc2025.12.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/animations/__init__.py", line 24, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'SceneAnimation'
> view name session-start
opened ChimeraX session
> open
> /Users/manellab/Desktop/Sebastian/20260516_LBD_7KC_ribbons_and_ligand.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11-rc2025.12.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 847, in restore
cls = name.class_of(self)
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11-rc2025.12.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 228, in class_of
cls = bundle_info.get_class(class_name, session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11-rc2025.12.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 487, in get_class
return f(class_name)
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11-rc2025.12.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/animations/__init__.py", line 24, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'SceneAnimation'
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15X000JEFN/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: mBoot-18000.101.7
OS Loader Version: 11881.140.96.701.1
Software:
System Software Overview:
System Version: macOS 15.7.5 (24G624)
Kernel Version: Darwin 24.6.0
Time since boot: 27 minutes, 51 seconds
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
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: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11rc202512110057
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
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: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
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: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
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: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.18
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
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: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
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: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
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: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
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: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.20
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals-py: 3.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.3
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.6.1
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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