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Opened 3 years ago
Last modified 3 years ago
#8449 accepted defect
'CentroidModel' object has no attribute 'distance'
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-137-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
I try to measure the distance between two centroids, but I get this error.
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/pi-
> pi_stacking.cxs" format session
Log from Tue Jan 31 09:50:50 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/U-binding_colorCodingAndAInteraction.cxs"
Log from Mon Jan 30 17:31:41 2023You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_1_multimer_v2_pred_0.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_1_multimer_v2_pred_1.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_1_multimer_v2_pred_2.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_1_multimer_v2_pred_3.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_1_multimer_v2_pred_4.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_2_multimer_v2_pred_0.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_2_multimer_v2_pred_1.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_2_multimer_v2_pred_2.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_2_multimer_v2_pred_3.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_2_multimer_v2_pred_4.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_3_multimer_v2_pred_0.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_3_multimer_v2_pred_1.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_3_multimer_v2_pred_2.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_3_multimer_v2_pred_3.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_3_multimer_v2_pred_4.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_4_multimer_v2_pred_0.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_4_multimer_v2_pred_1.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_4_multimer_v2_pred_2.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_4_multimer_v2_pred_3.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc4/pabpc4lin28a/relaxed_model_4_multimer_v2_pred_4.pdb"
Chain information for relaxed_model_1_multimer_v2_pred_0.pdb #1
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_1_multimer_v2_pred_1.pdb #2
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_1_multimer_v2_pred_2.pdb #3
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_1_multimer_v2_pred_3.pdb #4
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_1_multimer_v2_pred_4.pdb #5
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_0.pdb #6
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_1.pdb #7
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_2.pdb #8
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_3.pdb #9
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_4.pdb #10
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_0.pdb #11
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_1.pdb #12
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_2.pdb #13
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_3.pdb #14
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_4.pdb #15
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_4_multimer_v2_pred_0.pdb #16
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_4_multimer_v2_pred_1.pdb #17
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_4_multimer_v2_pred_2.pdb #18
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_4_multimer_v2_pred_3.pdb #19
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_4_multimer_v2_pred_4.pdb #20
---
Chain | Description
A | No description available
B | No description available
> hide #1 models
> show #1 models
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> show #1 models
> hide #1 models
> show #2 models
> show #1 models
> hide #1 models
> show #1 models
> show #3 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> show #3 models
> hide #2 models
> hide #1 models
> hide #3 models
> show #4 models
> show #5 models
> hide #5 models
> hide #4 models
> show #6 models
> hide #6 models
> show #11 models
> hide #11 models
> show #16 models
> hide #16 models
> close #5
> close
> open "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_1_multimer_v2_pred_0.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_1_multimer_v2_pred_1.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_1_multimer_v2_pred_2.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_1_multimer_v2_pred_3.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_1_multimer_v2_pred_4.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_2_multimer_v2_pred_0.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_2_multimer_v2_pred_1.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_2_multimer_v2_pred_2.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_2_multimer_v2_pred_3.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_2_multimer_v2_pred_4.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_3_multimer_v2_pred_0.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_3_multimer_v2_pred_1.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_3_multimer_v2_pred_2.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_3_multimer_v2_pred_3.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_3_multimer_v2_pred_4.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_0.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_1.pdb"
> "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_2.pdb"
Chain information for relaxed_model_1_multimer_v2_pred_0.pdb #1
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_1_multimer_v2_pred_1.pdb #2
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_1_multimer_v2_pred_2.pdb #3
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_1_multimer_v2_pred_3.pdb #4
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_1_multimer_v2_pred_4.pdb #5
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_0.pdb #6
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_1.pdb #7
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_2.pdb #8
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_3.pdb #9
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_2_multimer_v2_pred_4.pdb #10
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_0.pdb #11
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_1.pdb #12
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_2.pdb #13
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_3.pdb #14
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_3_multimer_v2_pred_4.pdb #15
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_4_multimer_v2_pred_0.pdb #16
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_4_multimer_v2_pred_1.pdb #17
---
Chain | Description
A | No description available
B | No description available
Chain information for relaxed_model_4_multimer_v2_pred_2.pdb #18
---
Chain | Description
A | No description available
B | No description available
> hide target m
> show #1 models
> select
> #1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A#14/A#15/A#16/A#17/A#18/A
178650 atoms, 180558 bonds, 11448 residues, 18 models selected
> color (#1 & sel) hot pink
> select
> #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B
56772 atoms, 57456 bonds, 3762 residues, 18 models selected
> color (#1 & sel) cornflower blue
> select clear
> hide #1 models
> show #2 models
> show #1 models
> hide #1 models
> hide #2 models
> show target m
> select
> #1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A#14/A#15/A#16/A#17/A#18/A
178650 atoms, 180558 bonds, 11448 residues, 18 models selected
> color sel hot pink
> select
> #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B
56772 atoms, 57456 bonds, 3762 residues, 18 models selected
> color sel yellow
> color sel orange
> set bgColor white
> set bgColor black
> select clear
> hide target m
> show #1 models
> hide #1 models
> show #6 models
> hide #6 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #16 models
> ui tool show AlphaFold
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/session.cxs"
> ui tool show AlphaFold
> alphafold pae file '/home/klara/Dropbox (The Francis
> Crick)/klara/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_0.pdb'
Invalid "file" argument: File '/home/klara/Dropbox (The Francis
Crick)/klara/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_0.pdb'
does not exist
> alphafold pae file "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_0.pdb"
AlphaFold predicted aligned error (PAE) files must be in JSON (*.json) or
pickle (*.pkl) format, /home/klara/Dropbox (The Francis
Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_0.pdb
unrecognized format
> alphafold pae file "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_0.pdb"
AlphaFold predicted aligned error (PAE) files must be in JSON (*.json) or
pickle (*.pkl) format, /home/klara/Dropbox (The Francis
Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/relaxed_model_4_multimer_v2_pred_0.pdb
unrecognized format
> ls
Unknown command: ls
> ls
Unknown command: ls
> show #16 models
> hide #16 models
> show #1 models
> alphafold pae file result_model_1_multimer_v2_pred_0.pkl
Invalid "file" argument: File 'result_model_1_multimer_v2_pred_0.pkl' does not
exist
> show #1 models
> alphafold pae file "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/result_model_1_multimer_v2_pred_0.pkl"
> select add #1
13079 atoms, 13223 bonds, 845 residues, 1 model selected
> ui tool show AlphaFold
Must choose path to predicted aligned file
> alphafold pae #1 file "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/result_model_1_multimer_v2_pred_0.pkl"
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
13079 atoms, 845 residues, atom bfactor range 15.7 to 96.3
> color bfactor #1 palette alphafold
13079 atoms, 845 residues, atom bfactor range 15.7 to 96.3
> color bfactor #1 palette alphafold
13079 atoms, 845 residues, atom bfactor range 15.7 to 96.3
> color bfactor #1 palette alphafold
13079 atoms, 845 residues, atom bfactor range 15.7 to 96.3
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/202301_Alphafold/results_pabpc1/proteins/session.cxs"
[Repeated 1 time(s)]
> close session
> fetch 3TRZ
Unknown command: fetch 3TRZ
No atomic structure models chosen
> 3TRZ
Unknown command: 3TRZ
> PDB 3TRZ
Unknown command: PDB 3TRZ
> open /home/klara/Desktop/3trz.pdb
3trz.pdb title:
Mouse LIN28A In complex with let-7D microRNA pre-element [more info...]
Chain information for 3trz.pdb #1
---
Chain | Description | UniProt
A B C D E F | protein lin-28 homolog A | LN28A_MOUSE
U V W X Y Z | RNA (5'-
R(*GP*GP*GP*CP*ap*GP*GP*GP*ap*up*up*up*up*GP*CP*CP*CP*GP*GP*ap*G)- 3') |
Non-standard residues in 3trz.pdb #1
---
GMP — guanosine
ZN — zinc ion
> select /U/V/W/X/Y/Z
2718 atoms, 3042 bonds, 126 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 2718 atom styles
> select ~sel
5976 atoms, 6114 bonds, 54 pseudobonds, 792 residues, 3 models selected
> select protein
5964 atoms, 6114 bonds, 6 pseudobonds, 780 residues, 2 models selected
> select clear
> select protein
5964 atoms, 6114 bonds, 6 pseudobonds, 780 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select nucleic-acid
2718 atoms, 3042 bonds, 126 residues, 1 model selected
> color sel byhetero
> select clear
> select nucleic-acid
2718 atoms, 3042 bonds, 126 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 2718 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 2718 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> nucleotides sel fill
> style nucleic & sel stick
Changed 2718 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 2718 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 2718 atom styles
> color sel bynucleotide
> undo
> color sel bynucleotide
> color bfactor sel
2718 atoms, 126 residues, atom bfactor range 43.7 to 139
> color sel bynucleotide
> select /A
996 atoms, 1019 bonds, 9 pseudobonds, 132 residues, 3 models selected
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /B
996 atoms, 1019 bonds, 9 pseudobonds, 132 residues, 3 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /C
996 atoms, 1019 bonds, 9 pseudobonds, 132 residues, 3 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /D
996 atoms, 1019 bonds, 9 pseudobonds, 132 residues, 3 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /U
453 atoms, 507 bonds, 21 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /V
453 atoms, 507 bonds, 21 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /W
453 atoms, 507 bonds, 21 residues, 1 model selected
> select /X
453 atoms, 507 bonds, 21 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /W
453 atoms, 507 bonds, 21 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Show Sequence Viewer"
> sequence chain /E /F
Alignment identifier is 1
> select /E-F:38-48,53-61,64-75,92-100,103-110
768 atoms, 782 bonds, 98 residues, 1 model selected
> select /E-F:77-79,111-115,148-152,170-174
240 atoms, 236 bonds, 36 residues, 1 model selected
> select /E-F:38-48,53-61,64-75,92-100,103-110
768 atoms, 782 bonds, 98 residues, 1 model selected
> style sel stick
Changed 768 atom styles
> show sel atoms
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> transparency s 30
Missing or invalid "percent" argument: Expected a number
> transparency 30 surfaces
> transparency 90 surfaces
> select subtract #1.3
384 atoms, 391 bonds, 49 residues, 3 models selected
> select subtract #1.4
1 model selected
> select /E-F:35
14 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:35-179
1988 atoms, 2038 bonds, 2 pseudobonds, 260 residues, 2 models selected
> hide sel atoms
> select subtract #1.3
994 atoms, 1019 bonds, 1 pseudobond, 130 residues, 4 models selected
> select subtract #1.4
1 model selected
> select /E-F:88
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E-F:88-93
86 atoms, 84 bonds, 12 residues, 1 model selected
> select /E-F:56-57
28 atoms, 26 bonds, 4 residues, 1 model selected
> select /E-F:49-56
128 atoms, 130 bonds, 16 residues, 1 model selected
> select /E-F:38-48,53-61,64-75,92-100,103-110
768 atoms, 782 bonds, 98 residues, 1 model selected
> select /E-F:46
28 atoms, 30 bonds, 2 residues, 1 model selected
> select /E-F:46-58
222 atoms, 230 bonds, 26 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 222 atom styles
> select subtract #1.3
111 atoms, 115 bonds, 13 residues, 3 models selected
> select subtract #1.4
1 model selected
> select /E-F:46
28 atoms, 30 bonds, 2 residues, 1 model selected
> select /E-F:46
28 atoms, 30 bonds, 2 residues, 1 model selected
> select /E-F:38-48,53-61,64-75,92-100,103-110
768 atoms, 782 bonds, 98 residues, 1 model selected
> select /E-F:47
22 atoms, 22 bonds, 2 residues, 1 model selected
> select /E-F:47-48
38 atoms, 38 bonds, 4 residues, 1 model selected
> select /E-F:46
28 atoms, 30 bonds, 2 residues, 1 model selected
> select /E-F:46-47
50 atoms, 54 bonds, 4 residues, 1 model selected
> select /E-F:38-48,53-61,64-75,92-100,103-110
768 atoms, 782 bonds, 98 residues, 1 model selected
> select /E-F:48
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:48-49
30 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-F:50
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /E-F:50-51
38 atoms, 36 bonds, 4 residues, 1 model selected
> select /E-F:54
8 atoms, 6 bonds, 2 residues, 1 model selected
> select /E-F:54-55
30 atoms, 30 bonds, 4 residues, 1 model selected
> select /E-F:56
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:56-62
100 atoms, 98 bonds, 14 residues, 1 model selected
> hide sel atoms
> select clear
> hide #1.3 models
> hide #1.4 models
> select protein
1988 atoms, 2038 bonds, 2 pseudobonds, 260 residues, 2 models selected
> color bfactor sel
1988 atoms, 260 residues, 2 surfaces, atom bfactor range 36.2 to 164
> undo
> color (#!1 & sel) byhetero
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> select nucleic-acid
906 atoms, 1014 bonds, 42 residues, 1 model selected
> show sel cartoons
> hbonds sel reveal true
118 hydrogen bonds found
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select protein
1988 atoms, 2038 bonds, 2 pseudobonds, 260 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select ~sel
910 atoms, 1014 bonds, 57 pseudobonds, 46 residues, 2 models selected
> hbonds sel reveal true
118 hydrogen bonds found
> select /E-F:102
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E-F:102
18 atoms, 16 bonds, 2 residues, 1 model selected
> style sel stick
Changed 18 atom styles
> select /E-F:177
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E-F:177
18 atoms, 16 bonds, 2 residues, 1 model selected
> style sel stick
Changed 18 atom styles
> select /E-F:159
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E-F:159-160
36 atoms, 34 bonds, 4 residues, 1 model selected
> style sel stick
Changed 36 atom styles
> select /E-F:153
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E-F:153
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E-F:154
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:152-154
46 atoms, 44 bonds, 6 residues, 1 model selected
> select /E-F:155
14 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:155
14 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:153-154
34 atoms, 32 bonds, 4 residues, 1 model selected
> select /E-F:153-154
34 atoms, 32 bonds, 4 residues, 1 model selected
> select /E-F:153-179
418 atoms, 430 bonds, 54 residues, 1 model selected
> select /E-F:154-179
400 atoms, 412 bonds, 52 residues, 1 model selected
> select /E-F:77-79,111-115,148-152,170-174
240 atoms, 236 bonds, 36 residues, 1 model selected
> select /E-F:150-151
36 atoms, 34 bonds, 4 residues, 1 model selected
> select /E-F:150-151
36 atoms, 34 bonds, 4 residues, 1 model selected
> style sel stick
Changed 36 atom styles
> ui tool show "Side View"
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> select ::name="U"
160 atoms, 174 bonds, 4 pseudobonds, 8 residues, 2 models selected
> select ::name="A"
132 atoms, 144 bonds, 6 residues, 1 model selected
> select nucleic-acid
906 atoms, 1014 bonds, 57 pseudobonds, 42 residues, 2 models selected
> color (#!1 & sel) orange
> color (#!1 & sel) gray
> select ::name="U"
160 atoms, 174 bonds, 4 pseudobonds, 8 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> color (#!1 & sel) byhetero
> lighting shadows false
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> interfaces ~solvent
4 buried areas: E Y 1167, F Z 1162, E Z 835, F Y 830
Alignment identifier is 2
Alignment identifier is 3
> ~hbonds
> hbonds reveal true
309 hydrogen bonds found
> undo
Undo failed, probably because structures have been modified.
> undo
> ~hbonds
> select protein
1988 atoms, 2038 bonds, 2 pseudobonds, 260 residues, 2 models selected
> style sel stick
Changed 1988 atom styles
> hide sel atoms
> select ~sel
910 atoms, 1014 bonds, 46 residues, 1 model selected
> hbonds sel reveal true
118 hydrogen bonds found
> select clear
> select ::name="U"
160 atoms, 174 bonds, 4 pseudobonds, 8 residues, 2 models selected
> color (#!1 & sel) byhetero
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> select clear
> select /E-F:154
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:154
16 atoms, 14 bonds, 2 residues, 1 model selected
> ui mousemode right clip
> select clear
> select add /E:47
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select add /E:48
19 atoms, 18 bonds, 2 residues, 2 models selected
> select subtract /E:47
8 atoms, 7 bonds, 1 residue, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> select clear
> select add /E:71@CB
1 atom, 1 residue, 1 model selected
> select subtract /E:71
1 model selected
> select add /E:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) attribute name
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select add /E:45
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add /E:46
31 atoms, 30 bonds, 3 residues, 2 models selected
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select nucleic-acid
906 atoms, 1014 bonds, 57 pseudobonds, 42 residues, 2 models selected
> ~hbonds
> select ::name="U"
160 atoms, 174 bonds, 8 residues, 1 model selected
> hbonds sel reveal true
22 hydrogen bonds found
> select clear
> select protein
1988 atoms, 2038 bonds, 2 pseudobonds, 260 residues, 2 models selected
> hide sel atoms
> select ::name="U"
160 atoms, 174 bonds, 4 pseudobonds, 8 residues, 2 models selected
> hbonds sel reveal true
22 hydrogen bonds found
> select clear
> set bgColor white
> select protein
1988 atoms, 2038 bonds, 2 pseudobonds, 260 residues, 2 models selected
> color (#!1 & sel) hot pink
> color (#!1 & sel) light sea green
> color (#!1 & sel) byhetero
> color (#!1 & sel) #40bfb2ff
> color (#!1 & sel) #40bfabff
> color (#!1 & sel) #40bf8cff
> color (#!1 & sel) #4dbf91ff
> color (#!1 & sel) #41a27bff
> color (#!1 & sel) #46a27dff
> color (#!1 & sel) #429976ff
> color (#!1 & sel) #3e906eff
> color (#!1 & sel) #40906fff
> color (#!1 & sel) #429473ff
[Repeated 1 time(s)]
> color (#!1 & sel) #439675ff
> color (#!1 & sel) #449675ff
> color (#!1 & sel) #439473ff
[Repeated 1 time(s)]
> color (#!1 & sel) #449473ff
> color (#!1 & sel) #439373ff
> color (#!1 & sel) #459373ff
> color (#!1 & sel) #449273ff
> color (#!1 & sel) #459373ff
> color (#!1 & sel) #429372ff
> color (#!1 & sel) #429473ff
> color (#!1 & sel) #409472ff
> color (#!1 & sel) #3e906fff
> color (#!1 & sel) #3f906fff
> color (#!1 & sel) #419070ff
> color (#!1 & sel) #429372ff
> color (#!1 & sel) #459373ff
> color (#!1 & sel) #479978ff
> color (#!1 & sel) #4b997aff
> color (#!1 & sel) #4c9b7bff
> color (#!1 & sel) #509b7cff
> color (#!1 & sel) #519b7dff
> color (#!1 & sel) #569b7fff
> color (#!1 & sel) #59a184ff
> color (#!1 & sel) #5aa184ff
> color (#!1 & sel) #5ba286ff
> color (#!1 & sel) #5fa287ff
> color (#!1 & sel) #62a78bff
> color (#!1 & sel) #63a78cff
> color (#!1 & sel) #66a78dff
> color (#!1 & sel) #68ab90ff
[Repeated 2 time(s)]
> color (#!1 & sel) byhetero
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> select clear
> select add /E:54
4 atoms, 3 bonds, 1 residue, 1 model selected
> select subtract /E:54
Nothing selected
> select add /E:54
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add /E:55
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select ~sel
2883 atoms, 3035 bonds, 40 pseudobonds, 304 residues, 5 models selected
> select clear
> select add /E:55
11 atoms, 11 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select subtract /E:55
1 model selected
> select /E:46
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add /E:55
25 atoms, 26 bonds, 2 residues, 2 models selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> select clear
> select /E:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select /E:47
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select add /E:73
22 atoms, 22 bonds, 2 residues, 2 models selected
> show sel atoms
> select subtract /E:47
11 atoms, 11 bonds, 1 residue, 2 models selected
> select subtract /E:73
1 model selected
> select add /E:47
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /E-F:38-48,53-61,64-75,92-100,103-110
768 atoms, 782 bonds, 98 residues, 1 model selected
> select /E-F:69-70
28 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-F:68-70
42 atoms, 44 bonds, 6 residues, 1 model selected
> select /E-F:66-67
32 atoms, 30 bonds, 4 residues, 1 model selected
> select /E-F:65-67
42 atoms, 40 bonds, 6 residues, 1 model selected
> select /E-F:62
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /E-F:60-62
42 atoms, 40 bonds, 6 residues, 1 model selected
> select /E-F:60
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /E-F:56-60
68 atoms, 66 bonds, 10 residues, 1 model selected
> select /E-F:56-57
28 atoms, 26 bonds, 4 residues, 1 model selected
> select /E-F:56-57
28 atoms, 26 bonds, 4 residues, 1 model selected
> select /E-F:56
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:56-57
28 atoms, 26 bonds, 4 residues, 1 model selected
> style sel stick
Changed 28 atom styles
> style sel stick
Changed 28 atom styles
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> select /E-F:38-48,53-61,64-75,92-100,103-110
768 atoms, 782 bonds, 98 residues, 1 model selected
> select /E-F:55
22 atoms, 22 bonds, 2 residues, 1 model selected
> select /E-F:53-55
52 atoms, 54 bonds, 6 residues, 1 model selected
> show sel atoms
> select /E-F:51-52
24 atoms, 22 bonds, 4 residues, 1 model selected
> select /E-F:50-52
46 atoms, 44 bonds, 6 residues, 1 model selected
> select /E-F:51
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E-F:50-51
38 atoms, 36 bonds, 4 residues, 1 model selected
> select /E-F:50
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /E-F:50
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select /E-F:47
22 atoms, 22 bonds, 2 residues, 1 model selected
> select /E-F:47
22 atoms, 22 bonds, 2 residues, 1 model selected
> select /E-F:46
28 atoms, 30 bonds, 2 residues, 1 model selected
> select /E-F:44-46
58 atoms, 60 bonds, 6 residues, 1 model selected
> show sel atoms
> select subtract /E:45
49 atoms, 50 bonds, 5 residues, 3 models selected
> select subtract /E:46
35 atoms, 35 bonds, 4 residues, 3 models selected
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> select add /E:72
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /E:73
18 atoms, 17 bonds, 2 residues, 2 models selected
> select subtract /E:73
7 atoms, 6 bonds, 1 residue, 2 models selected
> select subtract /E:72
1 model selected
> select add /E:73
11 atoms, 11 bonds, 1 residue, 1 model selected
> select subtract /E:73
1 model selected
> select add /E:73
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add /E:53
11 atoms, 11 bonds, 1 residue, 1 model selected
> select subtract /E:53
1 model selected
> select add /E:53
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> select clear
> select ::name="U"
160 atoms, 174 bonds, 4 pseudobonds, 8 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 160 atom styles
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/CSD_uridine_interactions.tiff" width
> 1733 height 1004 supersample 3
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/U-binding.cxs"
——— End of log from Mon Jan 30 17:31:41 2023 ———
opened ChimeraX session
> select ::name="U"
160 atoms, 174 bonds, 4 pseudobonds, 8 residues, 2 models selected
> color (#!1 & sel) red
> ui tool show "Color Actions"
> color sel crimson
> color sel orange red
> color sel red
> color sel indian red
> color sel sienna
> color sel saddle brown
> color sel chocolate
> color sel brown
> color sel tomato
> color sel brown
> color sel fire brick
> color sel red
> color sel byhetero
> color sel byelement
> color sel byhetero
> color sel red
> color sel byhetero
> color (#!1 & sel) #bf3d3dff
> color (#!1 & sel) #bb3c3cff
> color (#!1 & sel) #bb3f3fff
> color (#!1 & sel) #cf4646ff
> color (#!1 & sel) #cf4a4aff
> color (#!1 & sel) #e05050ff
> color (#!1 & sel) #e45151ff
> color (#!1 & sel) #e45050ff
> color (#!1 & sel) #e34f4fff
> color (#!1 & sel) #e34545ff
> color (#!1 & sel) #df4444ff
> color (#!1 & sel) #df4040ff
> color (#!1 & sel) #e04040ff
> color (#!1 & sel) #e03d3dff
> color (#!1 & sel) #e13d3dff
> color (#!1 & sel) #e23d3dff
> color (#!1 & sel) #e24444ff
> color (#!1 & sel) #f74a4aff
> color (#!1 & sel) #f74b4bff
[Repeated 1 time(s)]
> color (#!1 & sel) #f75555ff
> color (#!1 & sel) #f65454ff
> color (#!1 & sel) #f65555ff
> color (#!1 & sel) #f65858ff
> color (#!1 & sel) #f55757ff
> color (#!1 & sel) #f55656ff
> color (#!1 & sel) #f55252ff
> color (#!1 & sel) #f75252ff
> color (#!1 & sel) #f75454ff
> color (#!1 & sel) #f95555ff
> color (#!1 & sel) #f95a5aff
> color (#!1 & sel) #f75a5aff
> color (#!1 & sel) #f75858ff
> color (#!1 & sel) #f65858ff
> color (#!1 & sel) #f65757ff
> color (#!1 & sel) #fd5959ff
> color (#!1 & sel) #fd5a5aff
> color (#!1 & sel) #ff5b5bff
> color (#!1 & sel) #ff5c5cff
> color (#!1 & sel) #ff5d5dff
> color (#!1 & sel) #ff6060ff
> color (#!1 & sel) #ff6464ff
> color (#!1 & sel) #ff6363ff
> color (#!1 & sel) #ff5b5bff
> color (#!1 & sel) #ff5a5aff
> color (#!1 & sel) #ff5858ff
> color (#!1 & sel) #ff5555ff
> color (#!1 & sel) #ff5454ff
> color (#!1 & sel) #ff4d4dff
> color (#!1 & sel) #ff4f4fff
> color (#!1 & sel) #ff5757ff
> color (#!1 & sel) #ff5c5cff
> color (#!1 & sel) #ff6060ff
> color (#!1 & sel) #ff6363ff
> color (#!1 & sel) #ff6565ff
> color (#!1 & sel) #ff6363ff
> color (#!1 & sel) #ff6262ff
> color (#!1 & sel) #ff5050ff
> color (#!1 & sel) #ff4d4dff
> color (#!1 & sel) #ff6161ff
> color (#!1 & sel) #ff8282ff
> color (#!1 & sel) #ff9696ff
> color (#!1 & sel) #ff9999ff
> color (#!1 & sel) #ff9797ff
> color (#!1 & sel) #ff8d8dff
> color (#!1 & sel) #ff7f7fff
> color (#!1 & sel) #ff7777ff
> color (#!1 & sel) #ff7676ff
> color (#!1 & sel) #ff7474ff
> color (#!1 & sel) #ff7373ff
> color (#!1 & sel) #ff7272ff
> color (#!1 & sel) #ff6e6eff
> color (#!1 & sel) #ff6d6dff
> color (#!1 & sel) #ff6c6cff
> color (#!1 & sel) #ff6b6bff
> color (#!1 & sel) #ff5a5aff
> color (#!1 & sel) #fa5858ff
> color (#!1 & sel) #fa5b5bff
> color (#!1 & sel) #fa5c5cff
> color (#!1 & sel) #f75b5bff
> color (#!1 & sel) #f75757ff
> color (#!1 & sel) #f15555ff
> color (#!1 & sel) #f15454ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f15353ff
> color (#!1 & sel) #f15050ff
> color (#!1 & sel) #f04f4fff
> color (#!1 & sel) #f04e4eff
> color (#!1 & sel) #f04a4aff
> color (#!1 & sel) #f94c4cff
> color (#!1 & sel) #f94a4aff
> color (#!1 & sel) #ff4c4cff
> color (#!1 & sel) #ff4444ff
> color (#!1 & sel) #ff1b1bff
> color (#!1 & sel) #ff1212ff
> color (#!1 & sel) #ff1414ff
> color (#!1 & sel) #fe1414ff
> color (#!1 & sel) #fe2727ff
> color (#!1 & sel) #f52626ff
> color (#!1 & sel) #f52f2fff
> color (#!1 & sel) #ae2222ff
> color (#!1 & sel) #ad2222ff
> color (#!1 & sel) #ad2121ff
> color (#!1 & sel) #ad2222ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ad2d2dff
> color (#!1 & sel) #af2d2dff
> color (#!1 & sel) #af4242ff
> color (#!1 & sel) #ad4141ff
> color (#!1 & sel) #ad6161ff
> color (#!1 & sel) #a55c5cff
> color (#!1 & sel) #a55b5bff
> color (#!1 & sel) #a05858ff
> color (#!1 & sel) #a05555ff
> color (#!1 & sel) #9f5454ff
> color (#!1 & sel) #9f4848ff
> color (#!1 & sel) #a94d4dff
> color (#!1 & sel) #a94646ff
> color (#!1 & sel) #bf5050ff
> color (#!1 & sel) #bf4f4fff
> color (#!1 & sel) #ce5555ff
> color (#!1 & sel) #cf5555ff
> color (#!1 & sel) #cf5f5fff
> color (#!1 & sel) #d26161ff
> color (#!1 & sel) #d26464ff
> color (#!1 & sel) #d26666ff
> color (#!1 & sel) #d36767ff
> color (#!1 & sel) #d37575ff
> color (#!1 & sel) #d37e7eff
> color (#!1 & sel) #cf7c7cff
> color (#!1 & sel) #cf8585ff
> color (#!1 & sel) #ce8484ff
> color (#!1 & sel) #ce8b8bff
> color (#!1 & sel) #ce8d8dff
> color (#!1 & sel) #cb8b8bff
> color (#!1 & sel) #cb7a7aff
> color (#!1 & sel) #e68a8aff
> color (#!1 & sel) #e68787ff
> color (#!1 & sel) #eb8b8bff
> color (#!1 & sel) #eb8a8aff
> color (#!1 & sel) #eb7171ff
> color (#!1 & sel) #f07373ff
> color (#!1 & sel) #f07575ff
> color (#!1 & sel) #f07474ff
> color (#!1 & sel) #f07070ff
> color (#!1 & sel) #ee6f6fff
> color (#!1 & sel) #ee6666ff
> color (#!1 & sel) #ee6161ff
> color (#!1 & sel) #f06161ff
> color (#!1 & sel) #f05a5aff
> color (#!1 & sel) #f45c5cff
[Repeated 3 time(s)]
> color sel byhetero
> select ::name="A"
132 atoms, 144 bonds, 6 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 132 atom styles
> select add /Y:9
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel forest green
> color sel byhetero
> hbonds sel reveal true
3 hydrogen bonds found
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/AUU_interactions.tif"
> width 1753 height 1038 supersample 3
> select /E:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /E:100
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add /E:104
23 atoms, 20 bonds, 3 residues, 2 models selected
> select subtract /E:104
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add /E:105@CB
16 atoms, 13 bonds, 3 residues, 2 models selected
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/AUU_interactions.tif"
> width 1753 height 1038 supersample 3
> select /E:104
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select subtract /E:104
1 model selected
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/AUU_interactions_1.tif"
> width 1753 height 1038 supersample 3
> select /Y:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /Y:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /Y:11
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add /Y:9
62 atoms, 66 bonds, 3 residues, 1 model selected
> select subtract /Y:9
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add /Y:9
62 atoms, 66 bonds, 3 residues, 1 model selected
> hbonds sel reveal true
8 hydrogen bonds found
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/AUU_interactions_1.tif"
> width 1753 height 1038 supersample 3
> ui tool show "Side View"
> select add /E:99
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select subtract /E:99
1 model selected
> select add /E:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select add /E:106
15 atoms, 13 bonds, 2 residues, 2 models selected
> select subtract /E:105
6 atoms, 5 bonds, 1 residue, 2 models selected
> show sel atoms
> hide sel atoms
> select subtract /E:106
1 model selected
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/pi-
> pi_stacking.cxs"
> select add /Y:11
20 atoms, 21 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add /Y:10
40 atoms, 42 bonds, 1 pseudobond, 2 residues, 2 models selected
> select add /Y:9
62 atoms, 66 bonds, 1 pseudobond, 3 residues, 2 models selected
> select /Y:9
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add /Y:10
42 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract /Y:9
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /Y:11
40 atoms, 42 bonds, 1 pseudobond, 2 residues, 2 models selected
> hbonds sel reveal true
5 hydrogen bonds found
> ~hbonds
> select :46.E & aromatic ring
Expected an objects specifier or a keyword
> select add /Y:5@N9
41 atoms, 42 bonds, 3 residues, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 41 atom styles
> undo
[Repeated 1 time(s)]
> select clear
> select add /Y:5
22 atoms, 24 bonds, 1 residue, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 22 atom styles
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/interactions_closeUp.tif"
> width 1753 height 1038 supersample 3
> select /Y:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /Y:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /Y:11
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add /Y:9
62 atoms, 66 bonds, 3 residues, 1 model selected
> hbonds sel reveal true
8 hydrogen bonds found
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/interactions_closeUp_1.tif"
> width 1753 height 1038 supersample 3
> select add /Y:10@C2
1 atom, 1 residue, 1 model selected
> select add /Y:10@N1
2 atoms, 1 residue, 1 model selected
> select subtract /Y:10@N1
1 atom, 1 residue, 1 model selected
> select add /Y:10@N1
2 atoms, 1 residue, 1 model selected
> select add /Y:10@C6
3 atoms, 1 residue, 1 model selected
> select add /Y:10@C5
4 atoms, 1 residue, 1 model selected
> select add /Y:10@C4
5 atoms, 1 residue, 1 model selected
> select add /Y:10@N3
6 atoms, 1 residue, 1 model selected
> toolshed show
> ui tool show Distances
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> ui tool show "Model Panel"
> ui tool show Distances
> ui tool show "Build Structure"
> ui tool show Axes/Planes/Centroids
No running or installed tool named "Axes/Planes/Centroids"
> ui tool show Axes/Planes/Centroids
No running or installed tool named "Axes/Planes/Centroids"
> ui tool show "Structure Analysis"
No running or installed tool named "Structure Analysis"
> ui tool show "Altloc Explorer"
> define centroid
Centroid 'centroid' placed at [34.40306176 68.26441992 52.1635652 ]
> hide #1.7 models
> show #1.7 models
> select add #1.7
7 atoms, 2 residues, 2 models selected
> define plane
Missing or invalid "atoms" argument: empty atom specifier
> select add #1
2899 atoms, 3052 bonds, 26 pseudobonds, 307 residues, 6 models selected
> select subtract #1
2 models selected
> select add #1.7
1 atom, 1 residue, 1 model selected
> delete atoms (#1.7 & sel)
> delete bonds (#1.7 & sel)
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/pi-
> pi_stacking.cxs"
——— End of log from Tue Jan 31 09:50:50 2023 ———
opened ChimeraX session
> select /E:55@CD2
1 atom, 1 residue, 1 model selected
> select /E:55@CG
1 atom, 1 residue, 1 model selected
> select add /E:55@CD2
2 atoms, 1 residue, 2 models selected
> select add /E:55@CE2
3 atoms, 1 residue, 2 models selected
> select add /E:55@CZ
4 atoms, 1 residue, 2 models selected
> select add /E:55@CE1
5 atoms, 1 residue, 2 models selected
> select add /E:55@CD1
6 atoms, 1 residue, 2 models selected
> ui tool show Axes/Planes/Centroids
> define plane sel
Plane 'plane' placed at [47.64033381 87.23733266 63.66333326] with normal
[-0.91291891 0.16670943 0.37254132] and radius 1.4
> define centroid sel radius 0.5
Centroid 'centroid' placed at [47.64033381 87.23733266 63.66333326]
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/pi-
> pi_stacking.cxs"
> select add #!1/Y:10@N3
1 atom, 1 residue, 1 model selected
> select add #!1/Y:10@C2
2 atoms, 1 residue, 1 model selected
> select add #!1/Y:10@N1
3 atoms, 1 residue, 1 model selected
> select add #!1/Y:10@C6
4 atoms, 1 residue, 1 model selected
> select add #!1/Y:10@C5
5 atoms, 1 residue, 1 model selected
> select add #!1/Y:10@C4
6 atoms, 1 residue, 1 model selected
> define plane sel
Plane 'plane' placed at [51.1710008 86.79616674 63.07033285] with normal [
0.94564073 -0.11258061 -0.30510524] and radius 1.4
> define centroid sel radius 0.5
Centroid 'centroid' placed at [51.1710008 86.79616674 63.07033285]
> select clear
> select add #!1/E:46@CD1
1 atom, 1 residue, 1 model selected
> select add #!1/E:46@CG
2 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CD2
3 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CE2
4 atoms, 1 residue, 2 models selected
> select add #!1/E:46@NE1
5 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CZ2
6 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CH2
7 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CZ3
8 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CE3
9 atoms, 1 residue, 2 models selected
> define plane sel
Plane 'plane' placed at [47.00344425 81.90888808 61.86822213] with normal [
0.74577282 -0.66151281 -0.07889046] and radius 2.4
> select clear
> select add #!1/Y:11@C2
1 atom, 1 residue, 1 model selected
> select add #!1/Y:11@N1
2 atoms, 1 residue, 1 model selected
> select add #!1/Y:11@N3
3 atoms, 1 residue, 1 model selected
> select add #!1/Y:11@C4
4 atoms, 1 residue, 1 model selected
> select add #!1/Y:11@C5
5 atoms, 1 residue, 1 model selected
> select add #!1/Y:11@C6
6 atoms, 1 residue, 1 model selected
> define plane sel
Plane 'plane' placed at [50.95666631 81.53816605 58.9993337 ] with normal
[-0.77214891 0.59940005 0.21096361] and radius 1.4
> define centroid sel radius 0.5
Centroid 'centroid' placed at [50.95666631 81.53816605 58.9993337 ]
> select clear
> select add #!1/E:46@CD1
1 atom, 1 residue, 1 model selected
> select add #!1/E:46@CG
2 atoms, 1 residue, 2 models selected
> select add #!1/E:46@NE1
3 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CE2
4 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CD2
5 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CE3
6 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CZ3
7 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CH2
8 atoms, 1 residue, 2 models selected
> select add #!1/E:46@CZ2
9 atoms, 1 residue, 2 models selected
> define centroid sel radius 0.5
Centroid 'centroid' placed at [47.00344425 81.90888808 61.86822213]
> select clear
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/pi-
> pi_stacking.cxs"
> lighting simple
> ui tool show "Side View"
> select #1.8
1 atom, 1 residue, 1 model selected
> select #1.10
1 atom, 1 residue, 1 model selected
> select #1.8
1 atom, 1 residue, 1 model selected
> select #1.10
1 atom, 1 residue, 1 model selected
> select #1.8
1 atom, 1 residue, 1 model selected
> ~select #1.8
Nothing selected
> select #1.10
1 atom, 1 residue, 1 model selected
> select #1.8
1 atom, 1 residue, 1 model selected
> select add #1.10
2 atoms, 2 residues, 2 models selected
No items chosen in table
> distance 1.8 1.10
Missing or invalid "objects" argument: invalid objects specifier
> distance sel
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
AttributeError: 'CentroidModel' object has no attribute 'distance'
AttributeError: 'CentroidModel' object has no attribute 'distance'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
See log for complete Python traceback.
> rename #1.8 c1
> rename #1.10 c2
> rename #1.13 c3
> rename #1.14 c4
> distance c1 c2
Missing or invalid "objects" argument: invalid objects specifier
> save "/home/klara/Dropbox (The Francis
> Crick)/klara/Projects/LIN28/results/AnalysisOfUBindingToCsd/pi-
> pi_stacking.cxs"
> distance c1.8 c1.10
Missing or invalid "objects" argument: invalid objects specifier
> ui tool show Distances
ID must be one or more integers separated by '.' characters
[Repeated 1 time(s)]
> distance #1.8 #1.10
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
AttributeError: 'CentroidModel' object has no attribute 'distance'
AttributeError: 'CentroidModel' object has no attribute 'distance'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
See log for complete Python traceback.
> ~distance #1.8 #1.10
[Repeated 1 time(s)]
> distance #1.8/centroid:1@centroid #1.10/centroid:1@centroid
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 254, in _create_distance
run(self.session, "distance %s %s" % tuple(a.string(style="command") for a in
sel_atoms))
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
AttributeError: 'CentroidModel' object has no attribute 'distance'
AttributeError: 'CentroidModel' object has no attribute 'distance'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
See log for complete Python traceback.
> distance #1.8/centroid:1@centroid #1.10/centroid:1@centroid
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 254, in _create_distance
run(self.session, "distance %s %s" % tuple(a.string(style="command") for a in
sel_atoms))
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
AttributeError: 'CentroidModel' object has no attribute 'distance'
AttributeError: 'CentroidModel' object has no attribute 'distance'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 620 (WHL GT2)
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: HP
Model: HP EliteBook 850 G6
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 30Gi 10Gi 10Gi 1.9Gi 9.7Gi 18Gi
Swap: 8.0Gi 0B 8.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 (Whiskey Lake) [8086:3ea0] (rev 02)
DeviceName: Onboard IGD
Subsystem: Hewlett-Packard Company UHD Graphics 620 (Whiskey Lake) [103c:8549]
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (3)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 'CentroidModel' object has no attribute 'distance' |
comment:2 by , 3 years ago
follow-up: 3 comment:3 by , 3 years ago
Thank you for your response! Cheers, Klara V V tor., 7. feb. 2023 ob 18:35 je oseba ChimeraX < ChimeraX-bugs-admin@cgl.ucsf.edu> napisala:
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Hi Klara,
--Eric