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Opened 21 months ago
Closed 21 months ago
#14490 closed defect (duplicate)
MatchMaker: 'NoneType' object has no attribute 'setChecked'
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.5.0-14-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J710_006_volume_map_sharp.mrc
Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.48, shown at level 0.0524, step 1, values float32
> open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v4.pdb
Chain information for fullmodel-v4.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
R | No description available
> volume #1 level 0.204
> show cartoons
> hide atoms
> volume #1 level 0.1434
> transparency 50
> surface dust #1 size 14.8
> select #2/R
1432 atoms, 1452 bonds, 92 residues, 1 model selected
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for fullmodel-v4.pdb
---
Chain | Description
2.2/A | No description available
2.2/B | No description available
2.2/C | No description available
2.2/D | No description available
2.2/E | No description available
2.2/R | No description available
> select clear
> clipper associate #1 toModel #2
Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #2.1.1.1, grid size
256,256,256, pixel 1.48, shown at step 1, values float32
> volume #2.1.1.1 level 0.0992
> select #2/R
1432 atoms, 1452 bonds, 92 residues, 1 model selected
> select clear
> select #2/R:38-108
1106 atoms, 1122 bonds, 71 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> hide #!2.1 models
> show #!2.1 models
> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J710_006_volume_map_sharp.mrc
Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.48, shown at level 0.0524, step 1, values float32
> volume #1 level 0.1585
> save /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb
> open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v4.pdb
Chain information for fullmodel-v4.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
R | No description available
> open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb
Chain information for fullmodel-v5.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
R | No description available
> hide #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #2.3 models
> hide #3-4 atoms
> show #3-4 cartoons
> transparency #1.1 50
> hide #3 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #4 models
> show #4 models
> open 5t35
5t35 title:
The PROTAC MZ1 in complex with the second bromodomain of Brd4 and
pVHL:ElonginC:ElonginB [more info...]
Chain information for 5t35 #5
---
Chain | Description | UniProt
A E | Bromodomain-containing protein 4 | BRD4_HUMAN
B F | Transcription elongation factor B polypeptide 2 | ELOB_HUMAN
C G | Transcription elongation factor B polypeptide 1 | ELOC_HUMAN
D H | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN
Non-standard residues in 5t35 #5
---
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide
5t35 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select #5/E
910 atoms, 918 bonds, 126 residues, 1 model selected
> delete sel
> select #5/G
693 atoms, 703 bonds, 1 pseudobond, 92 residues, 2 models selected
> delete sel
> select #5/F
811 atoms, 826 bonds, 105 residues, 1 model selected
> delete sel
> select #5/H
1265 atoms, 1294 bonds, 156 residues, 1 model selected
> delete sel
> ui tool show Matchmaker
> matchmaker #!5 to #4
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 fullmodel-v5.pdb, chain B (#4) with 5t35, chain D (#5), sequence
alignment score = 792.2
RMSD between 149 pruned atom pairs is 0.891 angstroms; (across all 149 pairs:
0.891)
> matchmaker #!5 to #4
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 fullmodel-v5.pdb, chain B (#4) with 5t35, chain D (#5), sequence
alignment score = 792.2
RMSD between 149 pruned atom pairs is 0.891 angstroms; (across all 149 pairs:
0.891)
> hide #4#!5 atoms
> select ::name="759"
69 atoms, 75 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select clear
> select #4/A
1835 atoms, 1858 bonds, 114 residues, 1 model selected
> color sel #5b42cdff
> select #4/B
2615 atoms, 2648 bonds, 160 residues, 1 model selected
> color sel #bfbfbfff
> color sel #fafafaff
[Repeated 1 time(s)]
> color sel forest green
> select #4/C
1647 atoms, 1663 bonds, 104 residues, 1 model selected
> color sel #bdbf40ff
> color sel #bdbf3aff
> color sel #ccce3fff
[Repeated 3 time(s)]
> select #4/D
1522 atoms, 1539 bonds, 97 residues, 1 model selected
> color sel #54bf40ff
> color sel #9abf93ff
> color sel #b0daa8ff
[Repeated 3 time(s)]
> select #4/E
10756 atoms, 10867 bonds, 658 residues, 1 model selected
> color sel #40a8bfff
> color sel #4daabfff
> color sel #4293a5ff
[Repeated 3 time(s)]
> select #4/R
1432 atoms, 1452 bonds, 92 residues, 1 model selected
> color sel #5ebf40ff
> color sel #5abf3aff
> color sel #60cb3eff
[Repeated 3 time(s)]
> select clear
> set bgColor white
> set bgColor #ffffff00
> lighting soft
> show #!1 models
> hide #!1 models
> save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
> height 803 supersample 3 transparentBackground true
> graphics silhouettes true
> save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
> height 803 supersample 3
> save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
> height 803 supersample 3 transparentBackground true
> open 5n4w
5n4w title:
Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex [more
info...]
Chain information for 5n4w #6
---
Chain | Description | UniProt
A | Cullin-2 | CUL2_HUMAN
B | Elongin-B | ELOB_HUMAN
C | Elongin-C | ELOC_HUMAN
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN
V | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN
Non-standard residues in 5n4w #6
---
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #!6 to #4
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 fullmodel-v5.pdb, chain E (#4) with 5n4w, chain A (#6), sequence
alignment score = 3288.4
RMSD between 377 pruned atom pairs is 1.063 angstroms; (across all 587 pairs:
3.224)
> matchmaker #!6 to #4
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 fullmodel-v5.pdb, chain E (#4) with 5n4w, chain A (#6), sequence
alignment score = 3288.4
RMSD between 377 pruned atom pairs is 1.063 angstroms; (across all 587 pairs:
3.224)
> select add #6
7719 atoms, 7841 bonds, 29 pseudobonds, 970 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #!6 models
> show #3 models
> hide #3 models
> show #3 models
> close #3
> close #2
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_28__npn-
> crosslinked-structure__final.cxs includeMaps true
> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map.mrc
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map_sharp.mrc
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J647_006_volume_map_sharp.mrc
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J659_007_volume_map.mrc
Opened cryosparc_P9_J635_008_volume_map.mrc as #2.1, grid size 480,480,480,
pixel 0.825, shown at level 0.00758, step 2, values float32
Opened cryosparc_P9_J635_008_volume_map_sharp.mrc as #2.2, grid size
480,480,480, pixel 0.825, shown at level 0.0194, step 2, values float32
Opened cryosparc_P9_J647_006_volume_map_sharp.mrc as #2.3, grid size
480,480,480, pixel 0.825, shown at level 0.0203, step 2, values float32
Opened cryosparc_P9_J659_007_volume_map.mrc as #2.4, grid size 480,480,480,
pixel 0.825, shown at level 0.00707, step 2, values float32
> volume #2.4 level 0.04195
> volume #2.3 level 0.07573
> volume #2.2 level 0.06618
> volume #2.1 level 0.03781
> surface dust #2.1 size 8.25
> surface dust #2.2 size 8.25
> surface dust #2.3 size 8.25
> surface dust #2.4 size 8.25
> volume flip #2.2
Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #3, grid size
480,480,480, pixel 0.825, shown at step 1, values float32
> close #2.2
> select add #2.3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2.3,0.98461,-0.13581,0.11,9.4722,-0.13019,-0.98986,-0.056778,424.6,0.1166,0.041583,-0.99231,332.63
> volume flip #2.3
Opened cryosparc_P9_J647_006_volume_map_sharp.mrc z flip as #7, grid size
480,480,480, pixel 0.825, shown at step 1, values float32
> close #2.3
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.94093,0.053579,0.33434,-66.51,-0.17685,0.91978,0.35032,-21.349,-0.28875,-0.38875,0.87493,94.987
> view matrix models
> #7,0.9958,-0.06531,0.064213,3.5056,-0.016537,-0.81777,-0.5753,480.25,0.090084,0.57182,-0.81542,197.79
> view matrix models
> #7,-0.94582,-0.18918,-0.2639,470.69,0.14941,-0.97515,0.16355,320.99,-0.28828,0.11526,0.95058,-18.388
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.94582,-0.18918,-0.2639,476.46,0.14941,-0.97515,0.16355,320.85,-0.28828,0.11526,0.95058,43.172
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.94582,-0.18918,-0.2639,476.75,0.14941,-0.97515,0.16355,319.58,-0.28828,0.11526,0.95058,47.965
> fitmap #3 inMap #1
Fit map cryosparc_P9_J635_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J710_006_volume_map_sharp.mrc using 260097 points
correlation = 0.7239, correlation about mean = 0.415, overlap = 7246
steps = 108, shift = 10.4, angle = 7.23 degrees
Position of cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#3) relative to
cryosparc_P7_J710_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99741254 0.03385855 0.06341789 -25.04544197
-0.04024254 0.99394367 0.10225709 -19.05719275
-0.05957154 -0.10454460 0.99273444 35.75883607
Axis -0.82141607 0.48851388 -0.29432945
Axis point 0.00000000 329.56848775 209.41103196
Rotation angle (degrees) 7.23164693
Shift along axis 0.73814676
> fitmap #7 inMap #1
Fit map cryosparc_P9_J647_006_volume_map_sharp.mrc z flip in map
cryosparc_P7_J710_006_volume_map_sharp.mrc using 215940 points
correlation = 0.7306, correlation about mean = 0.3854, overlap = 6936
steps = 208, shift = 9.46, angle = 21.8 degrees
Position of cryosparc_P9_J647_006_volume_map_sharp.mrc z flip (#7) relative to
cryosparc_P7_J710_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99893793 -0.00322217 0.04596451 381.28217401
0.00554917 -0.99870419 0.05058868 376.53393934
0.04574195 0.05079001 0.99766132 -20.33401849
Axis 0.02293995 0.02535860 0.99941518
Axis point 190.46107391 188.94352871 0.00000000
Rotation angle (degrees) 179.74857166
Shift along axis -2.02715908
> hide #!5 models
> hide #4 models
> show #4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> select clear
> surface dust #3 size 8.25
> surface dust #7 size 8.25
> hide #!3 models
> show #!3 models
> volume #7 level 0.07801
> volume #3 level 0.05626
> select clear
> transparency #3.1 50
> volume #!3 style surface
[Repeated 1 time(s)]
> open 6ttu
6ttu title:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]
Chain information for 6ttu #8
---
Chain | Description | UniProt
C | Cullin-1 | CUL1_HUMAN
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |
N | NEDD8 | NEDD8_HUMAN
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN
S | S-phase kinase-associated protein 1 | SKP1_HUMAN
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN
U | Polyubiquitin-C | UBC_HUMAN
Non-standard residues in 6ttu #8
---
ZN — zinc ion
> select add #8
12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select #8/I
58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected
> delete sel
> select #8/T
3085 atoms, 3146 bonds, 2 pseudobonds, 394 residues, 2 models selected
> delete sel
> select #8/S
891 atoms, 903 bonds, 3 pseudobonds, 123 residues, 2 models selected
> delete sel
> ui tool show Matchmaker
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> hide #!8 models
> hide #!3 models
> show #!8 models
> matchmaker #8/C to #4/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
alignment score = 1628.1
RMSD between 309 pruned atom pairs is 1.282 angstroms; (across all 619 pairs:
4.270)
> matchmaker #8/C to #4/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
alignment score = 1628.1
RMSD between 309 pruned atom pairs is 1.282 angstroms; (across all 619 pairs:
4.270)
> select #8/C:15-354
2540 atoms, 2582 bonds, 3 pseudobonds, 305 residues, 2 models selected
> delete sel
> select #8/C:703-776
582 atoms, 587 bonds, 1 pseudobond, 70 residues, 2 models selected
> delete sel
> ui tool show Matchmaker
> matchmaker #8/C to #4/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
alignment score = 1250.8
RMSD between 194 pruned atom pairs is 1.196 angstroms; (across all 316 pairs:
2.691)
> matchmaker #8/C to #4/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
alignment score = 1250.8
RMSD between 194 pruned atom pairs is 1.196 angstroms; (across all 316 pairs:
2.691)
> ui tool show Matchmaker
> matchmaker #8/R to #4/R pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 466.8
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)
> matchmaker #8/R to #4/R pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 466.8
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)
> ui tool show Matchmaker
> select #8/C
2606 atoms, 2650 bonds, 1 pseudobond, 326 residues, 2 models selected
> delete sel
> close #6
> show #!7 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> select add #4
19807 atoms, 20027 bonds, 1225 residues, 1 model selected
> select add #8
22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected
> combine sel
Remapping chain ID 'D' in 6ttu #8 to 'F'
Remapping chain ID 'R' in 6ttu #8 to 'S'
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 21 residues in model #6 to IUPAC-IUB
standards.
> select clear
> clipper associate #3 toModel #6
Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #6.1.1.1, grid
size 480,480,480, pixel 0.825, shown at step 1, values float32
> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map_sharp.mrc
Opened cryosparc_P9_J635_008_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 0.825, shown at level 0.0194, step 2, values float32
> volume #3 level 0.09358
> volume flip #3
Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #9, grid size
480,480,480, pixel 0.825, shown at step 1, values float32
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 2 maps.
> hide #!6.2 models
> show #!6.2 models
> select add #6.2
22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 8 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 2 maps.
> select add #6.2
22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 8 models selected
> select add #6
22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 15 models selected
> close #6
> hide #!9 models
> select add #4
19807 atoms, 20027 bonds, 1225 residues, 1 model selected
> select add #8
22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected
> combine sel
Remapping chain ID 'D' in 6ttu #8 to 'F'
Remapping chain ID 'R' in 6ttu #8 to 'S'
> hide #4 models
> select subtract #4
2984 atoms, 3047 bonds, 13 pseudobonds, 380 residues, 3 models selected
> hide #!8 models
> select subtract #8
Nothing selected
> select add #6
22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 3 models selected
> show #!9 models
> fitmap #6 inMap #9
Fit molecule combination (#6) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) using 22791 atoms
average map value = 0.0972, steps = 156
shifted from previous position = 11.3
rotated from previous position = 6.89 degrees
atoms outside contour = 12780, contour level = 0.093576
Position of combination (#6) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.99761374 -0.02131244 -0.06567050 24.02263064
0.01475408 0.99499981 -0.09878107 25.91855777
0.06744740 0.09757645 0.99293992 -32.41202814
Axis 0.81831656 -0.55476655 0.15030663
Axis point 0.00000000 350.66445652 246.92285576
Rotation angle (degrees) 6.89074657
Shift along axis 0.40762520
> select clear
> hide #!6 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #6/R to #4/R pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain R (#4) with combination, chain R (#6),
sequence alignment score = 927
RMSD between 89 pruned atom pairs is 0.000 angstroms; (across all 89 pairs:
0.000)
> matchmaker #6/R to #4/R pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain R (#4) with combination, chain R (#6),
sequence alignment score = 927
RMSD between 89 pruned atom pairs is 0.000 angstroms; (across all 89 pairs:
0.000)
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> ui tool show Matchmaker
> close #6
> show #4 models
> show #!8 models
> combine sel
No structures specified
> select add #4
19807 atoms, 20027 bonds, 1225 residues, 1 model selected
> select add #8
22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected
> select subtract #8
19807 atoms, 20027 bonds, 1225 residues, 1 model selected
> hide #!8 models
> hide #4 models
> show #4 models
> show #!9 models
> select add #9
19807 atoms, 20027 bonds, 1225 residues, 3 models selected
> fitmap #4 inMap #9
Fit molecule fullmodel-v5.pdb (#4) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) using 19807 atoms
average map value = 0.1121, steps = 152
shifted from previous position = 10.8
rotated from previous position = 6.89 degrees
atoms outside contour = 9792, contour level = 0.093576
Position of fullmodel-v5.pdb (#4) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) coordinates:
Matrix rotation and translation
0.99762593 -0.02091198 -0.06561397 23.93517264
0.01436000 0.99500528 -0.09878407 25.98670381
0.06735202 0.09760733 0.99294336 -32.41050705
Axis 0.81905399 -0.55453714 0.14710244
Axis point 0.00000000 350.60177499 247.72967437
Rotation angle (degrees) 6.88570607
Shift along axis 0.42594157
> select clear
> hide #!9 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #8/R to #4/R pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 499.8
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> matchmaker #8/R to #4/R pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 499.8
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)
> matchmaker #8/R to #4/R pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 499.8
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)
> ui tool show Matchmaker
[Repeated 1 time(s)]Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> matchmaker #!8 to #4
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 fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 476.4
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)
> matchmaker #!8 to #4
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 fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 476.4
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)
> select add #8
2984 atoms, 3047 bonds, 13 pseudobonds, 380 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.5203,0.56446,-0.64084,135.43,0.36003,-0.82545,-0.43475,422.57,-0.77438,-0.0045259,-0.6327,409.12
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.5203,0.56446,-0.64084,121.21,0.36003,-0.82545,-0.43475,360.91,-0.77438,-0.0045259,-0.6327,411.66
> view matrix models
> #8,0.5203,0.56446,-0.64084,67.915,0.36003,-0.82545,-0.43475,357.48,-0.77438,-0.0045259,-0.6327,425.56
> view matrix models
> #8,0.5203,0.56446,-0.64084,83.916,0.36003,-0.82545,-0.43475,369.99,-0.77438,-0.0045259,-0.6327,452.45
> view matrix models
> #8,0.5203,0.56446,-0.64084,75.872,0.36003,-0.82545,-0.43475,367.76,-0.77438,-0.0045259,-0.6327,456.02
> view matrix models
> #8,0.5203,0.56446,-0.64084,74.881,0.36003,-0.82545,-0.43475,370.35,-0.77438,-0.0045259,-0.6327,456.29
> view matrix models
> #8,0.5203,0.56446,-0.64084,75.862,0.36003,-0.82545,-0.43475,369.49,-0.77438,-0.0045259,-0.6327,457.55
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.2363,0.60838,-0.75765,130.06,0.41768,-0.76762,-0.48612,357.73,-0.87733,-0.20159,-0.43549,479.62
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.2363,0.60838,-0.75765,133.58,0.41768,-0.76762,-0.48612,354.6,-0.87733,-0.20159,-0.43549,486.99
> view matrix models
> #8,0.2363,0.60838,-0.75765,133.86,0.41768,-0.76762,-0.48612,354.1,-0.87733,-0.20159,-0.43549,487.38
> select clear
> select #8/R:19-39
184 atoms, 190 bonds, 21 residues, 1 model selected
> delete sel
Undo failed, probably because structures have been modified.
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!8 models
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for fullmodel-v5.pdb
---
Chain | Description
4.2/A | No description available
4.2/B | No description available
4.2/C | No description available
4.2/D | No description available
4.2/E | No description available
4.2/R | No description available
> clipper associate #9 toModel #4
Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #4.1.1.1, grid
size 480,480,480, pixel 0.825, shown at step 1, values float32
> view matrix models #4.2,1,0,0,0.56548,0,1,0,-4.8388,0,0,1,-5.2016
> show #!3 models
> hide #!3 models
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> volume #!4.1.1.1 style surface
> fitmap #4.2 inMap #4.1.1.1
Fit molecule fullmodel-v5.pdb (#4.2) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#4.1.1.1) using 19807 atoms
average map value = 0.1316, steps = 140
shifted from previous position = 7.11
rotated from previous position = 0.0441 degrees
atoms outside contour = 15522, contour level = 0.19368
Position of fullmodel-v5.pdb (#4.2) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#4.1.1.1) coordinates:
Matrix rotation and translation
0.99999973 -0.00058113 0.00045808 0.02446487
0.00058103 0.99999981 0.00021172 -0.18611887
-0.00045820 -0.00021146 0.99999987 0.13541812
Axis -0.27492671 0.59527919 0.75502185
Axis point 304.68612802 34.72877780 0.00000000
Rotation angle (degrees) 0.04409607
Shift along axis -0.01527510
> isolde sim resume
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 39 residues in model #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 50 residues in model #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /home/pinkie/Documents/Charlotte/2024_01_28/fulmodel-v6-crosslinked.pdb
> models #4
> hide #!4 models
> show #!4 models
> show #!7 models
> hide #!7 models
> hide #!4 models
> show #!3 models
> volume flip #3
Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #6, grid size
480,480,480, pixel 0.825, shown at step 1, values float32
> open /home/pinkie/Documents/Charlotte/2024_01_28/fulmodel-v6-crosslinked.pdb
Chain information for fulmodel-v6-crosslinked.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
R | No description available
> open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb
Chain information for fullmodel-v5.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
R | No description available
> hide #9-10 atoms
> show #9-10 cartoons
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> hide #10 models
> fitmap #9 inMap #6
Fit molecule fulmodel-v6-crosslinked.pdb (#9) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) using 19807 atoms
average map value = 0.1322, steps = 48
shifted from previous position = 0.00848
rotated from previous position = 0.0222 degrees
atoms outside contour = 7877, contour level = 0.093576
Position of fulmodel-v6-crosslinked.pdb (#9) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.99999993 -0.00034748 -0.00013386 0.09294722
0.00034750 0.99999993 0.00010561 -0.08510450
0.00013382 -0.00010566 0.99999999 0.00149379
Axis -0.27290890 -0.34577439 0.89775320
Axis point 239.58376669 271.68215520 0.00000000
Rotation angle (degrees) 0.02217725
Shift along axis 0.00540189
> hide #9 models
> show #10 models
> fitmap #10 inMap #6
Fit molecule fullmodel-v5.pdb (#10) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) using 19807 atoms
average map value = 0.1121, steps = 152
shifted from previous position = 10.8
rotated from previous position = 6.89 degrees
atoms outside contour = 9792, contour level = 0.093576
Position of fullmodel-v5.pdb (#10) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
0.99762593 -0.02091198 -0.06561397 23.93517264
0.01436000 0.99500528 -0.09878407 25.98670381
0.06735202 0.09760733 0.99294336 -32.41050705
Axis 0.81905399 -0.55453714 0.14710244
Axis point 0.00000000 350.60177499 247.72967437
Rotation angle (degrees) 6.88570607
Shift along axis 0.42594157
> show #9 models
> hide #!6 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> show #!5 models
> show #9-10#!5 cartoons
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #5
23537 atoms, 23790 bonds, 1 pseudobond, 1735 residues, 3 models selected
> help help:user
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.52174,-0.29947,0.79881,191.85,-0.34266,-0.78395,-0.5177,206.15,0.78126,-0.54383,0.3064,152.39,#4.2,1,-0.00058113,0.00045808,-0.80996,0.00058103,1,0.00021172,5.8066,-0.0004582,-0.00021146,1,0.83911
> select subtract #5
19807 atoms, 20027 bonds, 1225 residues, 1 model selected
> hide #9 models
> hide #10 models
> show #!6 models
> fitmap #5 inMap #6
Fit molecule 5t35 (#5) to map cryosparc_P9_J635_008_volume_map_sharp.mrc z
flip (#6) using 3730 atoms
average map value = 0.08285, steps = 112
shifted from previous position = 5.2
rotated from previous position = 3.59 degrees
atoms outside contour = 2412, contour level = 0.093576
Position of 5t35 (#5) relative to cryosparc_P9_J635_008_volume_map_sharp.mrc z
flip (#6) coordinates:
Matrix rotation and translation
-0.49489741 -0.35355994 0.79377070 195.33404698
-0.33737792 -0.76363743 -0.55048525 209.06766347
0.80078255 -0.54023443 0.25863887 152.81110365
Axis 0.50252548 -0.34374169 0.79329049
Axis point 48.43141862 138.03079969 0.00000000
Rotation angle (degrees) 179.41561301
Shift along axis 147.51865747
> show #9 models
> show #10 models
> hide #!6 models
> hide #!5 models
> select #9/R
1432 atoms, 1452 bonds, 92 residues, 1 model selected
> select clear
> select #9/R
1432 atoms, 1452 bonds, 92 residues, 1 model selected
> color sel lime
> select clear
> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J649_006_volume_map_sharp.mrc
Opened cryosparc_P9_J649_006_volume_map_sharp.mrc as #11, grid size
420,420,420, pixel 0.825, shown at level 0.0268, step 2, values float32
> volume #11 level 0.09477
> volume #11 level 0.07304
> select add #11
3 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.79578,-0.21636,0.56562,-21.157,-0.2012,-0.9754,-0.090028,385.2,0.57118,-0.042161,-0.81974,208.32
> volume flip #11
Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #12, grid size
420,420,420, pixel 0.825, shown at step 1, values float32
> select add #12
4 models selected
> close #11
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.79578,-0.21636,0.56562,-21.535,-0.2012,-0.9754,-0.090028,420.27,0.57118,-0.042161,-0.81974,256.69
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.97755,0.059009,-0.20229,370.12,-0.055777,-0.99821,-0.021647,387.2,-0.20321,-0.0098776,0.97909,50.616
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.97755,0.059009,-0.20229,369.93,-0.055777,-0.99821,-0.021647,388.27,-0.20321,-0.0098776,0.97909,64.412
> view matrix models
> #12,-0.97755,0.059009,-0.20229,390.8,-0.055777,-0.99821,-0.021647,385.58,-0.20321,-0.0098776,0.97909,68.302
Must specify one map, got 0
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> hide #!4.1 models
> hide #!4.2 models
> hide #4.3 models
> close #10
> fitmap #9 inMap #12
Fit molecule fulmodel-v6-crosslinked.pdb (#9) to map
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#12) using 19807 atoms
average map value = 0.1186, steps = 168
shifted from previous position = 7.18
rotated from previous position = 10.2 degrees
atoms outside contour = 7210, contour level = 0.073036
Position of fulmodel-v6-crosslinked.pdb (#9) relative to
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#12) coordinates:
Matrix rotation and translation
-0.99893072 -0.03543972 -0.02968888 383.81872944
0.03672114 -0.99836564 -0.04379003 372.34530599
-0.02808845 -0.04483342 0.99859951 -6.07997840
Axis -0.01445423 -0.02217085 0.99964970
Axis point 188.50734431 189.56827757 0.00000000
Rotation angle (degrees) 177.93156998
Shift along axis -19.88086512
> select clear
> surface dust #12 size 8.25
> volume #12 level 0.04915
> volume #4.1.1.1 level 0.1137
> show #!4.1 models
> show #!4.2 models
> show #4.3 models
> hide #!4.2 models
> hide #4.3 models
> hide #!4.1 models
> show #!6 models
> hide #!6 models
> open 8b3i
Summary of feedback from opening 8b3i fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /N:1
Atom H1 is not in the residue template for MET /U:1
Atom H1 is not in the residue template for MET /a:1
Atom H1 is not in the residue template for MET /d:1
note | Fetching compressed mmCIF 8b3i from
http://files.rcsb.org/download/8b3i.cif
8b3i title:
CRL4CSA-E2-Ub (state 2) [more info...]
Chain information for 8b3i #10
---
Chain | Description | UniProt
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN
N | NEDD8 | NEDD8_HUMAN
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN
U | Ubiquitin | UBC_HUMAN
a | DNA excision repair protein ERCC-8 | ERCC8_HUMAN
d | DNA damage-binding protein 1 | DDB1_HUMAN
e | Cullin-4A | CUL4A_HUMAN
Non-standard residues in 8b3i #10
---
ZN — zinc ion
> select #10/a
5627 atoms, 5686 bonds, 365 residues, 1 model selected
> delete sel
> select #10/d
17196 atoms, 17351 bonds, 6 pseudobonds, 1096 residues, 2 models selected
> delete sel
> ui tool show Matchmaker
> matchmaker #!10 to #9
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 fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
sequence alignment score = 1216.9
RMSD between 161 pruned atom pairs is 1.160 angstroms; (across all 614 pairs:
19.630)
> matchmaker #!10 to #9
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 fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
sequence alignment score = 1216.9
RMSD between 161 pruned atom pairs is 1.160 angstroms; (across all 614 pairs:
19.630)
> hide #!12 models
> hide #9 models
> hide #!4 models
> hide #!10 atoms
> show #!10 cartoons
> select #10/E:42-354
Nothing selected
> select #10/e:42-354
5160 atoms, 5206 bonds, 313 residues, 1 model selected
> delete sel
> show #9 models
> ui tool show Matchmaker
> matchmaker #!10 to #9
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 fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
sequence alignment score = 826.6
RMSD between 150 pruned atom pairs is 1.050 angstroms; (across all 315 pairs:
4.185)
> matchmaker #!10 to #9
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 fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
sequence alignment score = 826.6
RMSD between 150 pruned atom pairs is 1.050 angstroms; (across all 315 pairs:
4.185)
> show #!12 models
> hide #9 models
> show #9 models
> hide #!12 models
> open 6nyo
Summary of feedback from opening 6nyo fetched from pdb
---
note | Fetching compressed mmCIF 6nyo from
http://files.rcsb.org/download/6nyo.cif
6nyo title:
Crystal structure of a human Cdc34-ubiquitin thioester mimetic [more info...]
Chain information for 6nyo #11
---
Chain | Description | UniProt
A | Ubiquitin-conjugating enzyme E2 R2 | UB2R2_HUMAN
E | Ubiquitin |
Non-standard residues in 6nyo #11
---
EDO — 1,2-ethanediol (ethylene glycol)
PO4 — phosphate ion
U94 —
4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic
acid
> ui tool show Matchmaker
> matchmaker #11 to #10
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 8b3i, chain U (#10) with 6nyo, chain E (#11), sequence alignment
score = 312.7
RMSD between 71 pruned atom pairs is 0.646 angstroms; (across all 76 pairs:
1.638)
> matchmaker #11 to #10
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 8b3i, chain U (#10) with 6nyo, chain E (#11), sequence alignment
score = 312.7
RMSD between 71 pruned atom pairs is 0.646 angstroms; (across all 76 pairs:
1.638)
> show #!12 models
> hide #11 models
> hide #!10 models
> transparency #12.1 50
> volume #12 level 0.1357
> volume #12 level 0.09393
> show #!10 models
> hide #9 models
> volume #12 level 0.07005
> open
> /home/pinkie/Documents/Charlotte/2024_01_28/OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc
Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc as #13, grid
size 512,512,512, pixel 0.74, shown at level 0.0183, step 2, values float32
> volume #13 level 0.08943
> hide #!10 models
> volume #13 level 0.04837
> surface dust #13 size 7.4
> volume #13 level 0.04837
> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J846_005_volume_mask_refine.mrc
Opened cryosparc_P7_J846_005_volume_mask_refine.mrc as #14, grid size
512,512,512, pixel 0.74, shown at level 0.959, step 2, values float32
> ui mousemode right "map eraser"
[Repeated 1 time(s)]
Can only have one displayed volume when erasing
[Repeated 11 time(s)]
> volume erase #13 center 210.44,248.48,205.99 radius 24.248
Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy as #16,
grid size 512,512,512, pixel 0.74, shown at step 1, values float32
> volume erase #16 center 141.76,228.51,179.62 radius 24.248
> ui mousemode right "map eraser"
[Repeated 1 time(s)]
> volume gaussian #16
Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy gaussian as
#17, grid size 512,512,512, pixel 0.74, shown at step 1, values float32
> volume #17 level 0.02761
> close #17
> volume gaussian #16 sDev 3
Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy gaussian as
#17, grid size 512,512,512, pixel 0.74, shown at step 1, values float32
> surface dust #16 size 7.4
> save /home/pinkie/Documents/Charlotte/2024_01_28/J846-edited.mrc models #16
> close #17
> open /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J852_mask.mrc
Opened cryosparc_P7_J852_mask.mrc as #17, grid size 512,512,512, pixel 0.74,
shown at level 1, step 2, values float32
> volume #17 level 0.9908
> close #17
> close #16
> close #14
> close #13
> close #1
> volume #7 level 0.07099
> close #3
> volume #12 level 0.04968
> show #9 models
> hide #!12 models
> show #11 models
> select #11/E
705 atoms, 628 bonds, 161 residues, 1 model selected
> color sel yellow
> select clear
> show #!12 models
> hide #!12 models
> hide #9 models
> show #!8 models
> show #9 models
> hide #9 models
> hide #11 models
> view
> show #11 models
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #11/E:34
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> select clear
> hide #!8 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #!8 to #11
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 6nyo, chain E (#11) with 6ttu, chain U (#8), sequence alignment
score = 340
RMSD between 70 pruned atom pairs is 0.714 angstroms; (across all 75 pairs:
1.524)
> matchmaker #!8 to #11
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 6nyo, chain E (#11) with 6ttu, chain U (#8), sequence alignment
score = 340
RMSD between 70 pruned atom pairs is 0.714 angstroms; (across all 75 pairs:
1.524)
> show #9 models
Drag select of 27 residues, 1 atoms, 4 bonds
> select clear
> ui mousemode right translate
> select sequence YGH
92 atoms, 94 bonds, 6 residues, 2 models selected
> color (#9 & sel) orange red
> select clear
> hide #11 models
> open 6ttu
6ttu title:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]
Chain information for 6ttu #1
---
Chain | Description | UniProt
C | Cullin-1 | CUL1_HUMAN
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |
N | NEDD8 | NEDD8_HUMAN
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN
S | S-phase kinase-associated protein 1 | SKP1_HUMAN
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN
U | Polyubiquitin-C | UBC_HUMAN
Non-standard residues in 6ttu #1
---
ZN — zinc ion
> hide #!8 models
> show #!10 models
> hide #!1 models
> show #11 models
> select sequence YGH
92 atoms, 94 bonds, 6 residues, 2 models selected
> select sequence YGH
92 atoms, 94 bonds, 6 residues, 2 models selected
> select sequence YGH
92 atoms, 94 bonds, 6 residues, 2 models selected
> select sequence YGH
92 atoms, 94 bonds, 6 residues, 2 models selected
> select sequence YGH
92 atoms, 94 bonds, 6 residues, 2 models selected
> select sequence YGH
92 atoms, 94 bonds, 6 residues, 2 models selected
> select clear
> show #!12 models
> open
> /home/pinkie/Documents/Charlotte/2024_01_28/UBE2R1AF-P49427-F1-model_v4.pdb
UBE2R1AF-P49427-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1
(P49427) [more info...]
Chain information for UBE2R1AF-P49427-F1-model_v4.pdb #3
---
Chain | Description | UniProt
A | ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN
> ui tool show Matchmaker
> matchmaker #3 to #11
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 6nyo, chain A (#11) with UBE2R1AF-P49427-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 920.3
RMSD between 162 pruned atom pairs is 1.029 angstroms; (across all 188 pairs:
1.823)
> matchmaker #3 to #11
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 6nyo, chain A (#11) with UBE2R1AF-P49427-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 920.3
RMSD between 162 pruned atom pairs is 1.029 angstroms; (across all 188 pairs:
1.823)
> volume #12 level 0.02057
> volume #12 level 0.04386
> hide #!10 models
> hide #!12 models
> hide #11 models
> select #9/R
1432 atoms, 1452 bonds, 92 residues, 1 model selected
> delete sel
> show #11 models
> hide #11 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!1 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #!1 to #8
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 6ttu, chain D (#8) with 6ttu, chain D (#1), sequence alignment
score = 782.4
RMSD between 146 pruned atom pairs is 0.000 angstroms; (across all 146 pairs:
0.000)
> select add #1
12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select #1/I
58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected
> delete sel
> select #1/T
3085 atoms, 3146 bonds, 2 pseudobonds, 394 residues, 2 models selected
> delete sel
> select #1/S
891 atoms, 903 bonds, 3 pseudobonds, 123 residues, 2 models selected
> delete sel
> select #1/C
5728 atoms, 5820 bonds, 6 pseudobonds, 701 residues, 2 models selected
> delete sel
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 545.23.08
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: NOVATECH LTD
Model: PC-BX25094
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen Threadripper PRO 3955WX 16-Cores
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 251Gi 19Gi 2.1Gi 232Mi 229Gi 229Gi
Swap: 2.0Gi 965Mi 1.1Gi
Graphics:
2b:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Kernel driver in use: ast
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 21 months ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker: 'NoneType' object has no attribute 'setChecked' |
comment:2 by , 21 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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