Opened 4 years ago

Closed 4 years ago

#5535 closed defect (duplicate)

Matchmaker: 'NoneType' object has no attribute 'setChecked'

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open /Users/rachelmccole/Downloads/emd_11912.map format ccp4

Opened emd_11912.map as #1, grid size 312,312,312, pixel 1.75, shown at level
0.00157, step 2, values float32  

> volume #1 level 0.001573

> volume #1 level 0.02191

> open 6c24

6c24 title:  
Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Extended
Active State [more info...]  
  
Chain information for 6c24 #2  
---  
Chain | Description  
A M Q | Polycomb protein SUZ12  
B | Protein Jumonji  
C K | Histone-lysine N-methyltransferase EZH2  
E | Protein Jumonji  
L | Polycomb protein EED  
N | Histone-binding protein RBBP4  
O | JARID2-substrate  
P | Zinc finger protein AEBP2  
Z | SUZ12  
  

> select #2

13346 atoms, 13657 bonds, 6 pseudobonds, 1772 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,10.116,0,1,0,190,0,0,1,0

> view matrix models #2,1,0,0,10.104,0,1,0,189.8,0,0,1,0.085491

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.44586,0.88677,-0.12188,-14.475,-0.13415,-0.068433,-0.9886,465.46,-0.88499,0.45712,0.088444,171.33

> view matrix models
> #2,0.0030847,0.44541,-0.89532,194.84,-0.64602,-0.68253,-0.34178,523.62,-0.76331,0.57945,0.28564,115.64

> view matrix models
> #2,-0.058194,-0.28355,-0.95719,300.9,-0.72873,-0.64326,0.23486,455.57,-0.68232,0.7112,-0.1692,147.14

> view matrix models
> #2,0.21856,-0.38542,-0.89648,270.89,-0.73671,-0.66763,0.10742,475.86,-0.63992,0.63697,-0.42986,184.28

> view matrix models
> #2,0.03335,-0.051147,-0.99813,265.75,-0.6943,-0.71955,0.013674,488.93,-0.71891,0.69255,-0.059509,140.07

> view matrix models
> #2,-0.054133,-0.37833,-0.92409,307.92,-0.73172,-0.61469,0.29452,444.78,-0.67945,0.69212,-0.24356,158.64

> view matrix models
> #2,-0.076855,-0.44041,-0.8945,314.71,-0.73593,-0.58024,0.34891,434.1,-0.67269,0.6851,-0.27952,163.25

> view matrix models
> #2,-0.061042,-0.3894,-0.91904,309.52,-0.73249,-0.608,0.30626,442.55,-0.67803,0.69189,-0.24812,159.07

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.061042,-0.3894,-0.91904,334.73,-0.73249,-0.608,0.30626,434.1,-0.67803,0.69189,-0.24812,356.44

> view matrix models
> #2,-0.061042,-0.3894,-0.91904,423.5,-0.73249,-0.608,0.30626,427.23,-0.67803,0.69189,-0.24812,349.88

> ui mousemode right "rotate selected models"

> ui tool show "Fit to Segments"

> ui tool show "Color Zone"

> ui tool show "Fit in Map"

Fit molecule 6c24 (#2) to map emd_11912.map (#1) using 13346 atoms  
average map value = 0.01767, steps = 264  
shifted from previous position = 57.9  
rotated from previous position = 26.1 degrees  
atoms outside contour = 8258, contour level = 0.021907  
  
Position of 6c24 (#2) relative to emd_11912.map (#1) coordinates:  
Matrix rotation and translation  
0.18249426 -0.47672752 -0.85989925 404.06004155  
-0.91690442 -0.39824629 0.02619513 448.67271149  
-0.35493962 0.78366496 -0.50979123 275.06807967  
Axis 0.74908928 -0.49937282 -0.43530684  
Axis point 0.00000000 312.42704304 332.50141943  
Rotation angle (degrees) 149.62922010  
Shift along axis -41.11692525  
  

> volume #1 level 0.02529

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #1 level 0.004974

> view matrix models
> #2,0.10064,-0.47028,-0.87676,432.77,-0.91777,-0.38414,0.1007,424.09,-0.38415,0.79453,-0.47027,270.14

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.10064,-0.47028,-0.87676,431.85,-0.91777,-0.38414,0.1007,412.11,-0.38415,0.79453,-0.47027,270.58

> select #1

2 models selected  

> view matrix models #1,1,0,0,34.015,0,1,0,12.596,0,0,1,-108.72

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> ~select #1

Nothing selected  

> select #1

2 models selected  

> ~select #1

Nothing selected  

> set bgColor white

> volume #1 level 0.007129

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select #2

13346 atoms, 13657 bonds, 6 pseudobonds, 1772 residues, 2 models selected  

> view matrix models
> #2,0.10064,-0.47028,-0.87676,336.27,-0.91777,-0.38414,0.1007,410.89,-0.38415,0.79453,-0.47027,213.09

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.43243,0.47132,-0.76868,272.88,-0.74133,-0.67111,0.0055523,436.39,-0.51325,0.57225,0.63961,115.26

> view matrix models
> #2,-0.84508,0.53415,-0.022702,221.89,-0.53299,-0.84505,-0.042616,437.84,-0.041948,-0.023914,0.99883,83.939

> view matrix models
> #2,0.30478,0.3178,-0.89784,215.46,0.36104,-0.91088,-0.19986,353.35,-0.88134,-0.26324,-0.39235,397.06

> view matrix models
> #2,-0.75125,-0.25179,-0.6101,382.55,0.50415,-0.81551,-0.28422,334.25,-0.42598,-0.5211,0.73959,227.14

> view matrix models
> #2,-0.17653,0.93828,-0.29743,122.53,0.3765,-0.21483,-0.90116,354.58,-0.90944,-0.27106,-0.31534,391.74

> view matrix models
> #2,-0.19048,0.92261,-0.33543,131.08,0.33716,-0.25942,-0.905,365.56,-0.92198,-0.28548,-0.26165,388.26

> view matrix models
> #2,0.07836,-0.75233,-0.65411,345.65,0.40937,0.62254,-0.66698,216.66,0.909,-0.21551,0.35676,69.763

> view matrix models
> #2,0.65792,-0.70687,-0.25976,216.59,0.5978,0.69998,-0.39071,148.02,0.45801,0.10177,0.8831,20.08

> view matrix models
> #2,0.84448,-0.49606,0.20194,107.98,0.53557,0.77908,-0.32588,137.78,0.004326,0.38335,0.92359,37.185

> view matrix models
> #2,0.88244,-0.3809,0.27608,79.441,0.43897,0.87772,-0.19214,120.65,-0.16914,0.29075,0.94173,68.23

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.88244,-0.3809,0.27608,121.92,0.43897,0.87772,-0.19214,137.57,-0.16914,0.29075,0.94173,88.735

> view matrix models
> #2,0.88244,-0.3809,0.27608,144.09,0.43897,0.87772,-0.19214,142.1,-0.16914,0.29075,0.94173,62.797

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.91042,-0.24191,0.33558,115.72,0.27179,0.96133,-0.044353,133.94,-0.31188,0.13159,0.94097,100.64

> view matrix models
> #2,0.86577,-0.47377,0.16121,172.37,0.49636,0.85401,-0.15587,133.17,-0.063832,0.21497,0.97453,54.733

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.86577,-0.47377,0.16121,182.17,0.49636,0.85401,-0.15587,134.72,-0.063832,0.21497,0.97453,44.706

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.86587,-0.47507,0.15677,182.88,0.49531,0.77011,-0.40199,176.68,0.070241,0.42572,0.90212,10.898

> view matrix models
> #2,0.78469,-0.58043,-0.21762,253.98,0.56432,0.81416,-0.1367,128.64,0.25652,-0.015538,0.96641,33.945

> view matrix models
> #2,0.8384,-0.53749,-0.090471,225.65,0.28192,0.5697,-0.77199,275.68,0.46647,0.62173,0.62917,-28.537

> view matrix models
> #2,0.92322,-0.38427,-0.0028362,184.76,0.34798,0.8391,-0.41813,188.75,0.16306,0.38504,0.90838,3.4433

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.92322,-0.38427,-0.0028362,190.47,0.34798,0.8391,-0.41813,195.64,0.16306,0.38504,0.90838,2.4494

> view matrix models
> #2,0.92322,-0.38427,-0.0028362,175.8,0.34798,0.8391,-0.41813,185.6,0.16306,0.38504,0.90838,3.89

> view matrix models
> #2,0.92322,-0.38427,-0.0028362,175.89,0.34798,0.8391,-0.41813,185.41,0.16306,0.38504,0.90838,3.9172

> fitmap #2 inMap #1

Fit molecule 6c24 (#2) to map emd_11912.map (#1) using 13346 atoms  
average map value = 0.014, steps = 208  
shifted from previous position = 41.1  
rotated from previous position = 38 degrees  
atoms outside contour = 6652, contour level = 0.0071288  
  
Position of 6c24 (#2) relative to emd_11912.map (#1) coordinates:  
Matrix rotation and translation  
0.92541377 0.02250314 0.37828953 67.90093952  
0.03637711 0.98835055 -0.14778330 160.29655098  
-0.37720825 0.15052179 0.91381460 178.02881410  
Axis 0.36720061 0.92998497 0.01707825  
Axis point 445.61863766 0.00000000 80.22392081  
Rotation angle (degrees) 23.96560548  
Shift along axis 177.04707110  
  

> transparency (#!2 & sel) 60

> select #1

2 models selected  

> transparency #1.1 60

> view matrix models #1,1,0,0,37.324,0,1,0,13.919,0,0,1,-107.51

> view matrix models #1,1,0,0,38.555,0,1,0,16.898,0,0,1,-113.03

> select #2

13346 atoms, 13657 bonds, 6 pseudobonds, 1772 residues, 2 models selected  

> view matrix models
> #2,0.92541,0.022503,0.37829,99.888,0.036377,0.98835,-0.14778,174.22,-0.37721,0.15052,0.91381,71.174

Fit molecule 6c24 (#2) to map emd_11912.map (#1) using 13346 atoms  
average map value = 0.014, steps = 64  
shifted from previous position = 9.48  
rotated from previous position = 0.0153 degrees  
atoms outside contour = 6654, contour level = 0.0071288  
  
Position of 6c24 (#2) relative to emd_11912.map (#1) coordinates:  
Matrix rotation and translation  
0.92548554 0.02257636 0.37810953 67.88465189  
0.03621988 0.98837348 -0.14766848 160.31732460  
-0.37704725 0.15036013 0.91390766 178.03094701  
Axis 0.36705120 0.93004896 0.01680332  
Axis point 445.97367844 0.00000000 80.18618043  
Rotation angle (degrees) 23.95235878  
Shift along axis 177.01161486  
  

> volume #1 level 0.02314

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> open 7ksr

7ksr title:  
PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome [more info...]  
  
Chain information for 7ksr #3  
---  
Chain | Description  
A | Histone-lysine N-methyltransferase EZH1  
B | Polycomb protein EED  
C | Polycomb protein SUZ12  
D | Histone-binding protein RBBP4  
  
Non-standard residues in 7ksr #3  
---  
ZN — zinc ion  
  

> select #3

11863 atoms, 12131 bonds, 30 pseudobonds, 1531 residues, 3 models selected  

> color sel bychain

> style sel sphere

Changed 11863 atom styles  

> style sel sphere

Changed 11863 atom styles  

> show sel atoms

> hide sel cartoons

> hide sel surfaces

> ui tool show Matchmaker

> matchmaker #!3 to #2

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 6c24, chain M (#2) with 7ksr, chain C (#3), sequence alignment
score = 2867.9  
RMSD between 114 pruned atom pairs is 0.849 angstroms; (across all 122 pairs:
1.172)  
  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #1 level 0.006393

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> ~select #3

Nothing selected  

> hide #!3 models

> show #!3 models

> hide #!3 models

> volume #1 level 0.04616

> volume #1 level 0.01865

> select #2

13346 atoms, 13657 bonds, 6 pseudobonds, 1772 residues, 2 models selected  

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,37.758,0,1,0,15.35,0,0,1,-110.17

> ui mousemode right "translate selected atoms"

> ui mousemode right pivot

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.91318,-0.23885,-0.33024,229.86,0.17659,0.96215,-0.20757,170.15,0.36732,0.13123,0.92079,-28.308

> fitmap #2 inMap #1

Fit molecule 6c24 (#2) to map emd_11912.map (#1) using 13346 atoms  
average map value = 0.02028, steps = 160  
shifted from previous position = 13.5  
rotated from previous position = 22.9 degrees  
atoms outside contour = 6647, contour level = 0.018653  
  
Position of 6c24 (#2) relative to emd_11912.map (#1) coordinates:  
Matrix rotation and translation  
0.76664909 -0.09710820 -0.63468036 234.60276470  
0.12442570 0.99222777 -0.00151668 129.42510378  
0.62989476 -0.07780779 0.77277328 80.41242553  
Axis -0.05931983 -0.98326505 0.17225274  
Axis point -29.51420520 0.00000000 368.59035780  
Rotation angle (degrees) 40.01955019  
Shift along axis -127.32451623  
  

> ui tool show Matchmaker

> matchmaker #!3 to #2

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 6c24, chain M (#2) with 7ksr, chain C (#3), sequence alignment
score = 2867.9  
RMSD between 114 pruned atom pairs is 0.849 angstroms; (across all 122 pairs:
1.172)  
  

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> volume show

> volume hide

> volume show

> save /Users/rachelmccole/Documents/Structures/Muller_EMmodel_7ksr_6c24.cxs

> ~select #2

Nothing selected  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #1 level 0.01387

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!3 models

> show #!1 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!3 models

> open 6WKR

Summary of feedback from opening 6WKR fetched from pdb  
---  
warnings | Unknown polymer entity '14' near line 35601  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
6wkr title:  
PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome [more info...]  
  
Chain information for 6wkr #4  
---  
Chain | Description  
A | Polycomb protein SUZ12  
B E | Protein Jumonji  
C | Histone-lysine N-methyltransferase EZH2  
F T | Ubiquitin  
H | DNA (314-mer)  
I O | Histone H3.2  
J Q | Histone H4  
K R | Histone H2A type 1  
L | Polycomb protein EED  
M S | Histone H2B 1.1  
N | Histone-binding protein RBBP4  
P | Zinc finger protein AEBP2  
  
Non-standard residues in 6wkr #4  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> ui tool show Matchmaker

> matchmaker #!4 to #2

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 6c24, chain K (#2) with 6wkr, chain C (#4), sequence alignment
score = 3209.5  
RMSD between 269 pruned atom pairs is 0.963 angstroms; (across all 322 pairs:
1.972)  
  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> select #2/P#4/P

1831 atoms, 1868 bonds, 1 pseudobond, 258 residues, 3 models selected  
Alignment identifier is 1  

> select #4/P:50-116

417 atoms, 425 bonds, 67 residues, 1 model selected  

> select #4/P:50-116

417 atoms, 425 bonds, 67 residues, 1 model selected  

> select #2/P:232-276 #4/P:170-276

1107 atoms, 1132 bonds, 152 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [169-276] RMSD: 36.859  
  

> select #2/P:294-295 #4/P:294-295

40 atoms, 38 bonds, 4 residues, 2 models selected  

> select #2/P:277-295 #4/P:277-295

306 atoms, 309 bonds, 38 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [277-295] RMSD: 4.136  
  

> open
> /Users/rachelmccole/Documents/Structures/AEBP2_AF-Q6ZN18-F1-model_v1.pdb

AEBP2_AF-Q6ZN18-F1-model_v1.pdb title:  
Alphafold V2.0 prediction for zinc finger protein AEBP2 (Q6ZN18) [more
info...]  
  
Chain information for AEBP2_AF-Q6ZN18-F1-model_v1.pdb #5  
---  
Chain | Description  
A | zinc finger protein AEBP2  
  

> select #5

3810 atoms, 3874 bonds, 517 residues, 1 model selected  

> ~select #5

Nothing selected  

> hide #5 models

> show #5 models

> hide #5 models

> show #!3 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #5 models

> hide #!4 models

> hide #5 models

> show #5 models

> show #!4 models

> ui mousemode right zoom

Alignment identifier is 2  
Alignment identifier is 2/B  
Alignment identifier is 2/E  
Alignment identifier is 3  
Alignment identifier is 4  
Alignment identifier is 5  
Alignment identifier is 2/O  
Alignment identifier is 6  
Alignment identifier is 2/Z  
Alignment identifier is 3/A  
Alignment identifier is 7  
Alignment identifier is 8  
Alignment identifier is 4/H  
Alignment identifier is 9  
Alignment identifier is 10  
Alignment identifier is 11  
Alignment identifier is 12  
Alignment identifier is 5/A  

> ui mousemode right zoom

> ui mousemode right translate

> select down

Nothing selected  

> matchmaker #5 to #4/P pairing bs

Parameters  
---  
Chain pairing | bs  
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 6wkr, chain P (#4) with AEBP2_AF-Q6ZN18-F1-model_v1.pdb, chain A
(#5), sequence alignment score = 1290.4  
RMSD between 100 pruned atom pairs is 0.970 angstroms; (across all 193 pairs:
61.751)  
  

> ui mousemode right zoom

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right rotate

> select #2/B:113-116

31 atoms, 30 bonds, 4 residues, 1 model selected  

> select #5

3810 atoms, 3874 bonds, 517 residues, 1 model selected  
Destroying pre-existing alignment with identifier 5/A  
Alignment identifier is 5/A  

> select #4/P:50-100

295 atoms, 299 bonds, 51 residues, 1 model selected  

> select #3/A:31-123

685 atoms, 699 bonds, 1 pseudobond, 87 residues, 2 models selected  

> select #3/A:72

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:31-72

326 atoms, 330 bonds, 42 residues, 1 model selected  

> select #3

11863 atoms, 12131 bonds, 30 pseudobonds, 1531 residues, 3 models selected  

> hide #!4 models

> ~select #3

Nothing selected  

> select #5

3810 atoms, 3874 bonds, 517 residues, 1 model selected  

> show #5 target m

> select #5/A:517

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #5/A:517

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #5/A:220

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/A:1-220

1471 atoms, 1483 bonds, 220 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!4 models

> select #5

2339 atoms, 2390 bonds, 297 residues, 1 model selected  

> style sel sphere

Changed 2339 atom styles  

> show sel cartoons

> hide sel cartoons

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 2339 atom styles  

> color sel bychain

> rainbow sel

> color sel bychain

> color sel byhetero

> color sel byhetero

> color sel bychain

> color sel cyan

> matchmaker #5 to #4/P pairing bs

Parameters  
---  
Chain pairing | bs  
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 6wkr, chain P (#4) with AEBP2_AF-Q6ZN18-F1-model_v1.pdb, chain A
(#5), sequence alignment score = 1290.4  
RMSD between 100 pruned atom pairs is 0.970 angstroms; (across all 193 pairs:
61.751)  
  

> open
> /Users/rachelmccole/Documents/Structures/AEBP2_AF-Q6ZN18-F1-model_v1.pdb

AEBP2_AF-Q6ZN18-F1-model_v1.pdb title:  
Alphafold V2.0 prediction for zinc finger protein AEBP2 (Q6ZN18) [more
info...]  
  
Chain information for AEBP2_AF-Q6ZN18-F1-model_v1.pdb #6  
---  
Chain | Description  
A | zinc finger protein AEBP2  
  

> matchmaker #6/A to #4/P 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 6wkr, chain P (#4) with AEBP2_AF-Q6ZN18-F1-model_v1.pdb, chain A
(#6), sequence alignment score = 1290.4  
RMSD between 100 pruned atom pairs is 0.970 angstroms; (across all 193 pairs:
61.751)  
  

> show sel atoms

> ~select #5

Nothing selected  

> select #6

3810 atoms, 3874 bonds, 517 residues, 1 model selected  

> show sel atoms

> show sel atoms

> show sel atoms

> style sel sphere

Changed 3810 atom styles  

> matchmaker #5/A to #4/P 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 6wkr, chain P (#4) with AEBP2_AF-Q6ZN18-F1-model_v1.pdb, chain A
(#5), sequence alignment score = 1290.4  
RMSD between 100 pruned atom pairs is 0.970 angstroms; (across all 193 pairs:
61.751)  
  

> close #6

> show #4-5 target ab

> show #!2 models

> show #!3 models

> show #!1 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> hide #!4 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> close session

> open /Users/rachelmccole/Downloads/emd_11912.map format ccp4

Opened emd_11912.map as #1, grid size 312,312,312, pixel 1.75, shown at level
0.00157, step 2, values float32  

> open 6WKR

Summary of feedback from opening 6WKR fetched from pdb  
---  
warnings | Unknown polymer entity '14' near line 35601  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
6wkr title:  
PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome [more info...]  
  
Chain information for 6wkr #2  
---  
Chain | Description  
A | Polycomb protein SUZ12  
B E | Protein Jumonji  
C | Histone-lysine N-methyltransferase EZH2  
F T | Ubiquitin  
H | DNA (314-mer)  
I O | Histone H3.2  
J Q | Histone H4  
K R | Histone H2A type 1  
L | Polycomb protein EED  
M S | Histone H2B 1.1  
N | Histone-binding protein RBBP4  
P | Zinc finger protein AEBP2  
  
Non-standard residues in 6wkr #2  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> fitmap #2 inMap #1

Fit molecule 6wkr (#2) to map emd_11912.map (#1) using 29296 atoms  
average map value = 0.01252, steps = 284  
shifted from previous position = 60.6  
rotated from previous position = 17.1 degrees  
atoms outside contour = 11917, contour level = 0.0015727  
  
Position of 6wkr (#2) relative to emd_11912.map (#1) coordinates:  
Matrix rotation and translation  
0.96714772 -0.21269471 -0.13923453 123.66169049  
0.18897908 0.96787528 -0.16584434 12.89283393  
0.17003587 0.13408356 0.97627322 -14.56195846  
Axis 0.50919654 -0.52505759 0.68193358  
Axis point -113.78353881 488.21178833 0.00000000  
Rotation angle (degrees) 17.12821300  
Shift along axis 46.26833639  
  

> transparency 80

> transparency 60

> select #2

29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> show sel surfaces

> color sel bychain

> hide #!2 models

> show #!2 models

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87365,-0.31211,-0.37326,221.08,0.26468,0.94857,-0.17368,4.3017,0.40827,0.052943,0.91132,-31.153

> view matrix models
> #2,0.86819,-0.31841,-0.38062,225.47,0.27053,0.94669,-0.17488,3.771,0.41601,0.048858,0.90805,-31.075

> view matrix models
> #2,0.70327,-0.45813,-0.54362,332.87,0.45623,0.87728,-0.14911,-25.723,0.54522,-0.14315,0.82598,6.3916

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.70327,-0.45813,-0.54362,340.59,0.45623,0.87728,-0.14911,28.493,0.54522,-0.14315,0.82598,-29.736

> view matrix models
> #2,0.70327,-0.45813,-0.54362,342.66,0.45623,0.87728,-0.14911,43.939,0.54522,-0.14315,0.82598,-32.41

> view matrix models
> #2,0.70327,-0.45813,-0.54362,339.39,0.45623,0.87728,-0.14911,42.101,0.54522,-0.14315,0.82598,-25.895

> fitmap #2 inMap #1

Fit molecule 6wkr (#2) to map emd_11912.map (#1) using 29296 atoms  
average map value = 0.02831, steps = 300  
shifted from previous position = 11.2  
rotated from previous position = 40.4 degrees  
atoms outside contour = 7877, contour level = 0.0015727  
  
Position of 6wkr (#2) relative to emd_11912.map (#1) coordinates:  
Matrix rotation and translation  
0.31393755 -0.06985114 -0.94687065 431.57850921  
0.22236315 0.97496225 0.00180164 34.00016512  
0.92303729 -0.21111475 0.32160958 12.14951809  
Axis -0.11179404 -0.98181528 0.15343026  
Axis point 196.82996253 0.00000000 303.76222387  
Rotation angle (degrees) 72.22651276  
Shift along axis -79.76568320  
  

> open 7ksr

7ksr title:  
PRC2:EZH1_A from a dimeric PRC2 bound to a nucleosome [more info...]  
  
Chain information for 7ksr #3  
---  
Chain | Description  
A | Histone-lysine N-methyltransferase EZH1  
B | Polycomb protein EED  
C | Polycomb protein SUZ12  
D | Histone-binding protein RBBP4  
  
Non-standard residues in 7ksr #3  
---  
ZN — zinc ion  
  

> show sel surfaces

> ~select #2

18 models selected  

> select #3

11863 atoms, 12131 bonds, 30 pseudobonds, 1531 residues, 3 models selected  

> color sel bychain

> show sel surfaces

> hide sel cartoons

> hide sel atoms

> ui tool show Matchmaker

> matchmaker #!3 to #2

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 6wkr, chain A (#2) with 7ksr, chain C (#3), sequence alignment
score = 3077.9  
RMSD between 97 pruned atom pairs is 1.020 angstroms; (across all 387 pairs:
44.799)  
  

> matchmaker #3/A to #2/C 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 6wkr, chain C (#2) with 7ksr, chain A (#3), sequence alignment
score = 2277  
RMSD between 349 pruned atom pairs is 1.091 angstroms; (across all 394 pairs:
1.521)  
  

> ~select #3

4 models selected  

> select #2

29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected  

> select #1

2 models selected  

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!3 models

> show #!1 models

> open
> /Users/rachelmccole/Documents/Structures/EZH1-PRC2_nucleosome_emd_23103.map

Opened EZH1-PRC2_nucleosome_emd_23103.map as #4, grid size 300,300,300, pixel
1.35, shown at level 0.00529, step 2, values float32  

> volume #1 level 0.003874

> select #4

2 models selected  

> volume #1 level 0.003586

> volume #4 level -0.001743

> volume #4 level 0.004236

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 2 maps.  

> volume #4 level 0.005819

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 2 maps.  

> volume sel hide

> volume sel show

> volume sel style surface

> volume sel style mesh

> volume sel style image

> transparency #1.1#2.3-20#3.3-6 50

> volume sel showOutlineBox true

> volume sel showOutlineBox false

> volume sel style surface

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 2 maps.  

> hide #!2 models

> hide #!3 models

> fitmap #4 inMap #1

Fit map EZH1-PRC2_nucleosome_emd_23103.map in map emd_11912.map using 29487
points  
correlation = 0.4855, correlation about mean = 0.1661, overlap = 3.144  
steps = 568, shift = 70.9, angle = 34.7 degrees  
  
Position of EZH1-PRC2_nucleosome_emd_23103.map (#4) relative to emd_11912.map
(#1) coordinates:  
Matrix rotation and translation  
0.84419775 0.32644708 0.42516169 -83.97565821  
-0.22664604 0.93615838 -0.26877327 152.53994180  
-0.48575893 0.13053658 0.86429073 143.73245346  
Axis 0.35087482 0.80042883 -0.48600467  
Axis point 234.26564068 0.00000000 302.16015283  
Rotation angle (degrees) 34.68194143  
Shift along axis 22.77777860  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.55926,0.79704,-0.22794,-1.2759,-0.63661,0.2368,-0.73393,465.61,-0.531,0.55557,0.63983,107.47

> view matrix models
> #4,-0.63689,-0.016152,-0.77079,513.6,-0.3147,0.91814,0.24079,81.771,0.7038,0.39592,-0.58984,105.8

> view matrix models
> #4,-0.85478,-0.28591,-0.43313,552.63,-0.39034,0.90417,0.1735,112.7,0.34202,0.31737,-0.88448,251.18

> view matrix models
> #4,-0.4463,-0.89437,-0.030413,517.82,-0.1937,0.063369,0.97901,96.159,-0.87367,0.44282,-0.20152,355.45

> view matrix models
> #4,-0.52045,-0.85108,-0.069295,531.59,-0.16205,0.018766,0.9866,97.246,-0.83837,0.52471,-0.14768,321.56

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> fitmap #3 inMap #4

Fit molecule 7ksr (#3) to map EZH1-PRC2_nucleosome_emd_23103.map (#4) using
11863 atoms  
average map value = 0.003049, steps = 212  
shifted from previous position = 13.7  
rotated from previous position = 21.2 degrees  
atoms outside contour = 9627, contour level = 0.0058188  
  
Position of 7ksr (#3) relative to EZH1-PRC2_nucleosome_emd_23103.map (#4)
coordinates:  
Matrix rotation and translation  
-0.74519065 0.20044992 -0.63601161 397.83389175  
-0.53039189 -0.75625682 0.38309280 367.40588417  
-0.40419719 0.62281257 0.66987251 63.43630377  
Axis 0.29840894 -0.28856817 -0.90976948  
Axis point 250.15880049 126.25331811 0.00000000  
Rotation angle (degrees) 156.31780704  
Shift along axis -45.01686661  
  

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.52045,-0.85108,-0.069295,671.97,-0.16205,0.018766,0.9866,45.214,-0.83837,0.52471,-0.14768,261.37

> select #3

11863 atoms, 12131 bonds, 30 pseudobonds, 1531 residues, 3 models selected  

> view matrix models
> #3,0.86725,0.49615,-0.041448,-33.017,-0.28798,0.5678,0.77115,167.55,0.40614,-0.65684,0.6353,179.23

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.19925,-0.94945,0.24256,383.18,-0.53223,0.31268,0.78674,258.72,-0.82282,0.027666,-0.56763,497.25

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.19925,-0.94945,0.24256,563.07,-0.53223,0.31268,0.78674,103.63,-0.82282,0.027666,-0.56763,400.23

> ui mousemode right translate

> fitmap #3 inMap #4

Fit molecule 7ksr (#3) to map EZH1-PRC2_nucleosome_emd_23103.map (#4) using
11863 atoms  
average map value = 0.01087, steps = 320  
shifted from previous position = 15.6  
rotated from previous position = 39.2 degrees  
atoms outside contour = 3566, contour level = 0.0058188  
  
Position of 7ksr (#3) relative to EZH1-PRC2_nucleosome_emd_23103.map (#4)
coordinates:  
Matrix rotation and translation  
0.99999985 -0.00044289 -0.00040315 0.13680839  
0.00044335 0.99999926 0.00114663 -0.25278920  
0.00040264 -0.00114682 0.99999929 0.08891193  
Axis -0.88639228 -0.31142715 0.34252278  
Axis point 0.00000000 80.99522736 223.79783158  
Rotation angle (degrees) 0.07412346  
Shift along axis -0.01208611  
  

> hide #!4 models

> hide #!3 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> ui tool show Matchmaker

Traceback (most recent call last):  
File
"/private/var/folders/l8/3cj9gj7d5q95z3447bs163900000gn/T/AppTranslocation/F6FE9607-51D3-4214-A456-69D0132176F6/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/l8/3cj9gj7d5q95z3447bs163900000gn/T/AppTranslocation/F6FE9607-51D3-4214-A456-69D0132176F6/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File
"/private/var/folders/l8/3cj9gj7d5q95z3447bs163900000gn/T/AppTranslocation/F6FE9607-51D3-4214-A456-69D0132176F6/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, 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
"/private/var/folders/l8/3cj9gj7d5q95z3447bs163900000gn/T/AppTranslocation/F6FE9607-51D3-4214-A456-69D0132176F6/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> show #!4 models

> hide #!4 models

> matchmaker #!2 to #3

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 7ksr, chain C (#3) with 6wkr, chain A (#2), sequence alignment
score = 3077.9  
RMSD between 97 pruned atom pairs is 1.020 angstroms; (across all 387 pairs:
44.799)  
  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

Traceback (most recent call last):  
File
"/private/var/folders/l8/3cj9gj7d5q95z3447bs163900000gn/T/AppTranslocation/F6FE9607-51D3-4214-A456-69D0132176F6/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/l8/3cj9gj7d5q95z3447bs163900000gn/T/AppTranslocation/F6FE9607-51D3-4214-A456-69D0132176F6/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File
"/private/var/folders/l8/3cj9gj7d5q95z3447bs163900000gn/T/AppTranslocation/F6FE9607-51D3-4214-A456-69D0132176F6/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, 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
"/private/var/folders/l8/3cj9gj7d5q95z3447bs163900000gn/T/AppTranslocation/F6FE9607-51D3-4214-A456-69D0132176F6/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

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

Software:

    System Software Overview:

      System Version: macOS 11.5.2 (20G95)
      Kernel Version: Darwin 20.6.0
      Time since boot: 13 days 3:07

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 2880 x 1800
          UI Looks like: 1440 x 900 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Matchmaker: 'NoneType' object has no attribute 'setChecked'

comment:2 by Eric Pettersen, 4 years ago

Resolution: → duplicate
Status: accepted → closed

Duplicate of #5207

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