ISOLDE: addh step of sim start: z_align endpoints must be distinct

[jingjin.fan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here) When I start simulation, it shows this error C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\geometry\place.py", line 578, in z_align raise ValueError("z_align endpoints must be distinct")

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/J39_map_C3_LocalRefine_transparent.cxs

Opened cryosparc_P109_J38_006_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.0783, step 1, values float32  
Opened cryosparc_P109_J39_003_volume_map.mrc as #3, grid size 256,256,256,
pixel 0.85, shown at level 0.0773, step 1, values float32  
Opened cryosparc_P109_J39_003_volume_map.mrc z flip as #5, grid size
256,256,256, pixel 0.85, shown at level 0.0833, step 1, values float32  
Log from Wed Aug 14 19:16:04 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/J39_map_C3_LocalRefine.cxs

Opened cryosparc_P109_J38_006_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.0783, step 1, values float32  
Opened cryosparc_P109_J39_003_volume_map.mrc as #3, grid size 256,256,256,
pixel 0.85, shown at level 0.0773, step 1, values float32  
Opened cryosparc_P109_J39_003_volume_map.mrc z flip as #5, grid size
256,256,256, pixel 0.85, shown at level 0.0833, step 1, values float32  
Log from Wed Aug 14 14:59:22 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open Q:\\__BACKUP__\PROJECTS\TEM\img\raw\0578\J39_J40.cxs format session

Opened cryosparc_P102_J39_003_volume_map_sharp.mrc as #2, grid size
180,180,180, pixel 0.85, shown at level 0.129, step 1, values float32  
Opened cryosparc_P102_J40_004_volume_map_sharp.mrc as #3, grid size
180,180,180, pixel 0.85, shown at level 0.147, step 1, values float32  
Log from Fri Jul 12 17:47:46 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/chem-chem1822/OneDrive - Nexus365/__ESIBD-group-
> drive__/PROJECTS/TEM/img/raw/0578/1u7g.pdb1.gz" "C:/Users/chem-
> chem1822/OneDrive - Nexus365/__ESIBD-group-
> drive__/PROJECTS/TEM/img/raw/0578/cryosparc_P102_J39_003_volume_map_sharp.mrc"
> "C:/Users/chem-chem1822/OneDrive - Nexus365/__ESIBD-group-
> drive__/PROJECTS/TEM/img/raw/0578/cryosparc_P102_J40_004_volume_map_sharp.mrc"

1u7g.pdb1.gz title:  
Crystal structure of ammonia channel AMTB from E. Coli [more info...]  
  
Chain information for 1u7g.pdb1.gz  
---  
Chain | Description  
1.1/A | No description available  
1.2/A 1.3/A | No description available  
  
Opened cryosparc_P102_J39_003_volume_map_sharp.mrc as #2, grid size
180,180,180, pixel 0.85, shown at level 0.13, step 1, values float32  
Opened cryosparc_P102_J40_004_volume_map_sharp.mrc as #3, grid size
180,180,180, pixel 0.85, shown at level 0.133, step 1, values float32  

> color #1.1 #d55f05ff

> color #1.2 #706d7eff

> color #1.2 #716dacff

> color #1.3 #256451ff

> color #1.3 #1c7a5fff

> combine #1.1-3

Remapping chain ID 'A' in 1u7g.pdb1.gz #1.2 to 'B'  
Remapping chain ID 'A' in 1u7g.pdb1.gz #1.3 to 'C'  

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #1.1 models

> hide #1.2 models

> hide #1.3 models

> select add #4

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> ui mousemode right rotate

[Repeated 1 time(s)]

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.36007,-0.14009,0.92235,62.104,-0.27617,0.92834,0.24881,20.712,-0.89111,-0.34432,0.29558,5.3192

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.36007,-0.14009,0.92235,85.024,-0.27617,0.92834,0.24881,127.93,-0.89111,-0.34432,0.29558,113.43

> view matrix models
> #4,0.36007,-0.14009,0.92235,86.999,-0.27617,0.92834,0.24881,126.57,-0.89111,-0.34432,0.29558,118.64

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.0099323,0.038044,0.99923,112.31,-0.018713,0.99909,-0.038225,105.23,-0.99978,-0.019078,-0.0092114,120.86

> volume #2 level 0.1581

> hide #!3 models

> view matrix models
> #4,0.85394,0.46795,0.22761,53.417,-0.43186,0.88133,-0.1917,115.56,-0.29031,0.065399,0.9547,127.05

> ui tool show "Fit in Map"

> fitmap #4 inMap #2

Fit molecule combination (#4) to map
cryosparc_P102_J39_003_volume_map_sharp.mrc (#2) using 9747 atoms  
average map value = 0.07319, steps = 76  
shifted from previous position = 4.32  
rotated from previous position = 7.71 degrees  
atoms outside contour = 8584, contour level = 0.15811  
  
Position of combination (#4) relative to
cryosparc_P102_J39_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.90116436 0.41881726 0.11178058 48.87493810  
-0.39567127 0.90007373 -0.18251444 113.78426849  
-0.17705096 0.12024714 0.97682833 121.42498323  
Axis 0.33063929 0.31542660 -0.88948509  
Axis point 351.83879158 -77.84229649 0.00000000  
Rotation angle (degrees) 27.24798916  
Shift along axis -55.95515249  
  

> view #1.3 clip false

> show #!3 models

> view #4#2-3 clip false

> hide #!3 models

> combine #1.1-3

Remapping chain ID 'A' in 1u7g.pdb1.gz #1.2 to 'B'  
Remapping chain ID 'A' in 1u7g.pdb1.gz #1.3 to 'C'  

> hide #4 models

> hide #!2 models

> show #!3 models

> select subtract #4

Nothing selected  

> select add #3

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-21.135,0,1,0,-107.99,0,0,1,-48.678

> view #5#3 clip false

> view matrix models #3,1,0,0,-31.357,0,1,0,-90.784,0,0,1,-112.56

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.87663,0.48056,-0.024124,-53.011,-0.4381,0.8179,0.37298,-70.222,0.19897,-0.31639,0.92753,-101.3

> view matrix models
> #3,0.88394,0.43786,-0.16411,-39.692,-0.31303,0.81481,0.48795,-89.483,0.34738,-0.37994,0.85731,-103.81

> select add #5

9747 atoms, 8649 bonds, 2442 residues, 3 models selected  

> select subtract #3

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> view matrix models
> #5,-0.027223,0.33292,0.94256,94.11,-0.79105,0.56929,-0.22392,16.855,-0.61114,-0.75172,0.24786,-20.893

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.027223,0.33292,0.94256,94.497,-0.79105,0.56929,-0.22392,29.289,-0.61114,-0.75172,0.24786,-22.462

> fitmap #5 inMap #3

Fit molecule combination (#5) to map
cryosparc_P102_J40_004_volume_map_sharp.mrc (#3) using 9747 atoms  
average map value = 0.07256, steps = 136  
shifted from previous position = 1.31  
rotated from previous position = 15.7 degrees  
atoms outside contour = 7992, contour level = 0.13319  
  
Position of combination (#5) relative to
cryosparc_P102_J40_004_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.18391975 0.00986849 0.98289173 123.20280775  
-0.30366745 0.95046395 -0.06636549 113.63087593  
-0.93485807 -0.31067814 -0.17181236 106.75417738  
Axis -0.12474421 0.97918863 -0.16008909  
Axis point 118.47147138 0.00000000 7.35298177  
Rotation angle (degrees) 101.69103532  
Shift along axis 78.80704564  
  

> view matrix models
> #5,-0.14211,0.47588,0.86795,100.3,-0.64602,0.61977,-0.44558,23.974,-0.74997,-0.62404,0.21935,-16.614

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.36778,0.0015914,0.92991,100.36,-0.0070325,-0.99997,-0.00107,-33.289,0.92989,-0.0069332,0.36778,-73.228

> fitmap #5 inMap #3

Fit molecule combination (#5) to map
cryosparc_P102_J40_004_volume_map_sharp.mrc (#3) using 9747 atoms  
average map value = 0.07467, steps = 136  
shifted from previous position = 9.02  
rotated from previous position = 16.7 degrees  
atoms outside contour = 7957, contour level = 0.13319  
  
Position of combination (#5) relative to
cryosparc_P102_J40_004_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.02125273 0.47889586 0.87761443 122.53172655  
-0.69665945 -0.62251669 0.35656499 105.40190205  
0.71708712 -0.61897637 0.32039715 37.08321620  
Axis -0.63510673 0.10450810 -0.76532183  
Axis point 81.16093760 36.24497251 0.00000000  
Rotation angle (degrees) 129.82414481  
Shift along axis -95.18596622  
  

> view matrix models
> #5,-0.062981,0.58972,-0.80515,36.553,0.52373,-0.66721,-0.52965,-78.366,-0.84955,-0.45504,-0.26683,-24.081

> fitmap #5 inMap #3

Fit molecule combination (#5) to map
cryosparc_P102_J40_004_volume_map_sharp.mrc (#3) using 9747 atoms  
average map value = 0.0707, steps = 184  
shifted from previous position = 2.53  
rotated from previous position = 26.9 degrees  
atoms outside contour = 7993, contour level = 0.13319  
  
Position of combination (#5) relative to
cryosparc_P102_J40_004_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.27638065 0.28512139 -0.91777968 61.06713054  
0.88561690 -0.29530675 -0.35843639 9.70913667  
-0.37322441 -0.91186607 -0.17089125 62.95318169  
Axis -0.56383844 -0.55479713 0.61178947  
Axis point 57.61713573 46.33042419 0.00000000  
Rotation angle (degrees) 150.60881408  
Shift along axis -1.30450316  
  

> volume #3 level 0.1312

> volume #3 level 0.1468

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.28551,0.28218,0.91589,103.54,0.072695,-0.94654,0.31429,-32.967,0.95562,0.15631,0.24973,-70.574

> fitmap #5 inMap #3

Fit molecule combination (#5) to map
cryosparc_P102_J40_004_volume_map_sharp.mrc (#3) using 9747 atoms  
average map value = 0.07482, steps = 156  
shifted from previous position = 2.13  
rotated from previous position = 19.4 degrees  
atoms outside contour = 8364, contour level = 0.14678  
  
Position of combination (#5) relative to
cryosparc_P102_J40_004_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.22395567 0.43238293 0.87343510 110.25891842  
-0.62838605 -0.62097598 0.46852942 106.14185705  
0.74496634 -0.65378425 0.13263231 27.65624624  
Axis -0.72425076 0.08290338 -0.68453478  
Axis point 0.00000000 48.25758323 -75.50800405  
Rotation angle (degrees) 129.21217772  
Shift along axis -89.98724909  
  

> select add #3

9747 atoms, 8649 bonds, 2442 residues, 3 models selected  

> view matrix models
> #3,0.93355,0.27637,-0.22828,-26.977,-0.14483,0.87336,0.46504,-105.16,0.3279,-0.40107,0.85535,-101.04,#5,-0.13466,0.38128,0.9146,98.976,-0.23481,-0.909,0.34437,-15.568,0.96267,-0.16838,0.21193,-83.804

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.93355,0.27637,-0.22828,-37.335,-0.14483,0.87336,0.46504,-109.66,0.3279,-0.40107,0.85535,-47.99,#5,-0.13466,0.38128,0.9146,88.617,-0.23481,-0.909,0.34437,-20.069,0.96267,-0.16838,0.21193,-30.752

> view #5#3 clip false

> hide #!3 models

> hide #5 models

> show #4 models

> show #!2 models

> select subtract #3

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> select subtract #5

Nothing selected  

> view #4#2 clip false

> volume #2 level 0.1472

> volume #2 level 0.1291

> show #!3 models

> show #5 models

> select add #3

2 models selected  

> select add #5

9747 atoms, 8649 bonds, 2442 residues, 3 models selected  

> view matrix models
> #3,0.93355,0.27637,-0.22828,-27.012,-0.14483,0.87336,0.46504,-98.573,0.3279,-0.40107,0.85535,-44.901,#5,-0.13466,0.38128,0.9146,98.94,-0.23481,-0.909,0.34437,-8.9808,0.96267,-0.16838,0.21193,-27.663

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.023947,-0.33009,0.94365,-5.2609,-0.22037,0.91896,0.32704,-87.71,-0.97512,-0.21579,-0.050736,109.13,#5,0.91577,-0.40161,-0.008581,-11.559,-0.38318,-0.87975,0.28145,-5.424,-0.12058,-0.25446,-0.95954,-22.69

> view matrix models
> #3,0.11106,-0.28313,0.95263,-16.294,-0.22336,0.92693,0.30153,-86.08,-0.96839,-0.24626,0.039701,103.82,#5,0.91246,-0.39898,0.090694,-7.755,-0.40786,-0.86931,0.2792,-3.9822,-0.032552,-0.29175,-0.95594,-27.993

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.11106,-0.28313,0.95263,-24.011,-0.22336,0.92693,0.30153,-83.618,-0.96839,-0.24626,0.039701,104.49,#5,0.91246,-0.39898,0.090694,-15.473,-0.40786,-0.86931,0.2792,-1.5201,-0.032552,-0.29175,-0.95594,-27.327

> select add #4

19494 atoms, 17298 bonds, 4884 residues, 4 models selected  

> select add #2

19494 atoms, 17298 bonds, 4884 residues, 6 models selected  

> view #4-5#2-3 clip false

> select subtract #2

19494 atoms, 17298 bonds, 4884 residues, 4 models selected  

> select subtract #3

19494 atoms, 17298 bonds, 4884 residues, 2 models selected  

> select subtract #4

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> select subtract #5

Nothing selected  

> select add #5

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> select add #3

9747 atoms, 8649 bonds, 2442 residues, 3 models selected  

> view matrix models
> #3,0.11106,-0.28313,0.95263,-23.737,-0.22336,0.92693,0.30153,-83.91,-0.96839,-0.24626,0.039701,104.41,#5,0.91246,-0.39898,0.090694,-15.198,-0.40786,-0.86931,0.2792,-1.8123,-0.032552,-0.29175,-0.95594,-27.407

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.083424,-0.29023,0.95331,-21.186,-0.2005,0.9322,0.30135,-86.279,-0.97614,-0.21628,0.019575,104.34,#5,0.91125,-0.40696,0.063323,-16.428,-0.40619,-0.86258,0.3016,-1.1067,-0.068121,-0.30056,-0.95133,-25.701

> select subtract #5

2 models selected  

> select subtract #3

Nothing selected  

> select add #4

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> select add #2

9747 atoms, 8649 bonds, 2442 residues, 3 models selected  

> view matrix models
> #2,0.99534,0.071908,-0.064284,-4.5074,-0.086607,0.95966,-0.26749,32.383,0.042457,0.27181,0.96141,-23.386,#4,0.87989,0.47386,0.03534,44.516,-0.4104,0.79533,-0.44612,104.86,-0.23951,0.37804,0.89427,126.36

> ui tool show "Side View"

> view #4-5#2-3 clip false

> select add #5

19494 atoms, 17298 bonds, 4884 residues, 4 models selected  

> select add #3

19494 atoms, 17298 bonds, 4884 residues, 6 models selected  

> view #4-5#2-3 clip false

[Repeated 1 time(s)]

> select add #2

19494 atoms, 17298 bonds, 4884 residues, 7 models selected  

> select add #3

19494 atoms, 17298 bonds, 4884 residues, 8 models selected  

> select subtract #2

19494 atoms, 17298 bonds, 4884 residues, 5 models selected  

> select subtract #4

9747 atoms, 8649 bonds, 2442 residues, 4 models selected  

> save "C:/Users/chem-chem1822/OneDrive - Nexus365/__ESIBD-group-
> drive__/PROJECTS/TEM/img/raw/0578/J39_J40.cxs"

——— End of log from Fri Jul 12 17:47:46 2024 ———

opened ChimeraX session  

> show #!1 models

> hide #!1 models

> close #2

> close #3

> view #4-5#1 clip false

> close #5

> view #4#1 clip false

> save Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/colorful.cxs

> view #4#1 clip false

> view #4 clip false

> open
> Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/cryosparc_P109_J38_006_volume_map.mrc

Opened cryosparc_P109_J38_006_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.0783, step 1, values float32  

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-26.197,0,1,0,-16.399,0,0,1,-19.574

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.13747,0.075248,-0.98764,195.35,-0.8494,-0.52188,0.078462,235.22,-0.50953,0.84969,0.13566,35.103

> select subtract #2

Nothing selected  

> select add #4

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> view matrix models
> #4,-0.3992,-0.081849,-0.9132,52.893,-0.20887,-0.9617,0.1775,71.425,-0.89276,0.26159,0.36681,133.55

> view matrix models
> #4,-0.38674,-0.10347,-0.91637,51.591,-0.14201,-0.97515,0.17004,67.613,-0.91119,0.1959,0.36244,132.45

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.38674,-0.10347,-0.91637,61.394,-0.14201,-0.97515,0.17004,78.429,-0.91119,0.1959,0.36244,145.26

> ui tool show "Fit in Map"

> fitmap #4 inMap #2

Fit molecule combination (#4) to map cryosparc_P109_J38_006_volume_map.mrc
(#2) using 9747 atoms  
average map value = 0.07279, steps = 112  
shifted from previous position = 5.18  
rotated from previous position = 14.9 degrees  
atoms outside contour = 5619, contour level = 0.07834  
  
Position of combination (#4) relative to cryosparc_P109_J38_006_volume_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.63417762 0.77318603 0.00145935 99.79021417  
-0.77318603 0.63417892 -0.00068818 163.77470665  
-0.00145758 -0.00069192 0.99999870 146.08576025  
Axis -0.00000241 0.00188630 -0.99999822  
Axis point 223.25962912 -23.43096118 0.00000000  
Rotation angle (degrees) 50.64098383  
Shift along axis -145.77681257  
  

> view matrix models
> #4,-0.14392,-0.057883,-0.9879,47.767,-0.13527,-0.98777,0.077582,76.376,-0.9803,0.1448,0.13433,143.62

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.04821,-0.24189,0.96911,109.51,-0.98522,0.14816,0.085991,147.9,-0.16438,-0.95893,-0.23117,60.746

> fitmap #4 inMap #2

Fit molecule combination (#4) to map cryosparc_P109_J38_006_volume_map.mrc
(#2) using 9747 atoms  
average map value = 0.07382, steps = 132  
shifted from previous position = 2.32  
rotated from previous position = 9.1 degrees  
atoms outside contour = 5447, contour level = 0.07834  
  
Position of combination (#4) relative to cryosparc_P109_J38_006_volume_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.92998035 0.34924629 -0.11473270 68.37417556  
0.34979509 -0.93669002 -0.01597584 65.41039482  
-0.11304847 -0.02527572 -0.99326793 75.10476563  
Axis -0.98233900 -0.17790352 0.05796911  
Axis point 0.00000000 26.60952420 39.50696558  
Rotation angle (degrees) 179.72878697  
Shift along axis -74.44960222  
  

> view matrix models
> #4,-0.18435,0.32457,0.92772,134.69,0.72808,0.67916,-0.092931,76.951,-0.66023,0.65833,-0.36152,122.37

> fitmap #4 inMap #2

Fit molecule combination (#4) to map cryosparc_P109_J38_006_volume_map.mrc
(#2) using 9747 atoms  
average map value = 0.07382, steps = 112  
shifted from previous position = 2.02  
rotated from previous position = 8.29 degrees  
atoms outside contour = 5440, contour level = 0.07834  
  
Position of combination (#4) relative to cryosparc_P109_J38_006_volume_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
-0.17067889 -0.98306840 0.06667283 92.46229438  
-0.98209490 0.16425320 -0.09225245 156.46921685  
0.07973924 -0.08122459 -0.99350100 64.25738306  
Axis 0.64393322 -0.76296708 0.05684406  
Axis point 112.07077100 0.00000000 38.31843281  
Rotation angle (degrees) 179.50937659  
Shift along axis -56.18866883  
  

> view matrix models
> #4,0.052551,0.10247,0.99335,120.04,0.31062,-0.94705,0.081259,56.966,0.94908,0.30428,-0.081597,47.633

> fitmap #4 inMap #2

Fit molecule combination (#4) to map cryosparc_P109_J38_006_volume_map.mrc
(#2) using 9747 atoms  
average map value = 0.07382, steps = 92  
shifted from previous position = 0.681  
rotated from previous position = 3.21 degrees  
atoms outside contour = 5446, contour level = 0.07834  
  
Position of combination (#4) relative to cryosparc_P109_J38_006_volume_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
-0.76743014 0.63078454 -0.11472516 158.15169467  
0.63632130 0.77125846 -0.01598801 99.16420955  
0.07839776 -0.08527174 -0.99326861 64.19432376  
Axis -0.33755859 -0.94091791 0.02697573  
Axis point 59.42610179 0.00000000 36.50465165  
Rotation angle (degrees) 174.10966492  
Shift along axis -144.95915515  
  

> transparency 50

> volume #2 level 0.1755

> volume #2 level 0.07834

> view matrix models
> #4,0.15471,-0.017472,0.98781,111.65,0.32087,-0.94475,-0.066965,50.743,0.9344,0.32731,-0.14056,46.033

> view matrix models
> #4,-0.17537,-0.28054,-0.94369,45.17,0.6587,-0.74582,0.099307,46.693,-0.73168,-0.60419,0.31559,116.82

> fitmap #4 inMap #2

Fit molecule combination (#4) to map cryosparc_P109_J38_006_volume_map.mrc
(#2) using 9747 atoms  
average map value = 0.07228, steps = 72  
shifted from previous position = 2  
rotated from previous position = 7.25 degrees  
atoms outside contour = 5403, contour level = 0.07834  
  
Position of combination (#4) relative to cryosparc_P109_J38_006_volume_map.mrc
(#2) coordinates:  
Matrix rotation and translation  
-0.15360467 0.98535044 -0.07409551 139.57137677  
-0.98801717 -0.15200927 0.02674469 153.77405712  
0.01508968 0.07731575 0.99689246 147.64114253  
Axis 0.02559226 -0.04513354 -0.99865309  
Axis point 134.65683544 12.08685753 0.00000000  
Rotation angle (degrees) 98.87972287  
Shift along axis -150.81070408  
  

> ui tool show "Side View"

> transparency 0

> view #4#2 clip false

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.17218,-0.9784,0.11442,68.27,0.20048,0.078921,0.97651,124.73,-0.96445,0.19107,0.18256,146.07

> view matrix models
> #4,-0.047267,-0.47048,0.88115,106,-0.99073,0.13454,0.018689,145.34,-0.12734,-0.8721,-0.47247,52.087

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.047267,-0.47048,0.88115,155.69,-0.99073,0.13454,0.018689,150.48,-0.12734,-0.8721,-0.47247,49.94

> view #4#2 clip false

> view matrix models
> #4,-0.047267,-0.47048,0.88115,164.82,-0.99073,0.13454,0.018689,150.08,-0.12734,-0.8721,-0.47247,48.452

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.012548,0.13899,0.99021,182.91,-0.70045,-0.70549,0.1079,116.85,0.71359,-0.69495,0.088502,35.365

> view matrix models
> #4,0.042862,-0.026468,-0.99873,99.872,0.45565,-0.88911,0.043118,54.764,-0.88912,-0.45692,-0.026049,113.06

> open
> Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/cryosparc_P109_J39_003_volume_map.mrc

Opened cryosparc_P109_J39_003_volume_map.mrc as #3, grid size 256,256,256,
pixel 0.85, shown at level 0.0773, step 1, values float32  

> color #3 #b2b2b2ff models

> hide #4 models

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.042862,-0.026468,-0.99873,100.62,0.45565,-0.88911,0.043118,61.588,-0.88912,-0.45692,-0.026049,110.57

> select subtract #4

Nothing selected  

> select add #3

2 models selected  

> view matrix models #3,1,0,0,-13.096,0,1,0,98.364,0,0,1,-33.766

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.95368,-0.28144,0.10626,11.568,0.28327,0.95904,-0.002174,72.458,-0.1013,0.032175,0.99434,-25.745

> view matrix models
> #3,0.98706,0.15077,-0.05463,-22.469,-0.15026,0.98856,0.013346,114.46,0.056017,-0.0049644,0.99842,-39.112

> view matrix models
> #3,0.98313,-0.17133,0.063998,0.76506,0.17199,0.98509,-0.0049796,81.929,-0.06219,0.015903,0.99794,-28.569

> view matrix models
> #3,0.9693,0.23138,-0.083179,-26.378,-0.23018,0.97285,0.023978,123.7,0.086469,-0.0040962,0.99625,-42.27

> view matrix models
> #3,0.099291,0.95046,-0.29456,11.128,-0.91498,0.20355,0.34839,247.88,0.39109,0.23492,0.88986,-90.197

> view matrix models
> #3,-0.79668,0.59446,-0.10921,127.49,-0.52368,-0.5887,0.61578,264.25,0.30176,0.54777,0.78031,-103.29

> select add #2

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.13747,0.075248,-0.98764,214.78,-0.8494,-0.52188,0.078462,182.6,-0.50953,0.84969,0.13566,53.264,#3,-0.79668,0.59446,-0.10921,146.93,-0.52368,-0.5887,0.61578,211.63,0.30176,0.54777,0.78031,-85.13

> select subtract #2

2 models selected  

> view matrix models
> #3,-0.79668,0.59446,-0.10921,132.22,-0.52368,-0.5887,0.61578,212.46,0.30176,0.54777,0.78031,-84.54

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.044552,0.11276,-0.99262,199.08,-0.86096,-0.50832,-0.019104,308.42,-0.50673,0.85375,0.11973,40.281

> view matrix models
> #3,0.060316,-0.025477,-0.99785,203.56,-0.87531,-0.48186,-0.040606,309.37,-0.47979,0.87588,-0.051364,53.337

> hide #!2 models

> view matrix models
> #3,0.13064,0.05646,-0.98982,186.04,-0.86259,-0.48569,-0.14155,319.28,-0.48874,0.8723,-0.01475,50.76

> view #3 clip false

> show #4 models

> view matrix models
> #3,0.11458,0.048945,-0.99221,188.86,-0.75608,-0.64356,-0.11906,322.77,-0.64438,0.76383,-0.03673,81.955

> select subtract #3

Nothing selected  

> select add #4

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> view matrix models
> #4,-0.056375,-0.10249,0.99313,180.41,-0.56602,0.8227,0.052774,157.03,-0.82246,-0.55916,-0.10439,101.59

> view matrix models
> #4,-0.085757,-0.071047,0.99378,182.68,-0.10722,0.99232,0.06169,140.37,-0.99053,-0.10127,-0.092716,122.5

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.085757,-0.071047,0.99378,144.56,-0.10722,0.99232,0.06169,188.83,-0.99053,-0.10127,-0.092716,115.99

> view matrix models
> #4,-0.085757,-0.071047,0.99378,129.53,-0.10722,0.99232,0.06169,279.14,-0.99053,-0.10127,-0.092716,117.16

> view matrix models
> #4,-0.085757,-0.071047,0.99378,126.05,-0.10722,0.99232,0.06169,298.89,-0.99053,-0.10127,-0.092716,113.2

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.21515,0.028991,0.97615,134.21,0.76773,0.6228,0.15072,250.95,-0.60358,0.78184,-0.15625,116.65

> view matrix models
> #4,-0.042292,0.34405,0.938,133.2,0.21031,-0.91474,0.345,242.69,0.97672,0.21186,-0.033671,31.24

> view #4#3 clip false

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.042292,0.34405,0.938,152.91,0.21031,-0.91474,0.345,134.61,0.97672,0.21186,-0.033671,48.48

> fitmap #4 inMap #3

Fit molecule combination (#4) to map cryosparc_P109_J39_003_volume_map.mrc
(#3) using 9747 atoms  
average map value = 0.07202, steps = 92  
shifted from previous position = 2.17  
rotated from previous position = 6.74 degrees  
atoms outside contour = 5571, contour level = 0.077316  
  
Position of combination (#4) relative to cryosparc_P109_J39_003_volume_map.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.75853287 0.64987790 -0.04781814 161.36922056  
0.63946899 0.72825098 -0.24643437 87.85614201  
-0.12532864 -0.21750681 -0.96797908 65.57583687  
Axis 0.34691643 0.92955178 -0.12482979  
Axis point 65.20720484 0.00000000 37.38063315  
Rotation angle (degrees) 177.61050839  
Shift along axis 129.46264899  
  

> view #4#3 clip false

> flip #4

Unknown command: flip #4  

> view matrix models
> #4,0.068742,0.32592,0.9429,145.09,0.17689,-0.93414,0.30999,136.03,0.98183,0.14548,-0.12187,42.669

> volume flip #4

[Repeated 1 time(s)]

> volume flip #3

Opened cryosparc_P109_J39_003_volume_map.mrc z flip as #5, grid size
256,256,256, pixel 0.85, shown at step 1, values float32  

> fitmap #4 inMap #3

Fit molecule combination (#4) to map cryosparc_P109_J39_003_volume_map.mrc
(#3) using 9747 atoms  
average map value = 0.07202, steps = 112  
shifted from previous position = 1.54  
rotated from previous position = 0.0752 degrees  
atoms outside contour = 5565, contour level = 0.077316  
  
Position of combination (#4) relative to cryosparc_P109_J39_003_volume_map.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.75872120 0.64974527 -0.04661761 161.43204213  
0.63901969 0.72848083 -0.24692001 87.86891400  
-0.12647507 -0.21713304 -0.96791388 65.64866277  
Axis 0.34674677 0.92961167 -0.12485518  
Axis point 65.27385449 0.00000000 37.37832755  
Rotation angle (degrees) 177.53827132  
Shift along axis 129.46343195  
  

> view matrix models
> #4,0.069836,0.32554,0.94295,140.8,0.17746,-0.93423,0.30939,134.76,0.98165,0.14573,-0.12301,45.755

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.10003,0.13284,0.98608,135.77,0.02681,-0.99105,0.13079,133.39,0.99462,0.013354,-0.1027,42.306

> fitmap #4 inMap #3

Fit molecule combination (#4) to map cryosparc_P109_J39_003_volume_map.mrc
(#3) using 9747 atoms  
average map value = 0.074, steps = 116  
shifted from previous position = 3.78  
rotated from previous position = 9.71 degrees  
atoms outside contour = 5443, contour level = 0.077316  
  
Position of combination (#4) relative to cryosparc_P109_J39_003_volume_map.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.76843671 0.63621947 0.06877344 166.54452736  
0.63001297 0.77099458 -0.09301075 95.44450010  
-0.11219919 -0.02814473 -0.99328707 74.95690512  
Axis 0.33723505 0.94086733 -0.03226729  
Axis point 68.20574900 0.00000000 36.08919939  
Rotation angle (degrees) 174.48114560  
Shift along axis 143.54660868  
  

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.054117,0.13856,0.98887,137.82,0.1889,-0.97386,0.12612,123.22,0.9805,0.17997,-0.078876,45.507

> fitmap #4 inMap #3

Fit molecule combination (#4) to map cryosparc_P109_J39_003_volume_map.mrc
(#3) using 9747 atoms  
average map value = 0.07555, steps = 84  
shifted from previous position = 2.96  
rotated from previous position = 6.78 degrees  
atoms outside contour = 5340, contour level = 0.077316  
  
Position of combination (#4) relative to cryosparc_P109_J39_003_volume_map.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.75496851 0.65576083 -0.00050762 163.47416799  
0.65576093 0.75496775 -0.00112828 98.13095665  
-0.00035664 -0.00118471 -0.99999923 71.50328226  
Axis -0.35010110 -0.93671173 0.00060137  
Axis point 63.39705501 0.00000000 35.78553462  
Rotation angle (degrees) 179.99538268  
Shift along axis -149.10990343  
  

> transparency #5.1 50

> select subtract #4

Nothing selected  

> transparency #5.1 0

> view #4#5 clip false

> select add #4

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> view matrix models
> #4,-0.054051,0.11326,0.99209,141.65,0.14883,-0.98153,0.12016,127.25,0.98738,0.15415,0.036196,50.02

> fitmap #4 inMap #3

Fit molecule combination (#4) to map cryosparc_P109_J39_003_volume_map.mrc
(#3) using 9747 atoms  
average map value = 0.07555, steps = 52  
shifted from previous position = 1.13  
rotated from previous position = 0.0141 degrees  
atoms outside contour = 5338, contour level = 0.077316  
  
Position of combination (#4) relative to cryosparc_P109_J39_003_volume_map.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.75485010 0.65589715 -0.00047480 163.47095514  
0.65589714 0.75484916 -0.00129156 98.10848816  
-0.00048872 -0.00128637 -0.99999904 71.51046462  
Axis 0.34925457 0.93702748 -0.00086068  
Axis point 63.45182410 0.00000000 35.80006878  
Rotation angle (degrees) 179.99957413  
Shift along axis 148.96178014  
  

> view #5 clip false

> transparency #5.1 50

> select subtract #4

Nothing selected  

> volume #5 level 0.1706

> transparency #5.1 0

> select add #4

9747 atoms, 8649 bonds, 2442 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.053899,0.11337,0.99209,142.12,0.14867,-0.98155,0.12025,127.16,0.98742,0.15398,0.03605,49.981

> fitmap #4 inMap #3

Fit molecule combination (#4) to map cryosparc_P109_J39_003_volume_map.mrc
(#3) using 9747 atoms  
average map value = 0.07555, steps = 52  
shifted from previous position = 1.3  
rotated from previous position = 0.0191 degrees  
atoms outside contour = 5344, contour level = 0.077316  
  
Position of combination (#4) relative to cryosparc_P109_J39_003_volume_map.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.75490518 0.65583389 -0.00021455 163.50104421  
0.65583369 0.75490459 -0.00110005 98.12474378  
-0.00055948 -0.00097116 -0.99999936 71.51660928  
Axis 0.35003330 0.93673709 -0.00055975  
Axis point 63.42075981 0.00000000 35.78215264  
Rotation angle (degrees) 179.98945093  
Shift along axis 149.10786533  
  

> transparency #5.1 50

> volume #5 level 0.07531

> volume #5 level 0.08233

> select subtract #4

Nothing selected  

> volume #5 level 0.1937

> volume #5 level 0.08334

> transparency #5.1 0

> open
> Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/cryosparc_P109_J39_003_volume_map_sharp.mrc

Opened cryosparc_P109_J39_003_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 0.85, shown at level 0.0999, step 1, values float32  

> volume #6 level 0.3994

> color #6 #b2b2b2ff models

> select add #6

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.0060477,-0.14141,0.98993,16.665,0.020015,-0.98977,-0.14127,235.4,0.99978,0.018959,0.0088161,-2.1782

> close #6

> save Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/J39_map_LocalRefine.cxs

——— End of log from Wed Aug 14 14:59:22 2024 ———

opened ChimeraX session  

> volume #5 level 0.08334

> ui mousemode right clip

> hide #!5 models

> show #!5 models

> hide #4 models

> show #4 models

> transparency #5.1 50

> save
> Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/J39_map_C3_LocalRefine_transparent.cxs

——— End of log from Wed Aug 14 19:16:04 2024 ———

opened ChimeraX session  

> close #2-3

Removed all altlocs in #4 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 60 residues in model #4 to IUPAC-IUB
standards.  

> hide #!5 models

> view matrix models #2.2,1,0,0,-0.67407,0,1,0,-1.0427,0,0,1,-0.33833

> show #!5 models

> volume #5 level 0.2117

> clipper associate #5 toModel #2

Opened cryosparc_P109_J39_003_volume_map.mrc z flip as #2.1.1.1, grid size
256,256,256, pixel 0.85, shown at step 1, values float32  

> volume #2.1.1.1 level 0.006851

> isolde sim start #2.2/A-C

Loading residue template for NH3 from internal database  
Loading residue template for NH4 from internal database  
Sim termination reason: None  
ISOLDE: stopped sim  

> addh #2.2

Summary of feedback from adding hydrogens to combination #2.2  
---  
warning | Unknown hybridization for atom (SE) of residue type MSE; not adding
hydrogens to it  
notes | Termini for combination (#2.2) chain A determined from SEQRES records  
No usable SEQRES records for combination (#2.2) chain B; guessing termini
instead  
No usable SEQRES records for combination (#2.2) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: combination #2.2/B ALA 3,
combination #2.2/C ALA 3, combination #2.2/B ALA 3, combination #2.2/C ALA 3  
Chain-initial residues that are not actual N termini: combination #2.2/A ALA 3  
Chain-final residues that are actual C termini: combination #2.2/A VAL 385,
combination #2.2/B VAL 385, combination #2.2/C VAL 385  
Chain-final residues that are not actual C termini: combination #2.2/B VAL
385, combination #2.2/C VAL 385  
Missing OXT added to C-terminal residue combination #2.2/A VAL 385  
Missing OXT added to C-terminal residue combination #2.2/B VAL 385  
Missing OXT added to C-terminal residue combination #2.2/C VAL 385  
4188 hydrogen bonds  
  
Traceback (most recent call last):  
File "C:\Users\chem-chem1822\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 76, in
_populate_unparameterised_residue_table  
self._ask_to_add_hydrogens_if_necessary(residues)  
File "C:\Users\chem-chem1822\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 226, in
_ask_to_add_hydrogens_if_necessary  
run(self.session, f'addh #{residues.unique_structures[0].id_string}')  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 372, in add_hydrogens  
_do_prune(hbond, pruned, rel_bond, processed, pruned_by)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1457, in _do_prune  
if not _tet2_check(da._addh_coord, prev[0]._addh_coord, prev[1]._addh_coord,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1411, in _tet2_check  
for pos in bond_positions(tet_pos, 4, 1.0, [], toward=toward,
toward2=toward2):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 89, in bond_positions  
return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 169, in tetra_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 253, in angle_pos  
xforms = [z_align(atom_pos, bond_pos)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
ValueError: z_align endpoints must be distinct  
  
ValueError: z_align endpoints must be distinct  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
  
See log for complete Python traceback.  
  

> isolde start

> set bgColor white

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Unknown hybridization for atom (SE) of residue type MSE; not adding
hydrogens to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
notes | Termini for 1u7g.pdb1.gz (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 1u7g.pdb1.gz #1.1/A ALA
3  
Chain-final residues that are actual C termini: 1u7g.pdb1.gz #1.1/A VAL 385  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue 1u7g.pdb1.gz #1.1/A VAL 385  
1310 hydrogen bonds  
Adding 'H' to 1u7g.pdb1.gz #1.1/A ALA 3  
No usable SEQRES records for 1u7g.pdb1.gz (#1.2) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: 1u7g.pdb1.gz #1.2/A ALA 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 1u7g.pdb1.gz #1.2/A VAL
385  
1309 hydrogen bonds  
1u7g.pdb1.gz #1.2/A VAL 385 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 1u7g.pdb1.gz (#1.3) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: 1u7g.pdb1.gz #1.3/A ALA 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 1u7g.pdb1.gz #1.3/A VAL
385  
1309 hydrogen bonds  
1u7g.pdb1.gz #1.3/A VAL 385 is not terminus, removing H atom from 'C'  
Termini for combination (#2.2) chain A determined from SEQRES records  
No usable SEQRES records for combination (#2.2) chain B; guessing termini
instead  
No usable SEQRES records for combination (#2.2) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: combination #2.2/B ALA 3,
combination #2.2/C ALA 3, combination #2.2/B ALA 3, combination #2.2/C ALA 3  
Chain-initial residues that are not actual N termini: combination #2.2/A ALA 3  
Chain-final residues that are actual C termini: combination #2.2/A VAL 385,
combination #2.2/B VAL 385, combination #2.2/C VAL 385, combination #2.2/B VAL
385, combination #2.2/C VAL 385  
Chain-final residues that are not actual C termini:  
4188 hydrogen bonds  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 176, in hbond_add_hydrogens  
hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 372, in add_hydrogens  
_do_prune(hbond, pruned, rel_bond, processed, pruned_by)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1457, in _do_prune  
if not _tet2_check(da._addh_coord, prev[0]._addh_coord, prev[1]._addh_coord,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1411, in _tet2_check  
for pos in bond_positions(tet_pos, 4, 1.0, [], toward=toward,
toward2=toward2):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 89, in bond_positions  
return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 169, in tetra_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 253, in angle_pos  
xforms = [z_align(atom_pos, bond_pos)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
ValueError: z_align endpoints must be distinct  
  
ValueError: z_align endpoints must be distinct  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
  
See log for complete Python traceback.  
  

> isolde restrain ligands #1

> select #1

21110 atoms, 20012 bonds, 2442 residues, 10 models selected  

> isolde sim start sel

If selection is not from the current model active in ISOLDE, all atoms must be
from the same model!  

> isolde tutorial

> volume #2.1.1.1 level 0.009671

> volume #2.1.1.1 level 0.004032

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  
C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py:275:
UserWarning: Tight layout not applied. The bottom and top margins cannot be
made large enough to accommodate all axes decorations.  
self.exec()  
C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py:275:
UserWarning: Tight layout not applied. tight_layout cannot make axes height
small enough to accommodate all axes decorations.  
self.exec()  

> isolde set simFidelityMode Lowest/Fastest

ISOLDE: setting sim fidelity mode to Lowest/Fastest  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = False  

> isolde set simFidelityMode Lowest/Fastest

ISOLDE: setting sim fidelity mode to Lowest/Fastest  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = False  

> isolde sim start #1.1/A #1.2/A #1.3/A
> #2.2/A:15,18-23,25-27,30,202-214,231,549,767/B:15-31,106,110,200,202-215,231,500,549,767/C:15,17-27,30,203-204,206-208,210-211,549,767

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.1/A #1.2/A #1.3/A
> #2.2/A:12-33,199-217,228-234,549,767/B:12-33,103-113,197-218,228-234,500,549,767/C:12-33,200-213,549,767

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.1/A #1.2/A #1.3/A
> #2.2/A:9-36,196-220,225-237,549,767/B:9-36,100-115,194-221,225-237,500,549,767/C:9-36,197-215,549,767

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.1/A #1.2/A #1.3/A
> #2.2/A:6-39,193-240,549,767/B:6-39,97-118,191-240,500,549,767/C:6-39,194-218,549,767

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde ignore {selection}

Expected a residues specifier or a keyword  

> isolde sim start #1.1/A #1.2/A #1.3/A
> #2.2/A:3-42,190-241,549,767/B:3-42,94-121,188-242,500,549,767/C:3-42,191-221,549,767

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde demo

Missing or invalid "demoName" argument: Expected one of 'clashes_intro',
'cryo_em_intro', or 'crystal_intro'  

> isolde demo #1

Missing or invalid "demoName" argument: Should be one of 'clashes_intro',
'cryo_em_intro', or 'crystal_intro'  

> isolde demo #2

Missing or invalid "demoName" argument: Should be one of 'clashes_intro',
'cryo_em_intro', or 'crystal_intro'  

> volume #2.1.1.1 level 0.007657

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Unknown hybridization for atom (SE) of residue type MSE; not adding
hydrogens to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
notes | Termini for 1u7g.pdb1.gz (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 1u7g.pdb1.gz #1.1/A ALA
3  
Chain-final residues that are actual C termini: 1u7g.pdb1.gz #1.1/A VAL 385  
Chain-final residues that are not actual C termini:  
759 hydrogen bonds  
No usable SEQRES records for 1u7g.pdb1.gz (#1.2) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: 1u7g.pdb1.gz #1.2/A ALA 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 1u7g.pdb1.gz #1.2/A VAL
385  
759 hydrogen bonds  
1u7g.pdb1.gz #1.2/A VAL 385 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 1u7g.pdb1.gz (#1.3) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: 1u7g.pdb1.gz #1.3/A ALA 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 1u7g.pdb1.gz #1.3/A VAL
385  
758 hydrogen bonds  
1u7g.pdb1.gz #1.3/A VAL 385 is not terminus, removing H atom from 'C'  
Termini for combination (#2.2) chain A determined from SEQRES records  
No usable SEQRES records for combination (#2.2) chain B; guessing termini
instead  
No usable SEQRES records for combination (#2.2) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: combination #2.2/B ALA 3,
combination #2.2/C ALA 3, combination #2.2/B ALA 3, combination #2.2/C ALA 3  
Chain-initial residues that are not actual N termini: combination #2.2/A ALA 3  
Chain-final residues that are actual C termini: combination #2.2/A VAL 385,
combination #2.2/B VAL 385, combination #2.2/C VAL 385, combination #2.2/B VAL
385, combination #2.2/C VAL 385  
Chain-final residues that are not actual C termini:  
4188 hydrogen bonds  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 176, in hbond_add_hydrogens  
hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 372, in add_hydrogens  
_do_prune(hbond, pruned, rel_bond, processed, pruned_by)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1457, in _do_prune  
if not _tet2_check(da._addh_coord, prev[0]._addh_coord, prev[1]._addh_coord,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1411, in _tet2_check  
for pos in bond_positions(tet_pos, 4, 1.0, [], toward=toward,
toward2=toward2):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 89, in bond_positions  
return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 169, in tetra_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 253, in angle_pos  
xforms = [z_align(atom_pos, bond_pos)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
ValueError: z_align endpoints must be distinct  
  
ValueError: z_align endpoints must be distinct  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
  
See log for complete Python traceback.  
  

> addh template true

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Unknown hybridization for atom (SE) of residue type MSE; not adding
hydrogens to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
notes | Termini for 1u7g.pdb1.gz (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 1u7g.pdb1.gz #1.1/A ALA
3  
Chain-final residues that are actual C termini: 1u7g.pdb1.gz #1.1/A VAL 385  
Chain-final residues that are not actual C termini:  
759 hydrogen bonds  
No usable SEQRES records for 1u7g.pdb1.gz (#1.2) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: 1u7g.pdb1.gz #1.2/A ALA 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 1u7g.pdb1.gz #1.2/A VAL
385  
759 hydrogen bonds  
1u7g.pdb1.gz #1.2/A VAL 385 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 1u7g.pdb1.gz (#1.3) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: 1u7g.pdb1.gz #1.3/A ALA 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 1u7g.pdb1.gz #1.3/A VAL
385  
758 hydrogen bonds  
1u7g.pdb1.gz #1.3/A VAL 385 is not terminus, removing H atom from 'C'  
Termini for combination (#2.2) chain A determined from SEQRES records  
No usable SEQRES records for combination (#2.2) chain B; guessing termini
instead  
No usable SEQRES records for combination (#2.2) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: combination #2.2/B ALA 3,
combination #2.2/C ALA 3, combination #2.2/B ALA 3, combination #2.2/C ALA 3  
Chain-initial residues that are not actual N termini: combination #2.2/A ALA 3  
Chain-final residues that are actual C termini: combination #2.2/A VAL 385,
combination #2.2/B VAL 385, combination #2.2/C VAL 385, combination #2.2/B VAL
385, combination #2.2/C VAL 385  
Chain-final residues that are not actual C termini:  
4188 hydrogen bonds  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 176, in hbond_add_hydrogens  
hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 372, in add_hydrogens  
_do_prune(hbond, pruned, rel_bond, processed, pruned_by)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1457, in _do_prune  
if not _tet2_check(da._addh_coord, prev[0]._addh_coord, prev[1]._addh_coord,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1411, in _tet2_check  
for pos in bond_positions(tet_pos, 4, 1.0, [], toward=toward,
toward2=toward2):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 89, in bond_positions  
return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 169, in tetra_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 253, in angle_pos  
xforms = [z_align(atom_pos, bond_pos)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
ValueError: z_align endpoints must be distinct  
  
ValueError: z_align endpoints must be distinct  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
  
See log for complete Python traceback.  
  

> fitmap #1 inMap #2

Fit molecules 1u7g.pdb1.gz (#1.1), 1u7g.pdb1.gz (#1.2), 1u7g.pdb1.gz (#1.3) to
map cryosparc_P109_J39_003_volume_map.mrc z flip (#2.1.1.1) using 21110 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 21110, contour level = 0.0076569  
  
Position of 1u7g.pdb1.gz (#1.1) relative to
cryosparc_P109_J39_003_volume_map.mrc z flip (#2.1.1.1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  
Position of 1u7g.pdb1.gz (#1.2) relative to
cryosparc_P109_J39_003_volume_map.mrc z flip (#2.1.1.1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  
Position of 1u7g.pdb1.gz (#1.3) relative to
cryosparc_P109_J39_003_volume_map.mrc z flip (#2.1.1.1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> clipper associate #2 toModel #1

Invalid "toModel" argument: must specify 1 structure, got 3 for "#1"  

> volume #2.1.1.1 level 0.00806

> hide #!2.1.1.1 models

> show #!2.1.1.1 models

> open
> Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/cryosparc_P102_J39_003_volume_map_sharp.mrc

Opened cryosparc_P102_J39_003_volume_map_sharp.mrc as #3, grid size
180,180,180, pixel 0.85, shown at level 0.13, step 1, values float32  

> volume #3 level 0.1428

> volume #2.1.1.1 level 0.007657

> hide #!3 models

> isolde sim start #1.1/A #1.2/A #1.3/A
> #2.2/A:3-45,187-244,549,767/B:3-45,91-124,185-245,500,549,767/C:3-45,188-224,549,767

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.1/A #1.2/A #1.3/A
> #2.2/A:3-48,184-247,549,767/B:3-48,88-127,182-248,500,549,767/C:3-48,185-227,549,767

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.1/A #1.2/A #1.3/A
> #2.2/A:3-51,181-250,549,767/B:3-51,85-130,179-251,500,549,767/C:3-51,182-230,549,767

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #2.2

Summary of feedback from adding hydrogens to combination #2.2  
---  
warning | Unknown hybridization for atom (SE) of residue type MSE; not adding
hydrogens to it  
notes | Termini for combination (#2.2) chain A determined from SEQRES records  
No usable SEQRES records for combination (#2.2) chain B; guessing termini
instead  
No usable SEQRES records for combination (#2.2) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: combination #2.2/B ALA 3,
combination #2.2/C ALA 3, combination #2.2/B ALA 3, combination #2.2/C ALA 3  
Chain-initial residues that are not actual N termini: combination #2.2/A ALA 3  
Chain-final residues that are actual C termini: combination #2.2/A VAL 385,
combination #2.2/B VAL 385, combination #2.2/C VAL 385, combination #2.2/B VAL
385, combination #2.2/C VAL 385  
Chain-final residues that are not actual C termini:  
4188 hydrogen bonds  
  
Traceback (most recent call last):  
File "C:\Users\chem-chem1822\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 76, in
_populate_unparameterised_residue_table  
self._ask_to_add_hydrogens_if_necessary(residues)  
File "C:\Users\chem-chem1822\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 226, in
_ask_to_add_hydrogens_if_necessary  
run(self.session, f'addh #{residues.unique_structures[0].id_string}')  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 372, in add_hydrogens  
_do_prune(hbond, pruned, rel_bond, processed, pruned_by)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1457, in _do_prune  
if not _tet2_check(da._addh_coord, prev[0]._addh_coord, prev[1]._addh_coord,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 1411, in _tet2_check  
for pos in bond_positions(tet_pos, 4, 1.0, [], toward=toward,
toward2=toward2):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 89, in bond_positions  
return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 169, in tetra_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 253, in angle_pos  
xforms = [z_align(atom_pos, bond_pos)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
ValueError: z_align endpoints must be distinct  
  
ValueError: z_align endpoints must be distinct  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 578, in z_align  
raise ValueError("z_align endpoints must be distinct")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 42,721,021,952
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-GB

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    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
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    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
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    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
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    ipykernel: 6.23.2
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[Eric Pettersen]

This error typically indicates that two atoms are directly on top of one another.

[jingjin.fan@…]

Dear Sir/Madam,

Thank you so much for your reply! I see. Do you think it is because of the atoms in PDB file are not correct? I would appreciate it if you could give me some guidance on how to solve this.

Best wishes,
Jingjin

-----------------------------------------------------------------------------------------------------------------------
Dr. Jingjin Fan
Department of Chemistry | University of Oxford |Southparks Parks Rd | Oxford | OX1 3QU
E-mail: jingjin.fan@chem.ox.ac.uk 


-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: 27 August 2024 5:06 pm
To: Jingjin Fan <jingjin.fan@chem.ox.ac.uk>; tcroll@altoslabs.com; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #15828: ISOLDE: addh step of sim start: z_align endpoints must be distinct (was: ChimeraX bug report submission)

#15828: ISOLDE: addh step of sim start: z_align endpoints must be distinct
------------------------------------+---------------------------
          Reporter:  jingjin.fan@\u2026  |      Owner:  Tristan Croll
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Third Party    |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+---------------------------
Changes (by pett):

 * cc: pett (added)
 * component:  Unassigned => Third Party
 * owner:  (none) => Tristan Croll
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => assigned
 * summary:  ChimeraX bug report submission => ISOLDE: addh step of sim
     start: z_align endpoints must be distinct

Comment:

 This error typically indicates that two atoms are directly on top of one  another.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15828#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

I'm not sure how you made the construct in 1u7g.pdb1.gz, but if I generate
the trimeric biological assembly by:

open 1u7g
sym #1 assembly 1
combine #2

... then

addh #3

works fine for me (with the caveat that I'm using ChimeraX 1.8, not 1.7).


On Tue, Aug 27, 2024 at 5:14 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>
>
>
>
>
>
>
>
>

[Tristan Croll]

The offending atoms will probably be the nitrogens in the three NH3
ligands, which sit exactly on the 3-fold axis. If you made your starting
model by rotating and combining three whole copies of the PDB entry, you’ll
have thee perfectly-overlapping nitrogens at each site.

One slightly-annoying bug you’ll probably run into if you take the approach
I suggested: ISOLDE might not properly discard the crystallographic
symmetry info causing a mess of nonsensical symmetry ghosts after
initialising it. Easiest fix is to save the combined model to PDB, open it
in a text editor to delete the CRYST1 line, save that and re-open in
ChimeraX. I’ll get around to fixing that properly one of these days.

… although come to think of it, it would probably be sensible if ChimeraX
itself had a way to discard symmetry metadata given the number of actions
that can render it invalid?

On Tue, 27 Aug 2024 at 17:27, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
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>

[Eric Pettersen]

Also, in case you want to find out where the problems in the original file are, after you open the structure in ChimeraX if you then open the attached Python file, all bonds shorter than 0.01 angstroms will be printed to the Log.

--Eric

short.py​

[Eric Pettersen]

Added by email2trac

[jingjin.fan@…]

Dear Sir/Madam,

My problem has been solved! Thank you so much for your helpful suggestions and fast feedback!

 Best wishes,
 Jingjin


-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: 27 August 2024 5:28 pm
To: Jingjin Fan <jingjin.fan@chem.ox.ac.uk>; tcroll@altoslabs.com
Cc: pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #15828: ISOLDE: addh step of sim start: z_align endpoints must be distinct

#15828: ISOLDE: addh step of sim start: z_align endpoints must be distinct
------------------------------------+---------------------------
          Reporter:  jingjin.fan@\u2026  |      Owner:  Tristan Croll
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Third Party    |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+---------------------------
Comment (by Tristan Croll):

 {{{
 I'm not sure how you made the construct in 1u7g.pdb1.gz, but if I generate  the trimeric biological assembly by:

 open 1u7g
 sym #1 assembly 1
 combine #2

 ... then

 addh #3

 works fine for me (with the caveat that I'm using ChimeraX 1.8, not 1.7).


 On Tue, Aug 27, 2024 at 5:14\u202fPM ChimeraX <ChimeraX-bugs-  admin@cgl.ucsf.edu>
 wrote:

 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 }}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15828#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker