ISOLDE: too many hydrogens for SER

[n.aleksandrova@…]

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Hello! 

I am using both ISOLDE and Coot for model building into an EM map. I needed to delete and manually add back a stretch of residues, which I did in Coot. When I opened the new model in ISOLDE, all of the newly added residues were unparametrised, so I went on to fix them using the Unparametrised Residues widget. However, when I tried to fix my SER residues, I got this error:

Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having 5 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (SER). If this template is built into ISOLDE, please report this using Help/Report a bug

Could you help me bypass the error? And additionally, do you know if there is a way to manually rebuild residues in Coot without them being read as unparametrised in ISOLDE?

I have attached the PDB with my model in case you need it. 

Thanks!

Nadia

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/alignments.cxs"

Opened emd_0149.map as #5, grid size 480,480,480, pixel 1.14, shown at level
0.0281, step 1, values float32  
Opened Zflip_J248.mrc as #1, grid size 560,560,560, pixel 1.5, shown at level
0.422, step 1, values float32  
Log from Fri Aug 30 13:07:45 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6H6E

6h6e title:  
PTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1,
TcdB2, TccC3) [more info...]  
  
Chain information for 6h6e #1  
---  
Chain | Description | UniProt  
A B C D E | TcdA1 | Q9RN43_PHOLU 1-2516  
F | TcdB2,TccC3 | Q8GF99_PHOLU 1-1479, Q8GF97_PHOLU 1480-2439  
  

> select add #1

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> select subtract #1

Nothing selected  

> select /A/B/C/D/E

95805 atoms, 97870 bonds, 10 pseudobonds, 12085 residues, 2 models selected  

> hide sel cartoons

> open
> /Users/nadia/Documents/Phenix/SepABC_holotoxin/SepBC_AF_relativetoJ200.pdb

Chain information for SepBC_AF_relativetoJ200.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select add #2

132523 atoms, 135055 bonds, 10 pseudobonds, 14506 residues, 3 models selected  

> select subtract #2

95805 atoms, 97870 bonds, 10 pseudobonds, 12085 residues, 2 models selected  

> select add #1

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,146.64,0,1,0,-21.108,0,0,1,190.53

> view matrix models #1,1,0,0,71.094,0,1,0,131.43,0,0,1,222.11

> view matrix models #1,1,0,0,144.96,0,1,0,161.64,0,0,1,236.07

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.33483,-0.86541,-0.37277,870.71,0.89871,-0.1744,-0.40237,373.48,0.2832,-0.46974,0.83615,342.56

> ui tool show Matchmaker

> matchmaker #!1 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 SepBC_AF_relativetoJ200.pdb, chain A (#2) with 6h6e, chain F (#1),
sequence alignment score = 4268  
RMSD between 1219 pruned atom pairs is 0.964 angstroms; (across all 1404
pairs: 1.943)  
  

> matchmaker #!1 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 SepBC_AF_relativetoJ200.pdb, chain A (#2) with 6h6e, chain F (#1),
sequence alignment score = 4268  
RMSD between 1219 pruned atom pairs is 0.964 angstroms; (across all 1404
pairs: 1.943)  
  

> select subtract #1

Nothing selected  

> hide #!1 models

> open /Users/nadia/Documents/Phenix/SepABC_holotoxin/J200_C1_1024box.mrc

Opened J200_C1_1024box.mrc as #3, grid size 560,560,560, pixel 1.5, shown at
level 0.159, step 4, values float32  

> volume #3 step 1

> volume #3 level 0.3476

> color #3 #b2b2b2a3 models

> vop zflip #3

> volume zflip #3

Expected a density maps specifier or a keyword  

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Best
> maps/ZFlip_J200.mrc"

Opened ZFlip_J200.mrc as #4, grid size 560,560,560, pixel 1.5, shown at level
0.159, step 4, values float32  

> hide #!3 models

> volume #4 step 1

> volume #4 level 0.3425

> select add #4

2 models selected  

> view matrix models
> #4,-0.42634,0.87115,0.24358,139.75,0.87834,0.33432,0.34167,-243.27,0.21621,0.35962,-0.9077,577.01

> volume #4 level 0.3694

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.42634,0.87115,0.24358,193.75,0.87834,0.33432,0.34167,-173.36,0.21621,0.35962,-0.9077,584.11

> color #4 #ffffb2bd models

> color #4 #f6ffe6bd models

> color #4 #b3baa8bd models

> select subtract #4

Nothing selected  

> select add #2

36718 atoms, 37185 bonds, 2421 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.83818,0.15414,-0.52315,1016.2,0.28872,-0.6884,-0.6654,985.63,-0.4627,-0.70877,0.5325,770.24

> view matrix models
> #2,-0.76825,-0.1564,-0.62075,1175.3,0.57503,-0.59473,-0.56182,765.19,-0.28132,-0.78856,0.54684,719.47

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.76825,-0.1564,-0.62075,1188.9,0.57503,-0.59473,-0.56182,762.97,-0.28132,-0.78856,0.54684,721.51

> view matrix models
> #2,-0.76825,-0.1564,-0.62075,1189.2,0.57503,-0.59473,-0.56182,757.21,-0.28132,-0.78856,0.54684,722.7

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.81029,-0.14021,-0.56901,1168.3,0.56029,-0.46996,-0.68207,785.25,-0.17178,-0.87148,0.45936,765.18

> ui tool show "Fit in Map"

> fitmap #2 inMap #4

Fit molecule SepBC_AF_relativetoJ200.pdb (#2) to map ZFlip_J200.mrc (#4) using
36718 atoms  
average map value = 0.2226, steps = 68  
shifted from previous position = 4.71  
rotated from previous position = 5.5 degrees  
atoms outside contour = 30977, contour level = 0.36942  
  
Position of SepBC_AF_relativetoJ200.pdb (#2) relative to ZFlip_J200.mrc (#4)
coordinates:  
Matrix rotation and translation  
0.77669055 -0.58810260 -0.22558181 472.08269052  
-0.58309225 -0.53585147 -0.61062808 1247.62613833  
0.23823361 0.60580407 -0.75910883 341.66309869  
Axis 0.93437531 -0.35626951 0.00384859  
Axis point 0.00000000 646.15954159 416.75486137  
Rotation angle (degrees) 139.38798929  
Shift along axis -2.07381748  
  

> select subtract #2

Nothing selected  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #!3 models

> hide #!4 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #!4 models

> hide #!4 models

> show #2 models

> hide #!3 models

> show #!4 models

> volume #4 level 0.4083

> hide #2 models

> show #!1 models

> hide #!4 models

> open /Users/nadia/Downloads/emd_0149.map

Opened emd_0149.map as #5, grid size 480,480,480, pixel 1.14, shown at level
0.00684, step 2, values float32  

> volume #5 step 1

> show #2 models

> hide #2 models

> select add #1

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 2 models selected  

> view matrix models
> #1,-0.34248,0.64498,0.68316,83.557,0.93883,0.20697,0.27524,-1.4556,0.036131,0.73564,-0.67641,668.64

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.34248,0.64498,0.68316,-96.458,0.93883,0.20697,0.27524,-7.4362,0.036131,0.73564,-0.67641,444.96

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.78474,-0.60782,-0.12141,225.78,-0.5963,-0.68687,-0.4155,900.1,0.16916,0.39845,-0.90146,581.04

> view matrix models
> #1,-0.71658,0.68194,0.14654,198.16,0.69576,0.68395,0.21938,-43.608,0.049379,0.25917,-0.96457,673.28

> view matrix models
> #1,0.73357,-0.61315,-0.29313,305.93,-0.57862,-0.78971,0.20385,687.73,-0.35648,0.020074,-0.93409,833.38

> view matrix models
> #1,0.60972,-0.71258,-0.34708,385.52,-0.7151,-0.68341,0.14687,718.8,-0.34186,0.15865,-0.92626,790.7

> view matrix models
> #1,0.72766,-0.57187,-0.37878,329.24,-0.60716,-0.79393,0.032264,761.41,-0.31917,0.2065,-0.92493,771.7

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.72766,-0.57187,-0.37878,362.65,-0.60716,-0.79393,0.032264,609.01,-0.31917,0.2065,-0.92493,757.95

> fitmap #1 inMap #5

Fit molecule 6h6e (#1) to map emd_0149.map (#5) using 112922 atoms  
average map value = 0.003412, steps = 2000  
shifted from previous position = 23.8  
rotated from previous position = 9.62 degrees  
atoms outside contour = 103032, contour level = 0.0068401  
  
Position of 6h6e (#1) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
0.71174946 -0.50235886 -0.49096665 391.98002823  
-0.52680341 -0.84408754 0.09997179 586.52122978  
-0.46464056 0.18748805 -0.86542322 777.44936479  
Axis 0.92509138 -0.27828021 -0.25839132  
Axis point 0.00000000 342.27839315 450.96386324  
Rotation angle (degrees) 177.28881716  
Shift along axis -1.48607230  
  

> volume #5 color #b2ffff80

> fitmap #1 inMap #5

Fit molecule 6h6e (#1) to map emd_0149.map (#5) using 112922 atoms  
average map value = 0.003412, steps = 2000  
shifted from previous position = 23.8  
rotated from previous position = 9.62 degrees  
atoms outside contour = 103032, contour level = 0.0068401  
  
Position of 6h6e (#1) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
0.71174946 -0.50235886 -0.49096665 391.98002823  
-0.52680341 -0.84408754 0.09997179 586.52122978  
-0.46464056 0.18748805 -0.86542322 777.44936479  
Axis 0.92509138 -0.27828021 -0.25839132  
Axis point 0.00000000 342.27839315 450.96386324  
Rotation angle (degrees) 177.28881716  
Shift along axis -1.48607230  
  

> fitmap #1 inMap #5

Fit molecule 6h6e (#1) to map emd_0149.map (#5) using 112922 atoms  
average map value = 0.003429, steps = 2000  
shifted from previous position = 0.642  
rotated from previous position = 0.31 degrees  
atoms outside contour = 103064, contour level = 0.0068401  
  
Position of 6h6e (#1) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
0.70965345 -0.50660373 -0.48963723 393.22237380  
-0.52918838 -0.84207268 0.10427475 585.29900132  
-0.46513613 0.18511140 -0.86566859 778.71754944  
Axis 0.92453087 -0.28021979 -0.25830126  
Axis point 0.00000000 343.03602215 451.20638056  
Rotation angle (degrees) 177.49436397  
Shift along axis -1.60986832  
  

> volume #5 level 0.02903

> select subtract #1

Nothing selected  

> select add #1

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 2 models selected  

> hide #!1 models

> select add #2

149640 atoms, 152593 bonds, 11 pseudobonds, 16652 residues, 3 models selected  

> select subtract #2

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 2 models selected  

> show #!1 models

> view matrix models
> #1,0.70965,-0.5066,-0.48964,400.14,-0.52919,-0.84207,0.10427,587.2,-0.46514,0.18511,-0.86567,785.34

> view matrix models
> #1,0.70965,-0.5066,-0.48964,392.63,-0.52919,-0.84207,0.10427,638.07,-0.46514,0.18511,-0.86567,784.26

> view matrix models
> #1,0.70965,-0.5066,-0.48964,398.55,-0.52919,-0.84207,0.10427,589.35,-0.46514,0.18511,-0.86567,789.91

> view matrix models
> #1,0.70965,-0.5066,-0.48964,310.96,-0.52919,-0.84207,0.10427,559.94,-0.46514,0.18511,-0.86567,771.3

> view matrix models
> #1,0.70965,-0.5066,-0.48964,377.88,-0.52919,-0.84207,0.10427,603.82,-0.46514,0.18511,-0.86567,795.28

> view matrix models
> #1,0.70965,-0.5066,-0.48964,401.08,-0.52919,-0.84207,0.10427,589.38,-0.46514,0.18511,-0.86567,779.43

> view matrix models
> #1,0.70965,-0.5066,-0.48964,394.61,-0.52919,-0.84207,0.10427,586.78,-0.46514,0.18511,-0.86567,779.53

> fitmap #1 inMap #5

Fit molecule 6h6e (#1) to map emd_0149.map (#5) using 112922 atoms  
average map value = 0.003416, steps = 2000  
shifted from previous position = 3.2  
rotated from previous position = 0.195 degrees  
atoms outside contour = 110597, contour level = 0.029032  
  
Position of 6h6e (#1) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
0.71162881 -0.50608804 -0.48729796 391.40973208  
-0.52765536 -0.84295704 0.10489624 584.39605314  
-0.46385799 0.18247819 -0.86691259 778.83936186  
Axis 0.92506811 -0.27949242 -0.25716334  
Axis point 0.00000000 342.50114167 450.44510725  
Rotation angle (degrees) 177.59670552  
Shift along axis -1.54253967  
  

> hide #!1 models

> show #!1 models

> view matrix models
> #1,0.71163,-0.50609,-0.4873,384.88,-0.52766,-0.84296,0.1049,486.49,-0.46386,0.18248,-0.86691,783.37

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.32071,-0.71163,-0.62508,595.88,-0.63021,-0.65299,0.42005,346.1,-0.70709,0.25922,-0.6579,750.42

> view matrix models
> #1,-0.78039,-0.46699,0.41582,437.45,-0.24755,0.84141,0.48036,-166.04,-0.5742,0.27194,-0.77223,754.37

> view matrix models
> #1,-0.77535,-0.46735,0.42475,432.8,-0.22217,0.83144,0.50927,-181.26,-0.59116,0.30049,-0.74849,742.62

> view matrix models
> #1,0.13599,0.97173,-0.19299,48.082,0.9617,-0.17628,-0.20989,30.088,-0.23798,-0.15706,-0.95849,844.45

> view matrix models
> #1,0.15096,0.97502,-0.16296,31.83,0.98278,-0.16579,-0.081563,-26.837,-0.10654,-0.14785,-0.98325,815.85

> view matrix models
> #1,0.18511,0.98137,-0.051405,-21.231,0.97573,-0.18977,-0.10924,-8.2778,-0.11696,-0.029936,-0.99269,791.8

> view matrix models
> #1,0.18686,0.98125,-0.047186,-23.267,0.97739,-0.19053,-0.091656,-15.177,-0.098928,-0.028993,-0.99467,787.42

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.18686,0.98125,-0.047186,0.13387,0.97739,-0.19053,-0.091656,75.161,-0.098928,-0.028993,-0.99467,800.54

> view matrix models
> #1,0.18686,0.98125,-0.047186,-143.13,0.97739,-0.19053,-0.091656,2.2573,-0.098928,-0.028993,-0.99467,797.28

> view matrix models
> #1,0.18686,0.98125,-0.047186,-126.57,0.97739,-0.19053,-0.091656,4.2934,-0.098928,-0.028993,-0.99467,827.07

> view matrix models
> #1,0.18686,0.98125,-0.047186,-126.55,0.97739,-0.19053,-0.091656,4.875,-0.098928,-0.028993,-0.99467,824.44

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.88373,0.46596,0.043604,-216.59,-0.46702,0.88407,0.017967,77.23,-0.030177,-0.036242,0.99889,54.108

> view matrix models
> #1,0.99742,-0.0037861,-0.071729,-82.535,0.0036031,0.99999,-0.0026806,-72.332,0.071739,0.0024152,0.99742,17.086

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.99742,-0.0037861,-0.071729,26.105,0.0036031,0.99999,-0.0026806,-7.4536,0.071739,0.0024152,0.99742,-24.619

> view matrix models
> #1,0.99742,-0.0037861,-0.071729,26.575,0.0036031,0.99999,-0.0026806,-0.29159,0.071739,0.0024152,0.99742,-23.559

> view matrix models
> #1,0.99742,-0.0037861,-0.071729,29.608,0.0036031,0.99999,-0.0026806,-2.329,0.071739,0.0024152,0.99742,-19.144

> view matrix models
> #1,0.99742,-0.0037861,-0.071729,26.906,0.0036031,0.99999,-0.0026806,-2.509,0.071739,0.0024152,0.99742,-18.601

> view matrix models
> #1,0.99742,-0.0037861,-0.071729,25.392,0.0036031,0.99999,-0.0026806,-0.40658,0.071739,0.0024152,0.99742,-18.129

> fitmap #1 inMap #5

Fit molecule 6h6e (#1) to map emd_0149.map (#5) using 112922 atoms  
average map value = 0.03076, steps = 120  
shifted from previous position = 8.77  
rotated from previous position = 4.12 degrees  
atoms outside contour = 52774, contour level = 0.029032  
  
Position of 6h6e (#1) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00006575 -0.00000502 0.01820303  
0.00006575 0.99999999 -0.00006422 0.00800605  
0.00000502 0.00006422 0.99999998 -0.01919741  
Axis 0.69770496 -0.05456957 0.71430382  
Axis point -120.54821677 292.24580919 0.00000000  
Rotation angle (degrees) 0.00527375  
Shift along axis -0.00144933  
  

> select subtract #1

Nothing selected  

> volume #5 level 0.01697

> save /Users/nadia/Desktop/PTC3_RelativetoMap.pdb models #1

> save /Users/nadia/Desktop/PTC3_RelativetoMap.pdb models #1 relModel #5

> open /Users/nadia/Desktop/PTC3_RelativetoMap.pdb

Chain information for PTC3_RelativetoMap.pdb #6  
---  
Chain | Description  
A B C D E | No description available  
F | No description available  
  

> select add #6

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 2 models selected  

> select subtract #6

Nothing selected  

> select add #6

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> close #1

> select subtract #6

Nothing selected  

> select #6/A

19161 atoms, 19574 bonds, 2 pseudobonds, 2417 residues, 2 models selected  

> select #6/A

19161 atoms, 19574 bonds, 2 pseudobonds, 2417 residues, 2 models selected  

> hide sel cartoons

> select #6/A

19161 atoms, 19574 bonds, 2 pseudobonds, 2417 residues, 2 models selected  

> select #6/B

19161 atoms, 19574 bonds, 2 pseudobonds, 2417 residues, 2 models selected  

> hide sel cartoons

> select #6/C

19161 atoms, 19574 bonds, 2 pseudobonds, 2417 residues, 2 models selected  

> hide sel cartoons

> select #6/D

19161 atoms, 19574 bonds, 2 pseudobonds, 2417 residues, 2 models selected  

> hide sel cartoons

> select #6/E

19161 atoms, 19574 bonds, 2 pseudobonds, 2417 residues, 2 models selected  

> hide sel cartoons

> show #!3 models

> select add #3

19161 atoms, 19574 bonds, 2 pseudobonds, 2417 residues, 4 models selected  

> view matrix models
> #3,1,0,0,12.719,0,1,0,42.966,0,0,1,-187.03,#6,1,0,0,12.719,0,1,0,42.966,0,0,1,-187.03

> view matrix models
> #3,1,0,0,-133.19,0,1,0,-127.3,0,0,1,-218.97,#6,1,0,0,-133.19,0,1,0,-127.3,0,0,1,-218.97

> undo

[Repeated 1 time(s)]

> select add #6

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 4 models selected  

> select subtract #6

2 models selected  

> view matrix models #3,1,0,0,-119.97,0,1,0,-165.99,0,0,1,-257.63

> view matrix models #3,1,0,0,-140.34,0,1,0,-149.29,0,0,1,-237.59

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.9643,-0.077851,0.25312,-196.21,0.05667,0.99433,0.089934,-207.14,-0.25868,-0.07238,0.96325,-84.904

> view matrix models
> #3,0.99623,0.020943,-0.084232,-113.18,-0.023182,0.9994,-0.025692,-128.93,0.083643,0.027548,0.99611,-282.26

> view matrix models
> #3,0.99983,0.0045837,-0.01764,-135,-0.0046823,0.99997,-0.0055493,-145.07,0.017614,0.005631,0.99983,-247.19

> view matrix models
> #3,0.99881,-0.012735,0.047019,-153.71,0.012031,0.99981,0.015233,-160.42,-0.047204,-0.014649,0.99878,-211.36

> view matrix models
> #3,0.8986,-0.43809,-0.024369,90.04,0.43867,0.89815,0.029763,-303.76,0.0088483,-0.037435,0.99926,-225.78

> view matrix models
> #3,-0.26202,-0.94636,-0.18906,849.59,0.96444,-0.24972,-0.086609,-10.48,0.034752,-0.20503,0.97814,-159.98

> view matrix models
> #3,-0.16789,-0.96753,-0.18894,818.7,0.98562,-0.16099,-0.051432,-69.653,0.019346,-0.19486,0.98064,-158.67

> view matrix models
> #3,-0.17086,-0.9692,-0.17736,815.94,0.98391,-0.15827,-0.082938,-57.286,0.052313,-0.18867,0.98065,-175

> view matrix models
> #3,-0.40053,-0.91064,-0.10151,857.67,0.88885,-0.35925,-0.28441,145.78,0.22253,-0.20414,0.95331,-228.97

> view matrix models
> #3,-0.72556,-0.68816,0.0018118,861.63,0.6736,-0.71074,-0.20276,345.76,0.14082,-0.14589,0.97923,-228.9

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.72556,-0.68816,0.0018118,880.1,0.6736,-0.71074,-0.20276,378.82,0.14082,-0.14589,0.97923,-211.51

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.71565,-0.69786,0.028883,868.93,0.68588,-0.70998,-0.15967,355.93,0.13193,-0.094457,0.98675,-231.73

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.71565,-0.69786,0.028883,863.22,0.68588,-0.70998,-0.15967,346.01,0.13193,-0.094457,0.98675,-236.12

> view matrix models
> #3,-0.71565,-0.69786,0.028883,843.48,0.68588,-0.70998,-0.15967,361.96,0.13193,-0.094457,0.98675,-243.7

> hide #!3 models

> select subtract #3

Nothing selected  

> show #!4 models

> select add #4

2 models selected  

> view matrix models
> #4,-0.42634,0.87115,0.24358,254.57,0.87834,0.33432,0.34167,-295.85,0.21621,0.35962,-0.9077,433.85

> view matrix models
> #4,-0.42634,0.87115,0.24358,28.386,0.87834,0.33432,0.34167,-352.34,0.21621,0.35962,-0.9077,339.16

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.31084,0.93512,0.17007,-12.696,0.94212,0.32679,-0.074914,-209.59,-0.12563,0.13694,-0.98258,589.43

> view matrix models
> #4,-0.29324,0.94526,-0.14315,98.845,0.95235,0.27566,-0.13056,-169.43,-0.083953,-0.17461,-0.98105,708.63

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.29324,0.94526,-0.14315,43.918,0.95235,0.27566,-0.13056,-180.73,-0.083953,-0.17461,-0.98105,699.83

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.79275,0.59601,-0.12778,371.22,0.60934,0.76931,-0.19202,-245.63,-0.016142,-0.23009,-0.97304,696.03

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.79275,0.59601,-0.12778,371.79,0.60934,0.76931,-0.19202,-243.39,-0.016142,-0.23009,-0.97304,702.22

> view matrix models
> #4,-0.79275,0.59601,-0.12778,371.39,0.60934,0.76931,-0.19202,-247.1,-0.016142,-0.23009,-0.97304,726.01

> view matrix models
> #4,-0.79275,0.59601,-0.12778,392.15,0.60934,0.76931,-0.19202,-255.49,-0.016142,-0.23009,-0.97304,697.15

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.78522,0.6191,0.011872,324.85,0.61873,0.78371,0.054553,-361.47,0.02447,0.050181,-0.99844,570.84

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.78522,0.6191,0.011872,337.22,0.61873,0.78371,0.054553,-340.12,0.02447,0.050181,-0.99844,574.04

> fitmap #4 inMap #5

Fit map ZFlip_J200.mrc in map emd_0149.map using 212364 points  
correlation = 0.4202, correlation about mean = 0.02371, overlap = 1287  
steps = 288, shift = 3.27, angle = 4.53 degrees  
  
Position of ZFlip_J200.mrc (#4) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
-0.73666555 0.67625558 -0.00149248 295.80389593  
0.67584230 0.73628907 0.03340028 -336.67383162  
0.02368602 0.02359615 -0.99944092 587.36116869  
Axis -0.36280548 -0.93173939 -0.01529367  
Axis point 211.30940537 0.00000000 297.77576771  
Rotation angle (degrees) 179.22582131  
Shift along axis 197.39008881  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.56292,0.82612,0.025634,156.98,0.82642,0.56212,0.032265,-315.63,0.012246,0.039347,-0.99915,584.59

> volume #4 color #b3baa8

> fitmap #4 inMap #5

Fit map ZFlip_J200.mrc in map emd_0149.map using 212364 points  
correlation = 0.5509, correlation about mean = 0.1223, overlap = 1959  
steps = 552, shift = 16.7, angle = 27.4 degrees  
  
Position of ZFlip_J200.mrc (#4) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
-0.11992069 0.99271029 0.01205329 -101.60988327  
0.99277556 0.11986248 0.00544404 -198.65615638  
0.00395961 0.01261906 -0.99991252 609.96027267  
Axis 0.66335108 0.74828399 0.00603461  
Axis point 38.35347785 0.00000000 305.71022546  
Rotation angle (degrees) 179.69013357  
Shift along axis -212.37337208  
  

> undo

[Repeated 2 time(s)]

> fitmap #4 inMap #5

Fit map ZFlip_J200.mrc in map emd_0149.map using 212364 points  
correlation = 0.5579, correlation about mean = 0.1059, overlap = 2014  
steps = 676, shift = 32.3, angle = 30 degrees  
  
Position of ZFlip_J200.mrc (#4) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
-0.98120065 0.19297496 -0.00243413 602.08229895  
0.19291409 0.98108955 0.01572961 -229.62080980  
0.00542351 0.01496432 -0.99987330 608.10401979  
Axis -0.09693299 -0.99526105 -0.00770954  
Axis point 311.61880483 0.00000000 305.55428144  
Rotation angle (degrees) 179.77382290  
Shift along axis 165.48280360  
  

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.9812,0.19297,-0.0024341,603.65,0.19291,0.98109,0.01573,-230.04,0.0054235,0.014964,-0.99987,601.09

> fitmap #4 inMap #5

Fit map ZFlip_J200.mrc in map emd_0149.map using 212364 points  
correlation = 0.5579, correlation about mean = 0.1059, overlap = 2014  
steps = 88, shift = 7.2, angle = 0.00222 degrees  
  
Position of ZFlip_J200.mrc (#4) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
-0.98120400 0.19295817 -0.00241153 602.08192744  
0.19289750 0.98109239 0.01575610 -229.62218214  
0.00540620 0.01499477 -0.99987294 608.09897717  
Axis -0.09692454 -0.99526176 -0.00772384  
Axis point 311.62077505 0.00000000 305.55029839  
Rotation angle (degrees) 179.77497164  
Shift along axis 165.48080383  
  

> view matrix models
> #4,-0.9812,0.19296,-0.0024115,602.33,0.1929,0.98109,0.015756,-230.66,0.0054062,0.014995,-0.99987,598.65

> view matrix models
> #4,-0.9812,0.19296,-0.0024115,600.39,0.1929,0.98109,0.015756,-228.84,0.0054062,0.014995,-0.99987,602.17

> select subtract #4

Nothing selected  

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!6 models

> show #!5 models

> show #!4 models

> hide #!5 models

> volume #4 level 0.325

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> select add #4

2 models selected  

> view matrix models
> #4,-0.9812,0.19296,-0.0024115,600.64,0.1929,0.98109,0.015756,-228.2,0.0054062,0.014995,-0.99987,601.22

> select subtract #4

Nothing selected  

> hide #!4 models

> volume #5 level 0.02807

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!6 models

> hide #!5 models

> hide #!4 models

> show #2 models

> hide #2 models

> show #2 models

> select add #2

36718 atoms, 37185 bonds, 2421 residues, 1 model selected  

> view matrix models
> #2,-0.78107,-0.068513,-0.62068,1093.5,0.56866,-0.48872,-0.66165,547.82,-0.258,-0.86975,0.42068,585.26

> view matrix models
> #2,-0.78107,-0.068513,-0.62068,987.73,0.56866,-0.48872,-0.66165,584.22,-0.258,-0.86975,0.42068,575.09

> view matrix models
> #2,-0.78107,-0.068513,-0.62068,983.49,0.56866,-0.48872,-0.66165,573.58,-0.258,-0.86975,0.42068,562.65

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.92373,0.38155,0.03375,456.21,0.29773,0.65979,0.68995,-615.79,0.24098,0.64738,-0.72307,428.44

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.92373,0.38155,0.03375,471.04,0.29773,0.65979,0.68995,-558,0.24098,0.64738,-0.72307,455.19

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.82347,0.47761,-0.30626,597.78,0.21208,0.75978,0.61462,-517.86,0.52623,0.44116,-0.72695,424.88

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.82347,0.47761,-0.30626,602.51,0.21208,0.75978,0.61462,-517.41,0.52623,0.44116,-0.72695,426.5

> ui tool show Matchmaker

> matchmaker #2 to #6

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 PTC3_RelativetoMap.pdb, chain F (#6) with
SepBC_AF_relativetoJ200.pdb, chain A (#2), sequence alignment score = 4268  
RMSD between 1218 pruned atom pairs is 0.963 angstroms; (across all 1404
pairs: 1.943)  
  

> select subtract #2

Nothing selected  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> show #!5 models

> hide #!6 models

> color #5 #fffaf480 models

> color #5 #fbfeff80 models

> volume #5 color #fbfeff9e

> volume #5 color #fbfeff6e

> volume #4 color #b2b6aaa7

> volume #4 color #b0b0b69d

> volume #4 color #b0b0b69e

> show #!6 models

> hide #!6 models

> volume #4 level 0.4027

> volume #4 level 0.3306

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Best
> maps/J248_LocalRef_Sharpened_1024.mrc"

Opened J248_LocalRef_Sharpened_1024.mrc as #1, grid size 560,560,560, pixel
1.5, shown at level 0.0422, step 4, values float32  

> hide #!1 models

> show #!1 models

> volume #1 step 1

> volume #1 level 0.1102

> volume #1 level 0.2341

> volume #1 level 0.2777

> select add #1

2 models selected  

> view matrix models #1,1,0,0,-226.76,0,1,0,-111.21,0,0,1,-184.51

> view matrix models #1,1,0,0,-157.24,0,1,0,-140.94,0,0,1,-241.59

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.19659,-0.94828,0.24925,621.08,0.97879,-0.20474,-0.0069489,-46.167,0.057622,0.2426,0.96841,-351.81

> view matrix models
> #1,-0.19251,-0.98103,0.022976,743.98,0.97412,-0.18823,0.12516,-115.87,-0.11846,0.046476,0.99187,-207.14

> view matrix models
> #1,-0.6492,-0.7555,0.08808,810.15,0.73464,-0.65281,-0.18479,331.19,0.19711,-0.055255,0.97882,-291.14

> view matrix models
> #1,-0.63575,-0.76985,0.056114,826.16,0.76828,-0.63813,-0.050402,245,0.07461,0.011068,0.99715,-276.25

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.63575,-0.76985,0.056114,825.98,0.76828,-0.63813,-0.050402,232.48,0.07461,0.011068,0.99715,-259.21

> volume #1 level 0.3301

> hide #!4 models

> hide #2 models

> show #!5 models

> fitmap #1 inMap #5

Fit map J248_LocalRef_Sharpened_1024.mrc in map emd_0149.map using 86943
points  
correlation = 0.5413, correlation about mean = 0.07846, overlap = 406.4  
steps = 168, shift = 10.9, angle = 4.74 degrees  
  
Position of J248_LocalRef_Sharpened_1024.mrc (#1) relative to emd_0149.map
(#5) coordinates:  
Matrix rotation and translation  
-0.60037798 -0.79964731 -0.01050991 864.40397028  
0.79941041 -0.59973295 -0.03554402 204.52158688  
0.02211954 -0.02974158 0.99931284 -223.98599110  
Axis 0.00362788 -0.02040105 0.99978529  
Axis point 382.64584066 316.19211421 0.00000000  
Rotation angle (degrees) 126.89848221  
Shift along axis -224.97439741  
  

> view matrix models
> #1,-0.60038,-0.79965,-0.01051,864.35,0.79941,-0.59973,-0.035544,204.59,0.02212,-0.029742,0.99931,-223.96

> view matrix models
> #1,-0.60038,-0.79965,-0.01051,952.42,0.79941,-0.59973,-0.035544,94.496,0.02212,-0.029742,0.99931,-240.34

> show #2 models

> hide #!5 models

> show #!5 models

> hide #2 models

> show #2 models

> close #1

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Best
> maps/Zflip_J248.mrc"

Opened Zflip_J248.mrc as #1, grid size 560,560,560, pixel 1.5, shown at level
0.0422, step 4, values float32  

> volume #1 step 1

> volume #1 level 0.1765

> volume #1 level 0.2794

> select add #1

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.64972,-0.75388,0.097593,976.21,-0.72473,0.65305,0.21976,373.92,-0.22941,0.072056,-0.97066,751.94

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.64972,-0.75388,0.097593,773.78,-0.72473,0.65305,0.21976,303.05,-0.22941,0.072056,-0.97066,686.8

> view matrix models
> #1,-0.64972,-0.75388,0.097593,828.66,-0.72473,0.65305,0.21976,224,-0.22941,0.072056,-0.97066,664.96

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.86912,-0.19645,0.45392,564.1,-0.18011,0.98043,0.079461,-93.496,-0.46065,-0.012695,-0.88749,768.88

> view matrix models
> #1,-0.60104,-0.79664,0.064079,837.69,-0.76215,0.54719,-0.34599,480.8,0.24057,-0.25679,-0.93605,592.42

> view matrix models
> #1,-0.81247,0.46818,0.34742,299.42,0.51998,0.85141,0.06866,-330.73,-0.26365,0.23643,-0.93519,598.32

> view matrix models
> #1,-0.82539,0.54715,0.13917,344.28,0.56441,0.79376,0.22671,-380.31,0.013573,0.26567,-0.96397,479.32

> view matrix models
> #1,-0.81396,0.58089,-0.0048364,375.44,0.58041,0.81358,0.034858,-328.61,0.024184,0.025566,-0.99938,587.55

> view matrix models
> #1,-0.85144,0.52442,-0.0061539,415.3,0.52424,0.85137,0.018557,-315.07,0.014971,0.012574,-0.99981,597.01

> fitmap #1 inMap #5

Fit map Zflip_J248.mrc in map emd_0149.map using 173804 points  
correlation = 0.6458, correlation about mean = 0.2227, overlap = 967.2  
steps = 188, shift = 7.21, angle = 20.1 degrees  
  
Position of Zflip_J248.mrc (#1) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
-0.97978281 0.19999196 -0.00537162 599.45197579  
0.19989815 0.97971055 0.01442081 -231.40020642  
0.00814668 0.01305548 -0.99988158 604.70005009  
Axis -0.10048472 -0.99491465 -0.00690417  
Axis point 310.37725119 0.00000000 304.20470467  
Rotation angle (degrees) 179.61074662  
Shift along axis 165.81274297  
  

> select subtract #1

Nothing selected  

> hide #!5 models

> volume #1 level 0.3544

> show #!5 models

> hide #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> ui mousemode right "translate selected models"

> select add #1

2 models selected  

> view matrix models
> #1,-0.97978,0.19999,-0.0053716,598.68,0.1999,0.97971,0.014421,-231.34,0.0081467,0.013055,-0.99988,601.3

> view matrix models
> #1,-0.97978,0.19999,-0.0053716,598.64,0.1999,0.97971,0.014421,-232.35,0.0081467,0.013055,-0.99988,598.33

> fitmap #1 inMap #5

Fit map Zflip_J248.mrc in map emd_0149.map using 65562 points  
correlation = 0.7473, correlation about mean = 0.2437, overlap = 572  
steps = 68, shift = 5.08, angle = 0.494 degrees  
  
Position of Zflip_J248.mrc (#1) relative to emd_0149.map (#5) coordinates:  
Matrix rotation and translation  
-0.97807425 0.20820899 -0.00444593 594.86969835  
0.20813888 0.97801655 0.01272129 -233.51562023  
0.00699688 0.01151699 -0.99990919 604.39080957  
Axis -0.10466468 -0.99448890 -0.00609309  
Axis point 308.84741800 0.00000000 303.79626984  
Rotation angle (degrees) 179.67036923  
Shift along axis 166.28423799  
  

> view matrix models
> #1,-0.97807,0.20821,-0.0044459,594.86,0.20814,0.97802,0.012721,-234.63,0.0069969,0.011517,-0.99991,600.65

> view matrix models
> #1,-0.97807,0.20821,-0.0044459,594.61,0.20814,0.97802,0.012721,-234.11,0.0069969,0.011517,-0.99991,599.56

> view matrix models
> #1,-0.97807,0.20821,-0.0044459,593.82,0.20814,0.97802,0.012721,-233.98,0.0069969,0.011517,-0.99991,597.32

> select subtract #1

Nothing selected  

> show #2 models

> hide #!5 models

> color #1 #c196c3ff models

> color #1 #c196c394 models

> color #1 #c3bec294 models

> volume #1 level 0.3841

> select add #2

36718 atoms, 37185 bonds, 2421 residues, 1 model selected  

> view matrix models
> #2,-0.70279,0.65495,-0.27773,463.15,0.37525,0.67296,0.63743,-563.98,0.60438,0.34376,-0.71872,422.01

> volume #1 level 0.4225

> save "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/SepBC_Rel.ativetoZflipJ248.pdb" models #2 relModel #1

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Best
> maps/Zflip_J248.mrc"

Opened Zflip_J248.mrc as #7, grid size 560,560,560, pixel 1.5, shown at level
0.0422, step 4, values float32  

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/SepBC_Rel.ativetoZflipJ248.pdb"

Chain information for SepBC_Rel.ativetoZflipJ248.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!7 models

> close #7

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #!1 models

> show #!1 models

> hide #8 models

> show #8 models

> hide #!1 models

> show #!1 models

> hide #8 models

> close #8

> select subtract #2

Nothing selected  

> save "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/Zflip_248.mrc" models #1

> save "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/SepBC_Rel.ativetoZflipJ248.pdb" models #2 relModel #1

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/Zflip_248.mrc"

Opened Zflip_248.mrc as #7, grid size 560,560,560, pixel 1.5, shown at level
0.0422, step 4, values float32  

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/SepBC_Rel.ativetoZflipJ248.pdb"

Chain information for SepBC_Rel.ativetoZflipJ248.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1 models

> hide #2 models

> hide #!7 models

> show #!7 models

> close #3

> close #4

> close #7

> show #!5 models

> show #!6 models

> show #2 models

> show #!1 models

> hide #8 models

> close #8

> hide #!5 models

> hide #2 models

> select add #6

112922 atoms, 115408 bonds, 11 pseudobonds, 14231 residues, 2 models selected  

> hide #!6 models

> select subtract #6

Nothing selected  

> show #2 models

> save "/Users/nadia/Desktop/SepABC holotoxin processing/Model building/1.mrc"
> models #1

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model building/1.mrc"

Opened 1.mrc as #3, grid size 560,560,560, pixel 1.5, shown at level 0.0422,
step 4, values float32  

> save "/Users/nadia/Desktop/SepABC holotoxin processing/Model building/1.pdb"
> models #2 displayedOnly true relModel #1.1

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model building/1.pdb"

> hide #!3 models

> show #!3 models

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model building/1.pdb"

> save "/Users/nadia/Desktop/SepABC holotoxin processing/Model building/1.pdb"
> models #2 relModel #1

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model building/1.pdb"

Chain information for 1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

Cell requested for row 2 is out of bounds for table with 6 rows! Resizing
table model.  

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Best
> maps/Zflip_J248.mrc"

Opened Zflip_J248.mrc as #7, grid size 560,560,560, pixel 1.5, shown at level
0.0422, step 4, values float32  

> close #4#3

> close #7

> save "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/alignments.cxs" includeMaps true

——— End of log from Fri Aug 30 13:07:45 2024 ———

opened ChimeraX session  

> ui tool show "Color Actions"

> set bgColor white

> close #1

> close #2

> close #6

> close #5

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/ISOLDErefine2_CootRefine1_SepAMono-coot-0.pdb"

Summary of feedback from opening /Users/nadia/Desktop/SepABC holotoxin
processing/Model building/ISOLDErefine2_CootRefine1_SepAMono-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 79 79 GLY A 1261 PHE A 1263 1 3  
Start residue of secondary structure not found: HELIX 80 80 SER A 1265 GLU A
1269 1 5  
End residue of secondary structure not found: SHEET 17 1717 VAL A1200 ASP
A1203 0  
Start residue of secondary structure not found: SHEET 18 1818 GLN A1214 ASN
A1221 0  
Start residue of secondary structure not found: SHEET 19 1919 GLN A1226 SER
A1233 0  
Start residue of secondary structure not found: SHEET 20 2020 GLN A1244 ASP
A1249 0  
Start residue of secondary structure not found: SHEET 21 2121 LEU A1254 ILE
A1257 0  
Start residue of secondary structure not found: SHEET 22 2222 TYR A1289 ASP
A1299 0  
2 messages similar to the above omitted  
  
Chain information for ISOLDErefine2_CootRefine1_SepAMono-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/ZFlipJ252_SepAC5.mrc"

Opened ZFlipJ252_SepAC5.mrc as #2, grid size 560,560,560, pixel 1.5, shown at
level 0.0217, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.3073

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 9 residues in model #1 to IUPAC-IUB
standards.  
Chain information for ISOLDErefine2_CootRefine1_SepAMono-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> clipper associate #2 toModel #1

Opened ZFlipJ252_SepAC5.mrc as #1.1.1.1, grid size 560,560,560, pixel 1.5,
shown at step 1, values float32  

> select clear

[Repeated 1 time(s)]Drag select of 2 residues  

> isolde sim start /A:1079-1087

Sim termination reason: None  
ISOLDE: stopped sim  
Fetching CCD HY3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/HY3/HY3.cif  
Fetching CCD THC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/THC/THC.cif  
Fetching CCD 0AF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/0AF/0AF.cif  
Fetching CCD 4PQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/4PQ/4PQ.cif  
Fetching CCD DAH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/DAH/DAH.cif  
Fetching CCD 3NF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/3NF/3NF.cif  
Fetching CCD 5CR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/5CR/5CR.cif  
Fetching CCD AAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/AAC/AAC.cif  
Fetching CCD CSO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CSO/CSO.cif  
Fetching CCD CSS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/CSS/CSS.cif  
Fetching CCD NMM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/NMM/NMM.cif  
Fetching CCD 2MR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/2MR/2MR.cif  
Fetching CCD DA2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/DA2/DA2.cif  
Fetching CCD AAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/AAG/AAG.cif  
Fetching CCD SAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/SAC/SAC.cif  
Failed to add atoms ['HB3', 'HB2'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Fetching CCD NLQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/NLQ/NLQ.cif  
Fetching CCD MEN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MEN/MEN.cif  
Fetching CCD HIC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/HIC/HIC.cif  
Fetching CCD PCA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/PCA/PCA.cif  
Fetching CCD AYA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/AYA/AYA.cif  
Fetching CCD ORN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ORN/ORN.cif  
Fetching CCD LYZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/LYZ/LYZ.cif  
Fetching CCD KCX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/KCX/KCX.cif  
Fetching CCD ALY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ALY/ALY.cif  
Failed to add atoms ['HB3', 'HB2'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
[Repeated 1 time(s)]Fetching CCD FME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FME/FME.cif  
Fetching CCD AME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/AME/AME.cif  
Fetching CCD N7P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/N7P/N7P.cif  
Fetching CCD SC2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/SC2/SC2.cif  

> ui mousemode right select

Drag select of 1 residues  

> ui mousemode right translate

> isolde sim start /A:1086-1097

Sim termination reason: None  
ISOLDE: stopped sim  
Fetching CCD LAY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/LAY/LAY.cif  
Fetching CCD NLG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NLG/NLG.cif  
Fetching CCD CGU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/CGU/CGU.cif  
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> save "/Users/nadia/Desktop/SepABC holotoxin processing/Model
> building/ISOLDErefine3_SepAMono_BugReport.pdb"




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3X/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 3 days, 3 hours, 26 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U2715H:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.3.7
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
File attachment: ISOLDErefine3_SepAMono_BugReport.pdb

ISOLDErefine3_SepAMono_BugReport.pdb​

[n.aleksandrova@…]

Added by email2trac

[Eric Pettersen]

Reported by Nadia Aleksandrova

[Tristan Croll]

So this is an annoyingly elusive bug that is reported from time to time,
which I've never been able to replicate locally. I can see *why *it happens
(ISOLDE uses an element-bond graph based approach to align the existing
atoms with the template, and for serine residues missing key hydrogen atoms
the graph can become symmetric so the backbone CA-C=O can in theory align
with the template CA-CB-OG and vice versa) but it never actually happens in
my hands. On my Windows machine the serine residues all complete
successfully. Will try on a Mac when I get the chance... and meanwhile I'll
try to figure out a solution.

For your immediate problem, the serines and histidines can be
straightforwardly corrected by simply re-running `addh` on your model. You
have a Phe and Tyr that have some extraneous bonds (one between the Phe and
Tyr, one between the Phe sidechain and backbone). You'll need to remove
those manually (ctrl-click on an offending bond and do `~bond sel`)
followed by either repeating `addh` or using ISOLDE's residue correction
widget.

On Tue, Sep 3, 2024 at 5:07 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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