Opened 4 years ago

Closed 4 years ago

#5203 closed defect (not a bug)

bigalpha.py: can't set residues.numbers

Reported by: shujun.cai@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/nus/Desktop/Alphafold2/bigalpha.py

executed bigalpha.py  

> bigalpha Q8WZ42 directory
> /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN/

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

No such file/path: AF-Q8WZ42-F1-model_v1.pdb.gz  

> open /Users/nus/Desktop/Alphafold2/bigalpha.py format python

FYI: command is replacing existing command: "bigalpha"  
executed bigalpha.py  

> open
> /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN/AF-Q8WZ42-F94-model_v1.pdb.gz
> format pdb

AF-Q8WZ42-F94-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F94-model_v1.pdb.gz #1  
---  
Chain | Description  
A | TITIN  
  

> close

> open
> /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN/AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #1  
---  
Chain | Description  
A | TITIN  
  

> open /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN/bigalpha.py

No such file/path:
/Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN/bigalpha.py  

> open /Users/nus/Desktop/Alphafold2/bigalpha.py

FYI: command is replacing existing command: "bigalpha"  
executed bigalpha.py  

> cd /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN/

Current working directory is:
/Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN  

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #2  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #2 palette alphafold

Fetching compressed palette alphafold from
http://www.colourlovers.com/api/palettes?keywords=alphafold&format=json&numResults=100  
Could not find palette alphafold at COLOURlovers.com using keyword search  

> close

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #1  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #1 palette alphafold

Could not find palette alphafold at COLOURlovers.com using keyword search  

> bigalpha Q8WZ42 directory
> /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #2  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #2 palette alphafold

Could not find palette alphafold at COLOURlovers.com using keyword search  

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #3  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #3 palette alphafold

Could not find palette alphafold at COLOURlovers.com using keyword search  

> close

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #1  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #1 palette alphafold

Could not find palette alphafold at COLOURlovers.com using keyword search  

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #2  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #2 palette alphafold

Could not find palette alphafold at COLOURlovers.com using keyword search  

> open bigalpha.py

No such file/path: bigalpha.py  

> cd /Users/nus/Desktop/Alphafold2

Current working directory is: /Users/nus/Desktop/Alphafold2  

> open bigalpha.py

FYI: command is replacing existing command: "bigalpha"  
executed bigalpha.py  

> close

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 0 mmCIF files  

> open AF-Q8WZ42-F0-model_v1.pdb.gz

No such file/path: AF-Q8WZ42-F0-model_v1.pdb.gz  

> cd /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN

Current working directory is:
/Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN  

> cd /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN

Current working directory is:
/Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN  

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #1  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #1 palette rainbow

10797 atoms, 1400 residues, atom bfactor range 24.8 to 96.7  

> hide #1 cartoons

> show #1 atoms

> style #1 sphere

Changed 10797 atom styles  

> open AF-Q8WZ42-F7-model_v1.pdb.gz

AF-Q8WZ42-F7-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F7-model_v1.pdb.gz #2  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #2 palette rainbow

11244 atoms, 1400 residues, atom bfactor range 26.2 to 97  

> hide #2 cartoons

> show #2 atoms

> style #2 sphere

Changed 11244 atom styles  

> align #2:196-200@CA toAtoms #1:1395-1399@CA

RMSD between 5 atom pairs is 1.585 angstroms  

> delete #2:1-200

> open AF-Q8WZ42-F13-model_v1.pdb.gz

AF-Q8WZ42-F13-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F13-model_v1.pdb.gz #3  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #3 palette rainbow

11015 atoms, 1400 residues, atom bfactor range 24.5 to 96.6  

> hide #3 cartoons

> show #3 atoms

> style #3 sphere

Changed 11015 atom styles  

> align #3:196-200@CA toAtoms #2:1395-1399@CA

RMSD between 5 atom pairs is 1.103 angstroms  

> delete #3:1-200

> open AF-Q8WZ42-F19-model_v1.pdb.gz

AF-Q8WZ42-F19-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F19-model_v1.pdb.gz #4  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #4 palette rainbow

10832 atoms, 1400 residues, atom bfactor range 22.8 to 96.8  

> hide #4 cartoons

> show #4 atoms

> style #4 sphere

Changed 10832 atom styles  

> align #4:196-200@CA toAtoms #3:1395-1399@CA

RMSD between 5 atom pairs is 0.465 angstroms  

> delete #4:1-200

> open AF-Q8WZ42-F25-model_v1.pdb.gz

AF-Q8WZ42-F25-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F25-model_v1.pdb.gz #5  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #5 palette rainbow

10810 atoms, 1400 residues, atom bfactor range 56.9 to 95.8  

> hide #5 cartoons

> show #5 atoms

> style #5 sphere

Changed 10810 atom styles  

> align #5:196-200@CA toAtoms #4:1395-1399@CA

RMSD between 5 atom pairs is 2.331 angstroms  

> delete #5:1-200

> open AF-Q8WZ42-F31-model_v1.pdb.gz

AF-Q8WZ42-F31-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F31-model_v1.pdb.gz #6  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #6 palette rainbow

10775 atoms, 1400 residues, atom bfactor range 32.6 to 96.2  

> hide #6 cartoons

> show #6 atoms

> style #6 sphere

Changed 10775 atom styles  

> align #6:196-200@CA toAtoms #5:1395-1399@CA

RMSD between 5 atom pairs is 0.738 angstroms  

> delete #6:1-200

> open AF-Q8WZ42-F37-model_v1.pdb.gz

AF-Q8WZ42-F37-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F37-model_v1.pdb.gz #7  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #7 palette rainbow

10739 atoms, 1400 residues, atom bfactor range 27.3 to 94.7  

> hide #7 cartoons

> show #7 atoms

> style #7 sphere

Changed 10739 atom styles  

> align #7:196-200@CA toAtoms #6:1395-1399@CA

RMSD between 5 atom pairs is 2.736 angstroms  

> delete #7:1-200

> open AF-Q8WZ42-F43-model_v1.pdb.gz

AF-Q8WZ42-F43-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F43-model_v1.pdb.gz #8  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #8 palette rainbow

10878 atoms, 1400 residues, atom bfactor range 4.74 to 96  

> hide #8 cartoons

> show #8 atoms

> style #8 sphere

Changed 10878 atom styles  

> align #8:196-200@CA toAtoms #7:1395-1399@CA

RMSD between 5 atom pairs is 0.761 angstroms  

> delete #8:1-200

> open AF-Q8WZ42-F49-model_v1.pdb.gz

AF-Q8WZ42-F49-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F49-model_v1.pdb.gz #9  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #9 palette rainbow

11339 atoms, 1400 residues, atom bfactor range 22.2 to 98.3  

> hide #9 cartoons

> show #9 atoms

> style #9 sphere

Changed 11339 atom styles  

> align #9:196-200@CA toAtoms #8:1395-1399@CA

RMSD between 5 atom pairs is 2.022 angstroms  

> delete #9:1-200

> open AF-Q8WZ42-F55-model_v1.pdb.gz

AF-Q8WZ42-F55-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F55-model_v1.pdb.gz #10  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #10 palette rainbow

10995 atoms, 1400 residues, atom bfactor range 24.9 to 98  

> hide #10 cartoons

> show #10 atoms

> style #10 sphere

Changed 10995 atom styles  

> align #10:196-200@CA toAtoms #9:1395-1399@CA

RMSD between 5 atom pairs is 0.848 angstroms  

> delete #10:1-200

> open AF-Q8WZ42-F61-model_v1.pdb.gz

AF-Q8WZ42-F61-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F61-model_v1.pdb.gz #11  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #11 palette rainbow

11076 atoms, 1400 residues, atom bfactor range 28.9 to 96.7  

> hide #11 cartoons

> show #11 atoms

> style #11 sphere

Changed 11076 atom styles  

> align #11:196-200@CA toAtoms #10:1395-1399@CA

RMSD between 5 atom pairs is 0.281 angstroms  

> delete #11:1-200

> open AF-Q8WZ42-F67-model_v1.pdb.gz

AF-Q8WZ42-F67-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F67-model_v1.pdb.gz #12  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #12 palette rainbow

11108 atoms, 1400 residues, atom bfactor range 17.2 to 96.2  

> hide #12 cartoons

> show #12 atoms

> style #12 sphere

Changed 11108 atom styles  

> align #12:196-200@CA toAtoms #11:1395-1399@CA

RMSD between 5 atom pairs is 1.087 angstroms  

> delete #12:1-200

> open AF-Q8WZ42-F73-model_v1.pdb.gz

AF-Q8WZ42-F73-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F73-model_v1.pdb.gz #13  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #13 palette rainbow

10961 atoms, 1400 residues, atom bfactor range 32.8 to 96.4  

> hide #13 cartoons

> show #13 atoms

> style #13 sphere

Changed 10961 atom styles  

> align #13:196-200@CA toAtoms #12:1395-1399@CA

RMSD between 5 atom pairs is 0.928 angstroms  

> delete #13:1-200

> open AF-Q8WZ42-F79-model_v1.pdb.gz

AF-Q8WZ42-F79-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F79-model_v1.pdb.gz #14  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #14 palette rainbow

10939 atoms, 1400 residues, atom bfactor range 31.6 to 96.9  

> hide #14 cartoons

> show #14 atoms

> style #14 sphere

Changed 10939 atom styles  

> align #14:196-200@CA toAtoms #13:1395-1399@CA

RMSD between 5 atom pairs is 1.711 angstroms  

> delete #14:1-200

> open AF-Q8WZ42-F85-model_v1.pdb.gz

AF-Q8WZ42-F85-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F85-model_v1.pdb.gz #15  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #15 palette rainbow

10952 atoms, 1400 residues, atom bfactor range 33.1 to 97.6  

> hide #15 cartoons

> show #15 atoms

> style #15 sphere

Changed 10952 atom styles  

> align #15:196-200@CA toAtoms #14:1395-1399@CA

RMSD between 5 atom pairs is 0.641 angstroms  

> delete #15:1-200

> open AF-Q8WZ42-F91-model_v1.pdb.gz

AF-Q8WZ42-F91-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F91-model_v1.pdb.gz #16  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #16 palette rainbow

10966 atoms, 1400 residues, atom bfactor range 50.4 to 96  

> hide #16 cartoons

> show #16 atoms

> style #16 sphere

Changed 10966 atom styles  

> align #16:196-200@CA toAtoms #15:1395-1399@CA

RMSD between 5 atom pairs is 1.802 angstroms  

> delete #16:1-200

> open AF-Q8WZ42-F97-model_v1.pdb.gz

AF-Q8WZ42-F97-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F97-model_v1.pdb.gz #17  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #17 palette rainbow

10886 atoms, 1400 residues, atom bfactor range 54 to 97  

> hide #17 cartoons

> show #17 atoms

> style #17 sphere

Changed 10886 atom styles  

> align #17:196-200@CA toAtoms #16:1395-1399@CA

RMSD between 5 atom pairs is 0.542 angstroms  

> delete #17:1-200

> open AF-Q8WZ42-F103-model_v1.pdb.gz

AF-Q8WZ42-F103-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F103-model_v1.pdb.gz #18  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #18 palette rainbow

10883 atoms, 1400 residues, atom bfactor range 36.8 to 96.9  

> hide #18 cartoons

> show #18 atoms

> style #18 sphere

Changed 10883 atom styles  

> align #18:196-200@CA toAtoms #17:1395-1399@CA

RMSD between 5 atom pairs is 2.342 angstroms  

> delete #18:1-200

> open AF-Q8WZ42-F109-model_v1.pdb.gz

AF-Q8WZ42-F109-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F109-model_v1.pdb.gz #19  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #19 palette rainbow

10863 atoms, 1400 residues, atom bfactor range 15.6 to 96.8  

> hide #19 cartoons

> show #19 atoms

> style #19 sphere

Changed 10863 atom styles  

> align #19:196-200@CA toAtoms #18:1395-1399@CA

RMSD between 5 atom pairs is 0.968 angstroms  

> delete #19:1-200

> open AF-Q8WZ42-F115-model_v1.pdb.gz

AF-Q8WZ42-F115-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F115-model_v1.pdb.gz #20  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #20 palette rainbow

10882 atoms, 1400 residues, atom bfactor range 44.7 to 96.8  

> hide #20 cartoons

> show #20 atoms

> style #20 sphere

Changed 10882 atom styles  

> align #20:196-200@CA toAtoms #19:1395-1399@CA

RMSD between 5 atom pairs is 1.242 angstroms  

> delete #20:1-200

> open AF-Q8WZ42-F121-model_v1.pdb.gz

AF-Q8WZ42-F121-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F121-model_v1.pdb.gz #21  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #21 palette rainbow

10876 atoms, 1400 residues, atom bfactor range 37.7 to 97.7  

> hide #21 cartoons

> show #21 atoms

> style #21 sphere

Changed 10876 atom styles  

> align #21:196-200@CA toAtoms #20:1395-1399@CA

RMSD between 5 atom pairs is 0.480 angstroms  

> delete #21:1-200

> open AF-Q8WZ42-F127-model_v1.pdb.gz

AF-Q8WZ42-F127-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F127-model_v1.pdb.gz #22  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #22 palette rainbow

10848 atoms, 1400 residues, atom bfactor range 32.1 to 97.4  

> hide #22 cartoons

> show #22 atoms

> style #22 sphere

Changed 10848 atom styles  

> align #22:196-200@CA toAtoms #21:1395-1399@CA

RMSD between 5 atom pairs is 2.398 angstroms  

> delete #22:1-200

> open AF-Q8WZ42-F133-model_v1.pdb.gz

AF-Q8WZ42-F133-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F133-model_v1.pdb.gz #23  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #23 palette rainbow

10875 atoms, 1400 residues, atom bfactor range 33.1 to 96.7  

> hide #23 cartoons

> show #23 atoms

> style #23 sphere

Changed 10875 atom styles  

> align #23:196-200@CA toAtoms #22:1395-1399@CA

RMSD between 5 atom pairs is 1.181 angstroms  

> delete #23:1-200

> open AF-Q8WZ42-F139-model_v1.pdb.gz

AF-Q8WZ42-F139-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F139-model_v1.pdb.gz #24  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #24 palette rainbow

10875 atoms, 1400 residues, atom bfactor range 44.4 to 96.7  

> hide #24 cartoons

> show #24 atoms

> style #24 sphere

Changed 10875 atom styles  

> align #24:196-200@CA toAtoms #23:1395-1399@CA

RMSD between 5 atom pairs is 0.895 angstroms  

> delete #24:1-200

> open AF-Q8WZ42-F145-model_v1.pdb.gz

AF-Q8WZ42-F145-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F145-model_v1.pdb.gz #25  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #25 palette rainbow

10871 atoms, 1400 residues, atom bfactor range 41.8 to 96.4  

> hide #25 cartoons

> show #25 atoms

> style #25 sphere

Changed 10871 atom styles  

> align #25:196-200@CA toAtoms #24:1395-1399@CA

RMSD between 5 atom pairs is 0.459 angstroms  

> delete #25:1-200

> open AF-Q8WZ42-F151-model_v1.pdb.gz

AF-Q8WZ42-F151-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F151-model_v1.pdb.gz #26  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #26 palette rainbow

10955 atoms, 1400 residues, atom bfactor range 55 to 96.3  

> hide #26 cartoons

> show #26 atoms

> style #26 sphere

Changed 10955 atom styles  

> align #26:196-200@CA toAtoms #25:1395-1399@CA

RMSD between 5 atom pairs is 1.067 angstroms  

> delete #26:1-200

> open AF-Q8WZ42-F157-model_v1.pdb.gz

AF-Q8WZ42-F157-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F157-model_v1.pdb.gz #27  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #27 palette rainbow

11139 atoms, 1400 residues, atom bfactor range 28 to 98  

> hide #27 cartoons

> show #27 atoms

> style #27 sphere

Changed 11139 atom styles  

> align #27:196-200@CA toAtoms #26:1395-1399@CA

RMSD between 5 atom pairs is 1.180 angstroms  

> delete #27:1-200

> open AF-Q8WZ42-F163-model_v1.pdb.gz

AF-Q8WZ42-F163-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F163-model_v1.pdb.gz #28  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #28 palette rainbow

11317 atoms, 1400 residues, atom bfactor range 25.2 to 94.8  

> hide #28 cartoons

> show #28 atoms

> style #28 sphere

Changed 11317 atom styles  

> align #28:196-200@CA toAtoms #27:1395-1399@CA

RMSD between 5 atom pairs is 1.715 angstroms  

> delete #28:1-200

> open AF-Q8WZ42-F166-model_v1.pdb.gz

AF-Q8WZ42-F166-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F166-model_v1.pdb.gz #29  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #29 palette rainbow

10581 atoms, 1350 residues, atom bfactor range 25.4 to 96.8  

> hide #29 cartoons

> show #29 atoms

> style #29 sphere

Changed 10581 atom styles  

> align #29:796-800@CA toAtoms #28:1395-1399@CA

RMSD between 5 atom pairs is 0.716 angstroms  

> delete #29:1-800

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "bigalpha.py", line 64, in open_multifile_alphafold_model  
File "bigalpha.py", line 102, in shift_residue_numbers  
AttributeError: can't set attribute  
  
AttributeError: can't set attribute  
  
File "bigalpha.py", line 102, in shift_residue_numbers  
  
See log for complete Python traceback.  
  

> bigalpha Q709C8

AlphaFold Q709C8 is split into 13 mmCIF files  

> open AF-Q709C8-F1-model_v1.pdb.gz

AF-Q709C8-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F1-model_v1.pdb.gz #30  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #30 palette rainbow

11171 atoms, 1400 residues, atom bfactor range 19.1 to 97.2  

> hide #30 cartoons

> show #30 atoms

> style #30 sphere

Changed 11171 atom styles  

> open AF-Q709C8-F7-model_v1.pdb.gz

AF-Q709C8-F7-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F7-model_v1.pdb.gz #31  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #31 palette rainbow

10972 atoms, 1400 residues, atom bfactor range 21.8 to 96.6  

> hide #31 cartoons

> show #31 atoms

> style #31 sphere

Changed 10972 atom styles  

> align #31:196-200@CA toAtoms #30:1395-1399@CA

RMSD between 5 atom pairs is 0.738 angstroms  

> delete #31:1-200

> open AF-Q709C8-F13-model_v1.pdb.gz

AF-Q709C8-F13-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F13-model_v1.pdb.gz #32  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #32 palette rainbow

10721 atoms, 1353 residues, atom bfactor range 28.1 to 94.7  

> hide #32 cartoons

> show #32 atoms

> style #32 sphere

Changed 10721 atom styles  

> align #32:196-200@CA toAtoms #31:1395-1399@CA

RMSD between 5 atom pairs is 1.442 angstroms  

> delete #32:1-200

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "bigalpha.py", line 64, in open_multifile_alphafold_model  
File "bigalpha.py", line 102, in shift_residue_numbers  
AttributeError: can't set attribute  
  
AttributeError: can't set attribute  
  
File "bigalpha.py", line 102, in shift_residue_numbers  
  
See log for complete Python traceback.  
  

> close

> bigalpha Q709C8

AlphaFold Q709C8 is split into 13 mmCIF files  

> open AF-Q709C8-F1-model_v1.pdb.gz

AF-Q709C8-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F1-model_v1.pdb.gz #1  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #1 palette rainbow

11171 atoms, 1400 residues, atom bfactor range 19.1 to 97.2  

> hide #1 cartoons

> show #1 atoms

> style #1 sphere

Changed 11171 atom styles  

> open AF-Q709C8-F7-model_v1.pdb.gz

AF-Q709C8-F7-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F7-model_v1.pdb.gz #2  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #2 palette rainbow

10972 atoms, 1400 residues, atom bfactor range 21.8 to 96.6  

> hide #2 cartoons

> show #2 atoms

> style #2 sphere

Changed 10972 atom styles  

> align #2:196-200@CA toAtoms #1:1395-1399@CA

RMSD between 5 atom pairs is 0.738 angstroms  

> delete #2:1-200

> open AF-Q709C8-F13-model_v1.pdb.gz

AF-Q709C8-F13-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F13-model_v1.pdb.gz #3  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #3 palette rainbow

10721 atoms, 1353 residues, atom bfactor range 28.1 to 94.7  

> hide #3 cartoons

> show #3 atoms

> style #3 sphere

Changed 10721 atom styles  

> align #3:196-200@CA toAtoms #2:1395-1399@CA

RMSD between 5 atom pairs is 1.442 angstroms  

> delete #3:1-200

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "bigalpha.py", line 64, in open_multifile_alphafold_model  
File "bigalpha.py", line 102, in shift_residue_numbers  
AttributeError: can't set attribute  
  
AttributeError: can't set attribute  
  
File "bigalpha.py", line 102, in shift_residue_numbers  
  
See log for complete Python traceback.  
  

> show atoms

> hide atoms

> hide atoms

> show atoms

> show cartoons

> hide atoms

> hide #2 models

> hide #3 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> show #3 models

> hide #2 models

> show #2 models

> hide #2 models

> close

> bigalpha Q709C8 directory
> /Users/nus/Desktop/Alphafold2/UP000005640_9606_HUMAN

AlphaFold Q709C8 is split into 13 mmCIF files  

> open AF-Q709C8-F1-model_v1.pdb.gz

AF-Q709C8-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F1-model_v1.pdb.gz #1  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #1 palette rainbow

11171 atoms, 1400 residues, atom bfactor range 19.1 to 97.2  

> hide #1 cartoons

> show #1 atoms

> style #1 sphere

Changed 11171 atom styles  

> open AF-Q709C8-F7-model_v1.pdb.gz

AF-Q709C8-F7-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F7-model_v1.pdb.gz #2  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #2 palette rainbow

10972 atoms, 1400 residues, atom bfactor range 21.8 to 96.6  

> hide #2 cartoons

> show #2 atoms

> style #2 sphere

Changed 10972 atom styles  

> align #2:196-200@CA toAtoms #1:1395-1399@CA

RMSD between 5 atom pairs is 0.738 angstroms  

> delete #2:1-200

> open AF-Q709C8-F13-model_v1.pdb.gz

AF-Q709C8-F13-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for vacuolar protein sorting-associated protein 13C
(Q709C8) [more info...]  
  
Chain information for AF-Q709C8-F13-model_v1.pdb.gz #3  
---  
Chain | Description  
A | vacuolar protein sorting-associated protein 13C  
  

> color bfactor #3 palette rainbow

10721 atoms, 1353 residues, atom bfactor range 28.1 to 94.7  

> hide #3 cartoons

> show #3 atoms

> style #3 sphere

Changed 10721 atom styles  

> align #3:196-200@CA toAtoms #2:1395-1399@CA

RMSD between 5 atom pairs is 1.442 angstroms  

> delete #3:1-200

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "bigalpha.py", line 64, in open_multifile_alphafold_model  
File "bigalpha.py", line 102, in shift_residue_numbers  
AttributeError: can't set attribute  
  
AttributeError: can't set attribute  
  
File "bigalpha.py", line 102, in shift_residue_numbers  
  
See log for complete Python traceback.  
  

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #4  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #4 palette rainbow

10797 atoms, 1400 residues, atom bfactor range 24.8 to 96.7  

> hide #4 cartoons

> show #4 atoms

> style #4 sphere

Changed 10797 atom styles  

> open AF-Q8WZ42-F7-model_v1.pdb.gz

AF-Q8WZ42-F7-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F7-model_v1.pdb.gz #5  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #5 palette rainbow

11244 atoms, 1400 residues, atom bfactor range 26.2 to 97  

> hide #5 cartoons

> show #5 atoms

> style #5 sphere

Changed 11244 atom styles  

> align #5:196-200@CA toAtoms #4:1395-1399@CA

RMSD between 5 atom pairs is 1.585 angstroms  

> delete #5:1-200

> open AF-Q8WZ42-F13-model_v1.pdb.gz

AF-Q8WZ42-F13-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F13-model_v1.pdb.gz #6  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #6 palette rainbow

11015 atoms, 1400 residues, atom bfactor range 24.5 to 96.6  

> hide #6 cartoons

> show #6 atoms

> style #6 sphere

Changed 11015 atom styles  

> align #6:196-200@CA toAtoms #5:1395-1399@CA

RMSD between 5 atom pairs is 1.103 angstroms  

> delete #6:1-200

> open AF-Q8WZ42-F19-model_v1.pdb.gz

AF-Q8WZ42-F19-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F19-model_v1.pdb.gz #7  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #7 palette rainbow

10832 atoms, 1400 residues, atom bfactor range 22.8 to 96.8  

> hide #7 cartoons

> show #7 atoms

> style #7 sphere

Changed 10832 atom styles  

> align #7:196-200@CA toAtoms #6:1395-1399@CA

RMSD between 5 atom pairs is 0.465 angstroms  

> delete #7:1-200

> open AF-Q8WZ42-F25-model_v1.pdb.gz

AF-Q8WZ42-F25-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F25-model_v1.pdb.gz #8  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #8 palette rainbow

10810 atoms, 1400 residues, atom bfactor range 56.9 to 95.8  

> hide #8 cartoons

> show #8 atoms

> style #8 sphere

Changed 10810 atom styles  

> align #8:196-200@CA toAtoms #7:1395-1399@CA

RMSD between 5 atom pairs is 2.331 angstroms  

> delete #8:1-200

> open AF-Q8WZ42-F31-model_v1.pdb.gz

AF-Q8WZ42-F31-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F31-model_v1.pdb.gz #9  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #9 palette rainbow

10775 atoms, 1400 residues, atom bfactor range 32.6 to 96.2  

> hide #9 cartoons

> show #9 atoms

> style #9 sphere

Changed 10775 atom styles  

> align #9:196-200@CA toAtoms #8:1395-1399@CA

RMSD between 5 atom pairs is 0.738 angstroms  

> delete #9:1-200

> open AF-Q8WZ42-F37-model_v1.pdb.gz

AF-Q8WZ42-F37-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F37-model_v1.pdb.gz #10  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #10 palette rainbow

10739 atoms, 1400 residues, atom bfactor range 27.3 to 94.7  

> hide #10 cartoons

> show #10 atoms

> style #10 sphere

Changed 10739 atom styles  

> align #10:196-200@CA toAtoms #9:1395-1399@CA

RMSD between 5 atom pairs is 2.736 angstroms  

> delete #10:1-200

> open AF-Q8WZ42-F43-model_v1.pdb.gz

AF-Q8WZ42-F43-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F43-model_v1.pdb.gz #11  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #11 palette rainbow

10878 atoms, 1400 residues, atom bfactor range 4.74 to 96  

> hide #11 cartoons

> show #11 atoms

> style #11 sphere

Changed 10878 atom styles  

> align #11:196-200@CA toAtoms #10:1395-1399@CA

RMSD between 5 atom pairs is 0.761 angstroms  

> delete #11:1-200

> open AF-Q8WZ42-F49-model_v1.pdb.gz

AF-Q8WZ42-F49-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F49-model_v1.pdb.gz #12  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #12 palette rainbow

11339 atoms, 1400 residues, atom bfactor range 22.2 to 98.3  

> hide #12 cartoons

> show #12 atoms

> style #12 sphere

Changed 11339 atom styles  

> align #12:196-200@CA toAtoms #11:1395-1399@CA

RMSD between 5 atom pairs is 2.022 angstroms  

> delete #12:1-200

> open AF-Q8WZ42-F55-model_v1.pdb.gz

AF-Q8WZ42-F55-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F55-model_v1.pdb.gz #13  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #13 palette rainbow

10995 atoms, 1400 residues, atom bfactor range 24.9 to 98  

> hide #13 cartoons

> show #13 atoms

> style #13 sphere

Changed 10995 atom styles  

> align #13:196-200@CA toAtoms #12:1395-1399@CA

RMSD between 5 atom pairs is 0.848 angstroms  

> delete #13:1-200

> open AF-Q8WZ42-F61-model_v1.pdb.gz

AF-Q8WZ42-F61-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F61-model_v1.pdb.gz #14  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #14 palette rainbow

11076 atoms, 1400 residues, atom bfactor range 28.9 to 96.7  

> hide #14 cartoons

> show #14 atoms

> style #14 sphere

Changed 11076 atom styles  

> align #14:196-200@CA toAtoms #13:1395-1399@CA

RMSD between 5 atom pairs is 0.281 angstroms  

> delete #14:1-200

> open AF-Q8WZ42-F67-model_v1.pdb.gz

AF-Q8WZ42-F67-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F67-model_v1.pdb.gz #15  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #15 palette rainbow

11108 atoms, 1400 residues, atom bfactor range 17.2 to 96.2  

> hide #15 cartoons

> show #15 atoms

> style #15 sphere

Changed 11108 atom styles  

> align #15:196-200@CA toAtoms #14:1395-1399@CA

RMSD between 5 atom pairs is 1.087 angstroms  

> delete #15:1-200

> open AF-Q8WZ42-F73-model_v1.pdb.gz

AF-Q8WZ42-F73-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F73-model_v1.pdb.gz #16  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #16 palette rainbow

10961 atoms, 1400 residues, atom bfactor range 32.8 to 96.4  

> hide #16 cartoons

> show #16 atoms

> style #16 sphere

Changed 10961 atom styles  

> align #16:196-200@CA toAtoms #15:1395-1399@CA

RMSD between 5 atom pairs is 0.928 angstroms  

> delete #16:1-200

> open AF-Q8WZ42-F79-model_v1.pdb.gz

AF-Q8WZ42-F79-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F79-model_v1.pdb.gz #17  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #17 palette rainbow

10939 atoms, 1400 residues, atom bfactor range 31.6 to 96.9  

> hide #17 cartoons

> show #17 atoms

> style #17 sphere

Changed 10939 atom styles  

> align #17:196-200@CA toAtoms #16:1395-1399@CA

RMSD between 5 atom pairs is 1.711 angstroms  

> delete #17:1-200

> open AF-Q8WZ42-F85-model_v1.pdb.gz

AF-Q8WZ42-F85-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F85-model_v1.pdb.gz #18  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #18 palette rainbow

10952 atoms, 1400 residues, atom bfactor range 33.1 to 97.6  

> hide #18 cartoons

> show #18 atoms

> style #18 sphere

Changed 10952 atom styles  

> align #18:196-200@CA toAtoms #17:1395-1399@CA

RMSD between 5 atom pairs is 0.641 angstroms  

> delete #18:1-200

> open AF-Q8WZ42-F91-model_v1.pdb.gz

AF-Q8WZ42-F91-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F91-model_v1.pdb.gz #19  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #19 palette rainbow

10966 atoms, 1400 residues, atom bfactor range 50.4 to 96  

> hide #19 cartoons

> show #19 atoms

> style #19 sphere

Changed 10966 atom styles  

> align #19:196-200@CA toAtoms #18:1395-1399@CA

RMSD between 5 atom pairs is 1.802 angstroms  

> delete #19:1-200

> open AF-Q8WZ42-F97-model_v1.pdb.gz

AF-Q8WZ42-F97-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F97-model_v1.pdb.gz #20  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #20 palette rainbow

10886 atoms, 1400 residues, atom bfactor range 54 to 97  

> hide #20 cartoons

> show #20 atoms

> style #20 sphere

Changed 10886 atom styles  

> align #20:196-200@CA toAtoms #19:1395-1399@CA

RMSD between 5 atom pairs is 0.542 angstroms  

> delete #20:1-200

> open AF-Q8WZ42-F103-model_v1.pdb.gz

AF-Q8WZ42-F103-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F103-model_v1.pdb.gz #21  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #21 palette rainbow

10883 atoms, 1400 residues, atom bfactor range 36.8 to 96.9  

> hide #21 cartoons

> show #21 atoms

> style #21 sphere

Changed 10883 atom styles  

> align #21:196-200@CA toAtoms #20:1395-1399@CA

RMSD between 5 atom pairs is 2.342 angstroms  

> delete #21:1-200

> open AF-Q8WZ42-F109-model_v1.pdb.gz

AF-Q8WZ42-F109-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F109-model_v1.pdb.gz #22  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #22 palette rainbow

10863 atoms, 1400 residues, atom bfactor range 15.6 to 96.8  

> hide #22 cartoons

> show #22 atoms

> style #22 sphere

Changed 10863 atom styles  

> align #22:196-200@CA toAtoms #21:1395-1399@CA

RMSD between 5 atom pairs is 0.968 angstroms  

> delete #22:1-200

> open AF-Q8WZ42-F115-model_v1.pdb.gz

AF-Q8WZ42-F115-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F115-model_v1.pdb.gz #23  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #23 palette rainbow

10882 atoms, 1400 residues, atom bfactor range 44.7 to 96.8  

> hide #23 cartoons

> show #23 atoms

> style #23 sphere

Changed 10882 atom styles  

> align #23:196-200@CA toAtoms #22:1395-1399@CA

RMSD between 5 atom pairs is 1.242 angstroms  

> delete #23:1-200

> open AF-Q8WZ42-F121-model_v1.pdb.gz

AF-Q8WZ42-F121-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F121-model_v1.pdb.gz #24  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #24 palette rainbow

10876 atoms, 1400 residues, atom bfactor range 37.7 to 97.7  

> hide #24 cartoons

> show #24 atoms

> style #24 sphere

Changed 10876 atom styles  

> align #24:196-200@CA toAtoms #23:1395-1399@CA

RMSD between 5 atom pairs is 0.480 angstroms  

> delete #24:1-200

> open AF-Q8WZ42-F127-model_v1.pdb.gz

AF-Q8WZ42-F127-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F127-model_v1.pdb.gz #25  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #25 palette rainbow

10848 atoms, 1400 residues, atom bfactor range 32.1 to 97.4  

> hide #25 cartoons

> show #25 atoms

> style #25 sphere

Changed 10848 atom styles  

> align #25:196-200@CA toAtoms #24:1395-1399@CA

RMSD between 5 atom pairs is 2.398 angstroms  

> delete #25:1-200

> open AF-Q8WZ42-F133-model_v1.pdb.gz

AF-Q8WZ42-F133-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F133-model_v1.pdb.gz #26  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #26 palette rainbow

10875 atoms, 1400 residues, atom bfactor range 33.1 to 96.7  

> hide #26 cartoons

> show #26 atoms

> style #26 sphere

Changed 10875 atom styles  

> align #26:196-200@CA toAtoms #25:1395-1399@CA

RMSD between 5 atom pairs is 1.181 angstroms  

> delete #26:1-200

> open AF-Q8WZ42-F139-model_v1.pdb.gz

AF-Q8WZ42-F139-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F139-model_v1.pdb.gz #27  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #27 palette rainbow

10875 atoms, 1400 residues, atom bfactor range 44.4 to 96.7  

> hide #27 cartoons

> show #27 atoms

> style #27 sphere

Changed 10875 atom styles  

> align #27:196-200@CA toAtoms #26:1395-1399@CA

RMSD between 5 atom pairs is 0.895 angstroms  

> delete #27:1-200

> open AF-Q8WZ42-F145-model_v1.pdb.gz

AF-Q8WZ42-F145-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F145-model_v1.pdb.gz #28  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #28 palette rainbow

10871 atoms, 1400 residues, atom bfactor range 41.8 to 96.4  

> hide #28 cartoons

> show #28 atoms

> style #28 sphere

Changed 10871 atom styles  

> align #28:196-200@CA toAtoms #27:1395-1399@CA

RMSD between 5 atom pairs is 0.459 angstroms  

> delete #28:1-200

> open AF-Q8WZ42-F151-model_v1.pdb.gz

AF-Q8WZ42-F151-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F151-model_v1.pdb.gz #29  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #29 palette rainbow

10955 atoms, 1400 residues, atom bfactor range 55 to 96.3  

> hide #29 cartoons

> show #29 atoms

> style #29 sphere

Changed 10955 atom styles  

> align #29:196-200@CA toAtoms #28:1395-1399@CA

RMSD between 5 atom pairs is 1.067 angstroms  

> delete #29:1-200

> open AF-Q8WZ42-F157-model_v1.pdb.gz

AF-Q8WZ42-F157-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F157-model_v1.pdb.gz #30  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #30 palette rainbow

11139 atoms, 1400 residues, atom bfactor range 28 to 98  

> hide #30 cartoons

> show #30 atoms

> style #30 sphere

Changed 11139 atom styles  

> align #30:196-200@CA toAtoms #29:1395-1399@CA

RMSD between 5 atom pairs is 1.180 angstroms  

> delete #30:1-200

> open AF-Q8WZ42-F163-model_v1.pdb.gz

AF-Q8WZ42-F163-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F163-model_v1.pdb.gz #31  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #31 palette rainbow

11317 atoms, 1400 residues, atom bfactor range 25.2 to 94.8  

> hide #31 cartoons

> show #31 atoms

> style #31 sphere

Changed 11317 atom styles  

> align #31:196-200@CA toAtoms #30:1395-1399@CA

RMSD between 5 atom pairs is 1.715 angstroms  

> delete #31:1-200

> open AF-Q8WZ42-F166-model_v1.pdb.gz

AF-Q8WZ42-F166-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F166-model_v1.pdb.gz #32  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #32 palette rainbow

10581 atoms, 1350 residues, atom bfactor range 25.4 to 96.8  

> hide #32 cartoons

> show #32 atoms

> style #32 sphere

Changed 10581 atom styles  

> align #32:796-800@CA toAtoms #31:1395-1399@CA

RMSD between 5 atom pairs is 0.716 angstroms  

> delete #32:1-800

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "bigalpha.py", line 64, in open_multifile_alphafold_model  
File "bigalpha.py", line 102, in shift_residue_numbers  
AttributeError: can't set attribute  
  
AttributeError: can't set attribute  
  
File "bigalpha.py", line 102, in shift_residue_numbers  
  
See log for complete Python traceback.  
  

> hide #1 models

> hide #2 models

> hide #3 models

> close

> open ../bigalpha.py

FYI: command is replacing existing command: "bigalpha"  
executed bigalpha.py  

> bigalpha Q8WZ42

AlphaFold Q8WZ42 is split into 166 mmCIF files  

> open AF-Q8WZ42-F1-model_v1.pdb.gz

AF-Q8WZ42-F1-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F1-model_v1.pdb.gz #1  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #1 palette redblue

10797 atoms, 1400 residues, atom bfactor range 24.8 to 96.7  

> hide #1 cartoons

> show #1 atoms

> style #1 sphere

Changed 10797 atom styles  

> open AF-Q8WZ42-F7-model_v1.pdb.gz

AF-Q8WZ42-F7-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F7-model_v1.pdb.gz #2  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #2 palette redblue

11244 atoms, 1400 residues, atom bfactor range 26.2 to 97  

> hide #2 cartoons

> show #2 atoms

> style #2 sphere

Changed 11244 atom styles  

> align #2:196-200@CA toAtoms #1:1395-1399@CA

RMSD between 5 atom pairs is 1.585 angstroms  

> delete #2:1-200

> open AF-Q8WZ42-F13-model_v1.pdb.gz

AF-Q8WZ42-F13-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F13-model_v1.pdb.gz #3  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #3 palette redblue

11015 atoms, 1400 residues, atom bfactor range 24.5 to 96.6  

> hide #3 cartoons

> show #3 atoms

> style #3 sphere

Changed 11015 atom styles  

> align #3:196-200@CA toAtoms #2:1395-1399@CA

RMSD between 5 atom pairs is 1.103 angstroms  

> delete #3:1-200

> open AF-Q8WZ42-F19-model_v1.pdb.gz

AF-Q8WZ42-F19-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F19-model_v1.pdb.gz #4  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #4 palette redblue

10832 atoms, 1400 residues, atom bfactor range 22.8 to 96.8  

> hide #4 cartoons

> show #4 atoms

> style #4 sphere

Changed 10832 atom styles  

> align #4:196-200@CA toAtoms #3:1395-1399@CA

RMSD between 5 atom pairs is 0.465 angstroms  

> delete #4:1-200

> open AF-Q8WZ42-F25-model_v1.pdb.gz

AF-Q8WZ42-F25-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F25-model_v1.pdb.gz #5  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #5 palette redblue

10810 atoms, 1400 residues, atom bfactor range 56.9 to 95.8  

> hide #5 cartoons

> show #5 atoms

> style #5 sphere

Changed 10810 atom styles  

> align #5:196-200@CA toAtoms #4:1395-1399@CA

RMSD between 5 atom pairs is 2.331 angstroms  

> delete #5:1-200

> open AF-Q8WZ42-F31-model_v1.pdb.gz

AF-Q8WZ42-F31-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F31-model_v1.pdb.gz #6  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #6 palette redblue

10775 atoms, 1400 residues, atom bfactor range 32.6 to 96.2  

> hide #6 cartoons

> show #6 atoms

> style #6 sphere

Changed 10775 atom styles  

> align #6:196-200@CA toAtoms #5:1395-1399@CA

RMSD between 5 atom pairs is 0.738 angstroms  

> delete #6:1-200

> open AF-Q8WZ42-F37-model_v1.pdb.gz

AF-Q8WZ42-F37-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F37-model_v1.pdb.gz #7  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #7 palette redblue

10739 atoms, 1400 residues, atom bfactor range 27.3 to 94.7  

> hide #7 cartoons

> show #7 atoms

> style #7 sphere

Changed 10739 atom styles  

> align #7:196-200@CA toAtoms #6:1395-1399@CA

RMSD between 5 atom pairs is 2.736 angstroms  

> delete #7:1-200

> open AF-Q8WZ42-F43-model_v1.pdb.gz

AF-Q8WZ42-F43-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F43-model_v1.pdb.gz #8  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #8 palette redblue

10878 atoms, 1400 residues, atom bfactor range 4.74 to 96  

> hide #8 cartoons

> show #8 atoms

> style #8 sphere

Changed 10878 atom styles  

> align #8:196-200@CA toAtoms #7:1395-1399@CA

RMSD between 5 atom pairs is 0.761 angstroms  

> delete #8:1-200

> open AF-Q8WZ42-F49-model_v1.pdb.gz

AF-Q8WZ42-F49-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F49-model_v1.pdb.gz #9  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #9 palette redblue

11339 atoms, 1400 residues, atom bfactor range 22.2 to 98.3  

> hide #9 cartoons

> show #9 atoms

> style #9 sphere

Changed 11339 atom styles  

> align #9:196-200@CA toAtoms #8:1395-1399@CA

RMSD between 5 atom pairs is 2.022 angstroms  

> delete #9:1-200

> open AF-Q8WZ42-F55-model_v1.pdb.gz

AF-Q8WZ42-F55-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F55-model_v1.pdb.gz #10  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #10 palette redblue

10995 atoms, 1400 residues, atom bfactor range 24.9 to 98  

> hide #10 cartoons

> show #10 atoms

> style #10 sphere

Changed 10995 atom styles  

> align #10:196-200@CA toAtoms #9:1395-1399@CA

RMSD between 5 atom pairs is 0.848 angstroms  

> delete #10:1-200

> open AF-Q8WZ42-F61-model_v1.pdb.gz

AF-Q8WZ42-F61-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F61-model_v1.pdb.gz #11  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #11 palette redblue

11076 atoms, 1400 residues, atom bfactor range 28.9 to 96.7  

> hide #11 cartoons

> show #11 atoms

> style #11 sphere

Changed 11076 atom styles  

> align #11:196-200@CA toAtoms #10:1395-1399@CA

RMSD between 5 atom pairs is 0.281 angstroms  

> delete #11:1-200

> open AF-Q8WZ42-F67-model_v1.pdb.gz

AF-Q8WZ42-F67-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F67-model_v1.pdb.gz #12  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #12 palette redblue

11108 atoms, 1400 residues, atom bfactor range 17.2 to 96.2  

> hide #12 cartoons

> show #12 atoms

> style #12 sphere

Changed 11108 atom styles  

> align #12:196-200@CA toAtoms #11:1395-1399@CA

RMSD between 5 atom pairs is 1.087 angstroms  

> delete #12:1-200

> open AF-Q8WZ42-F73-model_v1.pdb.gz

AF-Q8WZ42-F73-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F73-model_v1.pdb.gz #13  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #13 palette redblue

10961 atoms, 1400 residues, atom bfactor range 32.8 to 96.4  

> hide #13 cartoons

> show #13 atoms

> style #13 sphere

Changed 10961 atom styles  

> align #13:196-200@CA toAtoms #12:1395-1399@CA

RMSD between 5 atom pairs is 0.928 angstroms  

> delete #13:1-200

> open AF-Q8WZ42-F79-model_v1.pdb.gz

AF-Q8WZ42-F79-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F79-model_v1.pdb.gz #14  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #14 palette redblue

10939 atoms, 1400 residues, atom bfactor range 31.6 to 96.9  

> hide #14 cartoons

> show #14 atoms

> style #14 sphere

Changed 10939 atom styles  

> align #14:196-200@CA toAtoms #13:1395-1399@CA

RMSD between 5 atom pairs is 1.711 angstroms  

> delete #14:1-200

> open AF-Q8WZ42-F85-model_v1.pdb.gz

AF-Q8WZ42-F85-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F85-model_v1.pdb.gz #15  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #15 palette redblue

10952 atoms, 1400 residues, atom bfactor range 33.1 to 97.6  

> hide #15 cartoons

> show #15 atoms

> style #15 sphere

Changed 10952 atom styles  

> align #15:196-200@CA toAtoms #14:1395-1399@CA

RMSD between 5 atom pairs is 0.641 angstroms  

> delete #15:1-200

> open AF-Q8WZ42-F91-model_v1.pdb.gz

AF-Q8WZ42-F91-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F91-model_v1.pdb.gz #16  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #16 palette redblue

10966 atoms, 1400 residues, atom bfactor range 50.4 to 96  

> hide #16 cartoons

> show #16 atoms

> style #16 sphere

Changed 10966 atom styles  

> align #16:196-200@CA toAtoms #15:1395-1399@CA

RMSD between 5 atom pairs is 1.802 angstroms  

> delete #16:1-200

> open AF-Q8WZ42-F97-model_v1.pdb.gz

AF-Q8WZ42-F97-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F97-model_v1.pdb.gz #17  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #17 palette redblue

10886 atoms, 1400 residues, atom bfactor range 54 to 97  

> hide #17 cartoons

> show #17 atoms

> style #17 sphere

Changed 10886 atom styles  

> align #17:196-200@CA toAtoms #16:1395-1399@CA

RMSD between 5 atom pairs is 0.542 angstroms  

> delete #17:1-200

> open AF-Q8WZ42-F103-model_v1.pdb.gz

AF-Q8WZ42-F103-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F103-model_v1.pdb.gz #18  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #18 palette redblue

10883 atoms, 1400 residues, atom bfactor range 36.8 to 96.9  

> hide #18 cartoons

> show #18 atoms

> style #18 sphere

Changed 10883 atom styles  

> align #18:196-200@CA toAtoms #17:1395-1399@CA

RMSD between 5 atom pairs is 2.342 angstroms  

> delete #18:1-200

> open AF-Q8WZ42-F109-model_v1.pdb.gz

AF-Q8WZ42-F109-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F109-model_v1.pdb.gz #19  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #19 palette redblue

10863 atoms, 1400 residues, atom bfactor range 15.6 to 96.8  

> hide #19 cartoons

> show #19 atoms

> style #19 sphere

Changed 10863 atom styles  

> align #19:196-200@CA toAtoms #18:1395-1399@CA

RMSD between 5 atom pairs is 0.968 angstroms  

> delete #19:1-200

> open AF-Q8WZ42-F115-model_v1.pdb.gz

AF-Q8WZ42-F115-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F115-model_v1.pdb.gz #20  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #20 palette redblue

10882 atoms, 1400 residues, atom bfactor range 44.7 to 96.8  

> hide #20 cartoons

> show #20 atoms

> style #20 sphere

Changed 10882 atom styles  

> align #20:196-200@CA toAtoms #19:1395-1399@CA

RMSD between 5 atom pairs is 1.242 angstroms  

> delete #20:1-200

> open AF-Q8WZ42-F121-model_v1.pdb.gz

AF-Q8WZ42-F121-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F121-model_v1.pdb.gz #21  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #21 palette redblue

10876 atoms, 1400 residues, atom bfactor range 37.7 to 97.7  

> hide #21 cartoons

> show #21 atoms

> style #21 sphere

Changed 10876 atom styles  

> align #21:196-200@CA toAtoms #20:1395-1399@CA

RMSD between 5 atom pairs is 0.480 angstroms  

> delete #21:1-200

> open AF-Q8WZ42-F127-model_v1.pdb.gz

AF-Q8WZ42-F127-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F127-model_v1.pdb.gz #22  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #22 palette redblue

10848 atoms, 1400 residues, atom bfactor range 32.1 to 97.4  

> hide #22 cartoons

> show #22 atoms

> style #22 sphere

Changed 10848 atom styles  

> align #22:196-200@CA toAtoms #21:1395-1399@CA

RMSD between 5 atom pairs is 2.398 angstroms  

> delete #22:1-200

> open AF-Q8WZ42-F133-model_v1.pdb.gz

AF-Q8WZ42-F133-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F133-model_v1.pdb.gz #23  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #23 palette redblue

10875 atoms, 1400 residues, atom bfactor range 33.1 to 96.7  

> hide #23 cartoons

> show #23 atoms

> style #23 sphere

Changed 10875 atom styles  

> align #23:196-200@CA toAtoms #22:1395-1399@CA

RMSD between 5 atom pairs is 1.181 angstroms  

> delete #23:1-200

> open AF-Q8WZ42-F139-model_v1.pdb.gz

AF-Q8WZ42-F139-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F139-model_v1.pdb.gz #24  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #24 palette redblue

10875 atoms, 1400 residues, atom bfactor range 44.4 to 96.7  

> hide #24 cartoons

> show #24 atoms

> style #24 sphere

Changed 10875 atom styles  

> align #24:196-200@CA toAtoms #23:1395-1399@CA

RMSD between 5 atom pairs is 0.895 angstroms  

> delete #24:1-200

> open AF-Q8WZ42-F145-model_v1.pdb.gz

AF-Q8WZ42-F145-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F145-model_v1.pdb.gz #25  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #25 palette redblue

10871 atoms, 1400 residues, atom bfactor range 41.8 to 96.4  

> hide #25 cartoons

> show #25 atoms

> style #25 sphere

Changed 10871 atom styles  

> align #25:196-200@CA toAtoms #24:1395-1399@CA

RMSD between 5 atom pairs is 0.459 angstroms  

> delete #25:1-200

> open AF-Q8WZ42-F151-model_v1.pdb.gz

AF-Q8WZ42-F151-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F151-model_v1.pdb.gz #26  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #26 palette redblue

10955 atoms, 1400 residues, atom bfactor range 55 to 96.3  

> hide #26 cartoons

> show #26 atoms

> style #26 sphere

Changed 10955 atom styles  

> align #26:196-200@CA toAtoms #25:1395-1399@CA

RMSD between 5 atom pairs is 1.067 angstroms  

> delete #26:1-200

> open AF-Q8WZ42-F157-model_v1.pdb.gz

AF-Q8WZ42-F157-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F157-model_v1.pdb.gz #27  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #27 palette redblue

11139 atoms, 1400 residues, atom bfactor range 28 to 98  

> hide #27 cartoons

> show #27 atoms

> style #27 sphere

Changed 11139 atom styles  

> align #27:196-200@CA toAtoms #26:1395-1399@CA

RMSD between 5 atom pairs is 1.180 angstroms  

> delete #27:1-200

> open AF-Q8WZ42-F163-model_v1.pdb.gz

AF-Q8WZ42-F163-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F163-model_v1.pdb.gz #28  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #28 palette redblue

11317 atoms, 1400 residues, atom bfactor range 25.2 to 94.8  

> hide #28 cartoons

> show #28 atoms

> style #28 sphere

Changed 11317 atom styles  

> align #28:196-200@CA toAtoms #27:1395-1399@CA

RMSD between 5 atom pairs is 1.715 angstroms  

> delete #28:1-200

> open AF-Q8WZ42-F166-model_v1.pdb.gz

AF-Q8WZ42-F166-model_v1.pdb.gz title:  
Alphafold V2.0 prediction for titin (Q8WZ42) [more info...]  
  
Chain information for AF-Q8WZ42-F166-model_v1.pdb.gz #29  
---  
Chain | Description  
A | TITIN  
  

> color bfactor #29 palette redblue

10581 atoms, 1350 residues, atom bfactor range 25.4 to 96.8  

> hide #29 cartoons

> show #29 atoms

> style #29 sphere

Changed 10581 atom styles  

> align #29:796-800@CA toAtoms #28:1395-1399@CA

RMSD between 5 atom pairs is 0.716 angstroms  

> delete #29:1-800

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "../bigalpha.py", line 64, in open_multifile_alphafold_model  
shift_residue_numbers(models)  
File "../bigalpha.py", line 102, in shift_residue_numbers  
m.residues.numbers += rnext - rmin  
AttributeError: can't set attribute  
  
AttributeError: can't set attribute  
  
File "../bigalpha.py", line 102, in shift_residue_numbers  
m.residues.numbers += rnext - rmin  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.0.7
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 11.2.3 (20D91)
      Kernel Version: Darwin 20.3.0
      Time since boot: 14 days 16:38

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Cc: Eric Pettersen added
Component: Unassigned → Sequence
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → big_alpha.py: can't set residues.numbers

comment:2 by Eric Pettersen, 4 years ago

Resolution: → not a bug
Status: assigned → closed
Summary: big_alpha.py: can't set residues.numbers → bigalpha.py: can't set residues.numbers

Hi Shujun,

The bigalpha.py script uses features that are only available in the ChimeraX daily build. so you will have to use that in order to successfully run the script.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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