The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Menu Presets / Initial Styles / Original Look does not reset tube helices to normal ribbon helices.
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/goddard/ucsf/presentations/macromethods-jan2025/hsp90.cxs format
> session
Log from Fri Jan 3 16:58:58 2025UCSF ChimeraX version: 1.9.dev202411121724
(2024-11-12)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6x18
Summary of feedback from opening 6x18 fetched from pdb
---
note | Fetching compressed mmCIF 6x18 from http://files.rcsb.org/download/6x18.cif
6x18 title:
GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor [more
info...]
Chain information for 6x18 #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-394
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 5-62
N | Nanobody35 |
P | Glucagon | GLUC_HUMAN 7-36
R | Glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 10283 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> show surfaces
> lighting soft
> mlp
Map values for surface "6x18_A SES surface": minimum -29.68, mean -4.803,
maximum 24.45
Map values for surface "6x18_B SES surface": minimum -29.2, mean -5.737,
maximum 22.53
Map values for surface "6x18_G SES surface": minimum -24.48, mean -3.157,
maximum 23.07
Map values for surface "6x18_N SES surface": minimum -28.03, mean -7.085,
maximum 21.59
Map values for surface "6x18_P SES surface": minimum -24.59, mean -2.871,
maximum 22.26
Map values for surface "6x18_R SES surface": minimum -25.87, mean -0.3583,
maximum 24.51
To also show corresponding color key, enter the above mlp command and add key
true
> color bypolymer
> hide surfaces
> select /P:22
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
208 atoms, 212 bonds, 27 residues, 2 models selected
> select up
233 atoms, 238 bonds, 30 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> color sel byhetero
> hbonds sel reveal true
51 hydrogen bonds found
> mlp sel
Map values for surface "6x18_P SES surface": minimum -24.59, mean -2.871,
maximum 22.26
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select /R:210
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
86 atoms, 88 bonds, 11 residues, 2 models selected
> select up
1675 atoms, 1728 bonds, 203 residues, 2 models selected
> select up
1689 atoms, 1741 bonds, 205 residues, 2 models selected
> select up
2471 atoms, 2557 bonds, 304 residues, 2 models selected
> select up
3158 atoms, 3239 bonds, 404 residues, 2 models selected
> mlp sel
Map values for surface "6x18_R SES surface": minimum -25.87, mean -0.3583,
maximum 24.51
To also show corresponding color key, enter the above mlp command and add key
true
> select /P:7-36
233 atoms, 238 bonds, 28 pseudobonds, 30 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select /R:29-423
3138 atoms, 3239 bonds, 2 pseudobonds, 384 residues, 2 models selected
> hide sel surfaces
> select clear
> hide surfaces
> usage mlp
mlp [atoms] [spacing a number] [maxDistance a number] [method method] [nexp a
number] [color true or false] [palette a colormap] [range range] [transparency
a number] [surfaces a surfaces specifier] [map true or false] [key true or
false]
— display molecular lipophilic potential for selected models
method: one of brasseur, buckingham, dubost, fauchere, or type5
range: 2-tuple of numbers or full
> usage color
color [objects] [color [what]] [target characters from 'abcfmprs']
[transparency a number] [halfbond true or false]
— color objects
objects: an objects specifier or nothing
color: a color or one of byatom, bychain, byelement, byhetero, byidentity,
bymodel, bynucleotide, bypolymer, fromatoms, fromcartoons, fromribbons, or
random
what: a collection of one of All, atoms, bonds, cartoons, labels, models,
pseudobonds, ribbons, rings, or surfaces
Subcommands are:
* color bfactor
* color byattribute
* color cylindrical
* color delete
* color electrostatic
* color gradient
* color height
* color image
* color list
* color modify
* color name
* color radial
* color sample
* color sequential
* color show
* color single
* color zone
> mlp #1 map true
Opened mlp 6x18_A as #2, grid size 99,102,90, pixel 1, shown at step 1, values
float32
Map values for surface "6x18_A SES surface": minimum -29.68, mean -4.803,
maximum 24.45
Opened mlp 6x18_B as #3, grid size 77,84,75, pixel 1, shown at step 1, values
float32
Map values for surface "6x18_B SES surface": minimum -29.2, mean -5.737,
maximum 22.53
Opened mlp 6x18_G as #4, grid size 54,79,70, pixel 1, shown at step 1, values
float32
Map values for surface "6x18_G SES surface": minimum -24.48, mean -3.157,
maximum 23.07
Opened mlp 6x18_N as #5, grid size 55,63,58, pixel 1, shown at step 1, values
float32
Map values for surface "6x18_N SES surface": minimum -28.03, mean -7.085,
maximum 21.59
Opened mlp 6x18_P as #6, grid size 38,61,49, pixel 1, shown at step 1, values
float32
Map values for surface "6x18_P SES surface": minimum -24.59, mean -2.871,
maximum 22.26
Opened mlp 6x18_R as #7, grid size 66,131,75, pixel 1, shown at step 1, values
float32
Map values for surface "6x18_R SES surface": minimum -25.87, mean -0.3583,
maximum 24.51
> hide #!2-7 target m
> hide surfaces
> show #!2-7 target m
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select clear
> select /P:34@N
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
208 atoms, 212 bonds, 27 residues, 2 models selected
> select up
233 atoms, 238 bonds, 30 residues, 2 models selected
> show sel cartoons
> select clear
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /P:34
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
208 atoms, 212 bonds, 27 residues, 2 models selected
> select up
233 atoms, 238 bonds, 30 residues, 2 models selected
> show sel atoms
> ~hbonds
> select sel :< 5
746 atoms, 726 bonds, 92 residues, 1 model selected
> show sel atoms
> select clear
> color :ALA,VAL,LEU,ILE,PRO,PHE,CYS orange
> color bypolymer
> color :ALA,VAL,LEU,ILE,PRO,PHE,CYS & (/P :< 5) orange
> show #!5 models
> hide #!5 models
> color /P yellow
> color :ALA,VAL,LEU,ILE,PRO,PHE,CYS & (/P :< 5) orange
> close
> open 1ah8
1ah8 title:
Structure of the orthorhombic form of the N-terminal domain of the yeast HSP90
chaperone [more info...]
Chain information for 1ah8 #1
---
Chain | Description | UniProt
A B | HEAT SHOCK PROTEIN 90 | HSP82_YEAST 1-220
Non-standard residues in 1ah8 #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
> ui tool show "Unit Cell"
> unitcell #1
> unitcell delete #1
> color bychain
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select :GOL
24 atoms, 20 bonds, 4 residues, 1 model selected
> hbonds sel reveal true
30 hydrogen bonds found
> select clear
> show surfaces
> lighting soft
> ui tool show "Crystal Contacts"
> unitcell #1
> open 8jr6
8jr6 title:
Hsp90a N-terminal domain [more info...]
Chain information for 8jr6
---
Chain | Description | UniProt
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A | Heat shock protein HSP 90-alpha | HS90A_HUMAN 1-237
> crystalcontacts delete #1
[Repeated 1 time(s)]
> close #2
> hide surfaces
> mmaker #2 to #1/A
No molecules/chains to match specified
> mmaker #3 to #1/A
Computing secondary structure
[Repeated 10 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.1), sequence alignment
score = 739
RMSD between 79 pruned atom pairs is 1.243 angstroms; (across all 214 pairs:
3.679)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.2), sequence alignment
score = 737.8
RMSD between 108 pruned atom pairs is 1.297 angstroms; (across all 214 pairs:
3.651)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.3), sequence alignment
score = 706
RMSD between 92 pruned atom pairs is 1.152 angstroms; (across all 214 pairs:
4.390)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.4), sequence alignment
score = 734.8
RMSD between 89 pruned atom pairs is 1.181 angstroms; (across all 214 pairs:
4.043)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.5), sequence alignment
score = 750.4
RMSD between 88 pruned atom pairs is 1.201 angstroms; (across all 214 pairs:
4.531)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.6), sequence alignment
score = 749.2
RMSD between 108 pruned atom pairs is 1.249 angstroms; (across all 214 pairs:
4.284)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.7), sequence alignment
score = 707.8
RMSD between 69 pruned atom pairs is 1.175 angstroms; (across all 214 pairs:
4.062)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.8), sequence alignment
score = 747.4
RMSD between 92 pruned atom pairs is 1.371 angstroms; (across all 214 pairs:
3.816)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.9), sequence alignment
score = 740.2
RMSD between 106 pruned atom pairs is 1.316 angstroms; (across all 214 pairs:
3.511)
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.10), sequence alignment
score = 744.4
RMSD between 110 pruned atom pairs is 1.192 angstroms; (across all 214 pairs:
3.981)
> mmaker #3.1 to #1/A show true
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ah8, chain A (#1) with 8jr6, chain A (#3.1), sequence alignment
score = 739
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 1ah8 #1/A, 8jr6 #3.1/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 79 pruned atom pairs is 1.243 angstroms; (across all 214 pairs:
3.679)
> open 2fwz
Summary of feedback from opening 2fwz fetched from pdb
---
notes | Fetching compressed mmCIF 2fwz from http://files.rcsb.org/download/2fwz.cif
Fetching CCD H71 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/H71/H71.cif
2fwz title:
Structure of human Hsp90-alpha bound to the potent water soluble inhibitor
PU-H71 [more info...]
Chain information for 2fwz #2
---
Chain | Description
A | Heat shock protein HSP 90-alpha
Non-standard residues in 2fwz #2
---
H71 —
8-[(6-iodo-1,3-benzodioxol-5-yl)thio]-9-[3-(isopropylamino)propyl]-9H-purin-6-amine
110 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #2 to #1/A
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ah8, chain A (#1) with 2fwz, chain A (#2), sequence alignment
score = 812.2
RMSD between 187 pruned atom pairs is 0.802 angstroms; (across all 208 pairs:
1.241)
> hide #!3 models
> open /Users/goddard/Downloads/Hsp90_NTD_PU-H71_attr.defattr
No such file/path: /Users/goddard/Downloads/Hsp90_NTD_PU-H71_attr.defattr
> open /Users/goddard/Downloads/Hsp90_NTD_PU-H71_attr.defattr
Summary of feedback from opening
/Users/goddard/Downloads/Hsp90_NTD_PU-H71_attr.defattr
---
note | Assigned attribute 'csp' to 2456 residues using match mode: any
> ui tool show "Render/Select by Attribute"
> color byattribute r:csp #!1 target absc palette
> 0,blue:0.0582462,white:0.113116,red
3986 atoms, 967 residues, 2 surfaces, atom csp range 0 to 0.64
> hide #2 models
> show #2 models
> select add #2
1981 atoms, 1688 bonds, 531 residues, 1 model selected
> hide sel cartoons
> select clear
> hide
> show :H71
> color byattribute r:csp #!1 target absc palette
> 0.000844148,white:0.113116,red
3986 atoms, 967 residues, 2 surfaces, atom csp range 0 to 0.64
> color byattribute r:csp #!1 target absc palette
> 0.000844148,white:0.141817,red
3986 atoms, 967 residues, 2 surfaces, atom csp range 0 to 0.64
> color byattribute r:csp #!1 target absc palette
> 0.000844148,white:0.141817,red
3986 atoms, 967 residues, 2 surfaces, atom csp range 0 to 0.64
> color byattribute r:csp #!1 target absc palette
> 0.000844148,white:0.420386,red
3986 atoms, 967 residues, 2 surfaces, atom csp range 0 to 0.64
> color byattribute r:csp #!1 target absc palette
> 0.000844148,white:0.141817,red
3986 atoms, 967 residues, 2 surfaces, atom csp range 0 to 0.64
> hide #1/B ribbons
> show #2#!1 surfaces
> close #1.3
> hide #!2 models
> show #!2 models
> close #2.1
> color #1 tan
> color byattribute r:csp #!1 target absc palette
> 0.000844148,white:0.141817,red
3986 atoms, 967 residues, 1 surfaces, atom csp range 0 to 0.64
> hide #2#!1 surfaces
> show #2#!1 surfaces
> close #1.3
> close #2.1
> hide #1.2 models
> show #2 ribbons
> select #2/A:1001@C1'
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> select sel :< 4
2133 atoms, 2033 bonds, 11 pseudobonds, 183 residues, 13 models selected
> show sel & #2#!1 atoms
> hide solvent
> select #1/A:221@O3
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel
> show #!3 models
> save /Users/goddard/ucsf/presentations/macromethods-jan2025/hsp90.cxs
——— End of log from Fri Jan 3 16:58:58 2025 ———
opened ChimeraX session
> close
> open 1ah8
1ah8 title:
Structure of the orthorhombic form of the N-terminal domain of the yeast HSP90
chaperone [more info...]
Chain information for 1ah8 #1
---
Chain | Description | UniProt
A B | HEAT SHOCK PROTEIN 90 | HSP82_YEAST 1-220
Non-standard residues in 1ah8 #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
Associated 1ah8 chain A to 1ah8, chain A with 0 mismatches
Associated 1ah8 chain B to 1ah8, chain A with 0 mismatches
> open 4z1f format mmcif fromDatabase pdb
4z1f title:
Crystal structure of human Trap1 with PU-H71 [more info...]
Chain information for 4z1f #2
---
Chain | Description | UniProt
A | Heat shock protein 75 kDa, mitochondrial | TRAP1_HUMAN 60-561
Non-standard residues in 4z1f #2
---
H71 —
8-[(6-iodo-1,3-benzodioxol-5-yl)thio]-9-[3-(isopropylamino)propyl]-9H-purin-6-amine
> mmaker #1 to #2
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4z1f, chain A (#2) with 1ah8, chain B (#1), sequence alignment
score = 523.2
RMSD between 138 pruned atom pairs is 0.944 angstroms; (across all 180 pairs:
6.324)
> mmaker #1 to #2 show true
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4z1f, chain A (#2) with 1ah8, chain B (#1), sequence alignment
score = 523.2
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 1ah8 #1/B, 4z1f #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 138 pruned atom pairs is 0.944 angstroms; (across all 180 pairs:
6.324)
> close
> open 2fwz format mmcif fromDatabase pdb
2fwz title:
Structure of human Hsp90-alpha bound to the potent water soluble inhibitor
PU-H71 [more info...]
Chain information for 2fwz #1
---
Chain | Description
A | Heat shock protein HSP 90-alpha
Non-standard residues in 2fwz #1
---
H71 —
8-[(6-iodo-1,3-benzodioxol-5-yl)thio]-9-[3-(isopropylamino)propyl]-9H-purin-6-amine
110 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 64 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 138 days, 5 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
alphashape: 1.3.1
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.23.0
ChimeraX-clix: 0.1.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepSSETracer: 1.1
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-maskChains: 1.1
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NIHPresets: 1.1.19
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-TetraScape: 0.2
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
click: 8.1.7
click-log: 0.4.0
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
fsspec: 2024.3.1
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib-metadata: 4.0.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
joblib: 1.4.2
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
llvmlite: 0.42.0
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.59.1
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
pooch: 1.8.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynndescent: 0.5.12
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyvista: 0.44.1
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
Rtree: 1.3.0
scikit-learn: 1.4.2
scipy: 1.14.0
scooby: 0.10.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
shapely: 2.0.6
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
sympy: 1.12
tables: 3.10.1
tcia_utils: 1.5.1
threadpoolctl: 3.5.0
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
torch: 2.1.2
tornado: 6.4.2
tqdm: 4.66.4
traitlets: 5.14.3
trimesh: 4.4.7
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
umap-learn: 0.5.6
urllib3: 2.2.3
vtk: 9.3.1
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
zipp: 3.19.2
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Okay, "fixed". "Fixed" is in quotes because although the tube helices are now undone, the structure still doesn't look 100% like it did initially, because as far as I can tell there is no simple way to reset the XSectionManager (structure.ribbon_xs_mgr) back to its default values.
Fix: https://github.com/RBVI/ChimeraX/commit/e3c2f1d8e35629ed8cddee3ac2007a88708abff3