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Opened 21 months ago
Closed 21 months ago
#14583 closed defect (can't reproduce)
Non-ASCII PDB
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J223_open/cryosparc_P113_J223_009_volume_map.mrc
Opened cryosparc_P113_J223_009_volume_map.mrc as #1, grid size 180,180,180,
pixel 1.35, shown at level 0.094, step 1, values float32
> set bgColor white
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/4A9_Fab_210811.pdb
Chain information for 4A9_Fab_210811.pdb #2
---
Chain | Description
H | No description available
L | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_1to112.pdb
Chain information for AaRseP_1to112.pdb #3
---
Chain | Description
A | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_113to207.pdb
Chain information for AaRseP_113to207.pdb #4
---
Chain | Description
A | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_208to297.pdb
Chain information for AaRseP_208to297.pdb #5
---
Chain | Description
A | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_298to393.pdb
Chain information for AaRseP_298to393.pdb #6
---
Chain | Description
A | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_394to429.pdb
Chain information for AaRseP_394to429.pdb #7
---
Chain | Description
A | No description available
> transparency 50
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,15.929,0,1,0,-110.19,0,0,1,-126.33
> view matrix models #1,1,0,0,-90.657,0,1,0,-114.88,0,0,1,-121.4
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.29362,0.23568,0.92641,-84.907,0.82054,0.55932,0.11777,-172.97,-0.49041,0.79474,-0.35761,12.685
> view matrix models
> #1,0.31836,0.21865,0.92241,-154.54,0.59163,0.71445,-0.37355,-102.22,-0.74069,0.66464,0.098094,-0.032025
> view matrix models
> #1,0.45236,-0.89104,-0.037711,87.482,0.84427,0.44148,-0.30382,-107.62,0.28737,0.1056,0.95198,-162.07
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.45236,-0.89104,-0.037711,105.95,0.84427,0.44148,-0.30382,-99.2,0.28737,0.1056,0.95198,-255.35
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> select add #2
3347 atoms, 3428 bonds, 1 pseudobond, 434 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.6504,-0.56469,-0.50803,26.409,0.70523,0.20046,0.68005,-49.433,-0.28218,-0.80059,0.52862,21.999
> view matrix models
> #2,0.9285,0.068747,-0.36491,11.424,0.047474,-0.99663,-0.066962,-4.5401,-0.36828,0.04485,-0.92863,59.325
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.9285,0.068747,-0.36491,17.906,0.047474,-0.99663,-0.066962,-4.4623,-0.36828,0.04485,-0.92863,-15.386
> fitmap #2 inMap #1
Fit molecule 4A9_Fab_210811.pdb (#2) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 3347 atoms
average map value = 0.1758, steps = 140
shifted from previous position = 12.2
rotated from previous position = 34.6 degrees
atoms outside contour = 620, contour level = 0.094015
Position of 4A9_Fab_210811.pdb (#2) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.20917010 -0.97608399 0.05922761 109.92495464
-0.94690025 -0.18704739 0.26152090 156.46182440
-0.24418800 -0.11078499 -0.96337890 191.50739581
Axis -0.77375155 0.63057904 0.06065164
Axis point 0.00000000 138.01099741 88.97318885
Rotation angle (degrees) 166.07893496
Shift along axis 25.22218053
> select subtract #2
Nothing selected
> select add #3
907 atoms, 937 bonds, 112 residues, 1 model selected
> select add #4
1656 atoms, 1697 bonds, 207 residues, 2 models selected
> select add #5
2355 atoms, 2407 bonds, 297 residues, 3 models selected
> select add #6
3074 atoms, 3141 bonds, 393 residues, 4 models selected
> select add #7
3385 atoms, 3459 bonds, 429 residues, 5 models selected
> view matrix models
> #3,1,0,0,15.074,0,1,0,-3.2817,0,0,1,-104.04,#4,1,0,0,15.074,0,1,0,-3.2817,0,0,1,-104.04,#5,1,0,0,15.074,0,1,0,-3.2817,0,0,1,-104.04,#6,1,0,0,15.074,0,1,0,-3.2817,0,0,1,-104.04,#7,1,0,0,15.074,0,1,0,-3.2817,0,0,1,-104.04
> view matrix models
> #3,1,0,0,21.319,0,1,0,21.058,0,0,1,-114.69,#4,1,0,0,21.319,0,1,0,21.058,0,0,1,-114.69,#5,1,0,0,21.319,0,1,0,21.058,0,0,1,-114.69,#6,1,0,0,21.319,0,1,0,21.058,0,0,1,-114.69,#7,1,0,0,21.319,0,1,0,21.058,0,0,1,-114.69
> view matrix models
> #3,1,0,0,32.33,0,1,0,21.11,0,0,1,-111.68,#4,1,0,0,32.33,0,1,0,21.11,0,0,1,-111.68,#5,1,0,0,32.33,0,1,0,21.11,0,0,1,-111.68,#6,1,0,0,32.33,0,1,0,21.11,0,0,1,-111.68,#7,1,0,0,32.33,0,1,0,21.11,0,0,1,-111.68
> view matrix models
> #3,1,0,0,33.248,0,1,0,24.859,0,0,1,-110.24,#4,1,0,0,33.248,0,1,0,24.859,0,0,1,-110.24,#5,1,0,0,33.248,0,1,0,24.859,0,0,1,-110.24,#6,1,0,0,33.248,0,1,0,24.859,0,0,1,-110.24,#7,1,0,0,33.248,0,1,0,24.859,0,0,1,-110.24
> view matrix models
> #3,1,0,0,34.723,0,1,0,22.83,0,0,1,-109.13,#4,1,0,0,34.723,0,1,0,22.83,0,0,1,-109.13,#5,1,0,0,34.723,0,1,0,22.83,0,0,1,-109.13,#6,1,0,0,34.723,0,1,0,22.83,0,0,1,-109.13,#7,1,0,0,34.723,0,1,0,22.83,0,0,1,-109.13
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.84096,0.5185,-0.15471,32.65,-0.53707,0.76503,-0.35537,22.481,-0.065902,0.38195,0.92183,-110.34,#4,0.84096,0.5185,-0.15471,32.65,-0.53707,0.76503,-0.35537,22.481,-0.065902,0.38195,0.92183,-110.34,#5,0.84096,0.5185,-0.15471,32.65,-0.53707,0.76503,-0.35537,22.481,-0.065902,0.38195,0.92183,-110.34,#6,0.84096,0.5185,-0.15471,32.65,-0.53707,0.76503,-0.35537,22.481,-0.065902,0.38195,0.92183,-110.34,#7,0.84096,0.5185,-0.15471,32.65,-0.53707,0.76503,-0.35537,22.481,-0.065902,0.38195,0.92183,-110.34
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.84096,0.5185,-0.15471,32.675,-0.53707,0.76503,-0.35537,19.039,-0.065902,0.38195,0.92183,-110.83,#4,0.84096,0.5185,-0.15471,32.675,-0.53707,0.76503,-0.35537,19.039,-0.065902,0.38195,0.92183,-110.83,#5,0.84096,0.5185,-0.15471,32.675,-0.53707,0.76503,-0.35537,19.039,-0.065902,0.38195,0.92183,-110.83,#6,0.84096,0.5185,-0.15471,32.675,-0.53707,0.76503,-0.35537,19.039,-0.065902,0.38195,0.92183,-110.83,#7,0.84096,0.5185,-0.15471,32.675,-0.53707,0.76503,-0.35537,19.039,-0.065902,0.38195,0.92183,-110.83
> volume #1 level 0.1179
> select subtract #7
3074 atoms, 3141 bonds, 393 residues, 4 models selected
> select subtract #6
2355 atoms, 2407 bonds, 297 residues, 3 models selected
> select subtract #3
1448 atoms, 1470 bonds, 185 residues, 2 models selected
> select subtract #5
749 atoms, 760 bonds, 95 residues, 1 model selected
> fitmap #4 inMap #1
Fit molecule AaRseP_113to207.pdb (#4) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 749 atoms
average map value = 0.1896, steps = 104
shifted from previous position = 4.58
rotated from previous position = 16.8 degrees
atoms outside contour = 178, contour level = 0.1179
Position of AaRseP_113to207.pdb (#4) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.11467822 0.98863249 -0.09723527 111.94859165
-0.95565546 0.13651658 0.26093267 130.05969349
0.27124074 0.06300013 0.96044752 106.60810094
Axis -0.09952508 -0.18527831 -0.97763322
Axis point 109.82352831 -0.84905870 0.00000000
Rotation angle (degrees) 83.92552103
Shift along axis -139.46255409
> select add #5
1448 atoms, 1470 bonds, 185 residues, 2 models selected
> select subtract #4
699 atoms, 710 bonds, 90 residues, 1 model selected
> fitmap #5 inMap #1
Fit molecule AaRseP_208to297.pdb (#5) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 699 atoms
average map value = 0.1489, steps = 76
shifted from previous position = 1.56
rotated from previous position = 21.1 degrees
atoms outside contour = 211, contour level = 0.1179
Position of AaRseP_208to297.pdb (#5) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.03286915 0.99864964 -0.04023065 108.01222440
-0.90779892 -0.01299126 0.41920442 127.91417783
0.41811570 0.05030023 0.90700008 109.60340251
Axis -0.18489829 -0.22972755 -0.95553015
Axis point 88.56060591 11.96569705 0.00000000
Rotation angle (degrees) 93.98125859
Shift along axis -154.08604205
> select subtract #5
Nothing selected
> select add #7
311 atoms, 318 bonds, 36 residues, 1 model selected
> view matrix models
> #7,0.84096,0.5185,-0.15471,52.235,-0.53707,0.76503,-0.35537,22.025,-0.065902,0.38195,0.92183,-102.75
> view matrix models
> #7,0.84096,0.5185,-0.15471,46.26,-0.53707,0.76503,-0.35537,27.563,-0.065902,0.38195,0.92183,-104.72
> view matrix models
> #7,0.84096,0.5185,-0.15471,50.044,-0.53707,0.76503,-0.35537,29.775,-0.065902,0.38195,0.92183,-101.94
> fitmap #7 inMap #1
Fit molecule AaRseP_394to429.pdb (#7) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 311 atoms
average map value = 0.1193, steps = 216
shifted from previous position = 5.49
rotated from previous position = 34.7 degrees
atoms outside contour = 125, contour level = 0.1179
Position of AaRseP_394to429.pdb (#7) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.47292561 0.88083530 -0.02169194 119.90661426
-0.86522215 0.46891430 0.17751060 127.28199389
0.16652926 -0.06518096 0.98387979 104.57295315
Axis -0.13689246 -0.10616794 -0.98488011
Axis point 147.50064277 -27.20955955 0.00000000
Rotation angle (degrees) 62.42819691
Shift along axis -132.91939928
> volume #1 level 0.1348
> select subtract #7
Nothing selected
> select add #3
907 atoms, 937 bonds, 112 residues, 1 model selected
> fitmap #3 inMap #1
Fit molecule AaRseP_1to112.pdb (#3) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 907 atoms
average map value = 0.1438, steps = 148
shifted from previous position = 17
rotated from previous position = 35.3 degrees
atoms outside contour = 410, contour level = 0.13476
Position of AaRseP_1to112.pdb (#3) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49020724 0.87125328 -0.02479082 119.57137419
-0.86173435 0.48872781 0.13623151 125.85192255
0.13080811 -0.04541857 0.99036679 105.87237834
Axis -0.10383474 -0.08894339 -0.99060962
Axis point 152.26386706 -32.83417802 0.00000000
Rotation angle (degrees) 61.01039569
Shift along axis -128.48755537
> select add #6
1626 atoms, 1671 bonds, 208 residues, 2 models selected
> select subtract #3
719 atoms, 734 bonds, 96 residues, 1 model selected
> fitmap #6 inMap #1
Fit molecule AaRseP_298to393.pdb (#6) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 719 atoms
average map value = 0.1128, steps = 136
shifted from previous position = 6.38
rotated from previous position = 18.1 degrees
atoms outside contour = 493, contour level = 0.13476
Position of AaRseP_298to393.pdb (#6) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.11185114 0.93764636 -0.32910274 106.56256153
-0.99372028 0.10655574 -0.03414479 128.75661419
0.00305205 0.33085520 0.94367659 98.20696174
Axis 0.18310227 -0.16662547 -0.96887022
Axis point 125.57461512 -13.66335141 0.00000000
Rotation angle (degrees) 85.35155264
Shift along axis -97.09208527
> view matrix models
> #6,0.93592,0.31673,-0.15404,38.011,-0.3452,0.73814,-0.57964,12.92,-0.069889,0.59567,0.80018,-107.82
> view matrix models
> #6,0.93592,0.31673,-0.15404,45.566,-0.3452,0.73814,-0.57964,17.152,-0.069889,0.59567,0.80018,-109.56
> view matrix models
> #6,0.93592,0.31673,-0.15404,41.255,-0.3452,0.73814,-0.57964,21.976,-0.069889,0.59567,0.80018,-113.64
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.97025,-0.22263,-0.095162,42.447,0.15216,0.86643,-0.47554,18,0.18832,0.44691,0.87453,-115.13
> view matrix models
> #6,0.95378,-0.29041,-0.077203,42.824,0.22232,0.85482,-0.46889,17.466,0.20216,0.43006,0.87987,-115.18
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.95378,-0.29041,-0.077203,47.068,0.22232,0.85482,-0.46889,20.004,0.20216,0.43006,0.87987,-116.85
> view matrix models
> #6,0.95378,-0.29041,-0.077203,45.22,0.22232,0.85482,-0.46889,25.467,0.20216,0.43006,0.87987,-109.18
> view matrix models
> #6,0.95378,-0.29041,-0.077203,45.806,0.22232,0.85482,-0.46889,25.618,0.20216,0.43006,0.87987,-109.15
> fitmap #6 inMap #1
Fit molecule AaRseP_298to393.pdb (#6) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 719 atoms
average map value = 0.1394, steps = 100
shifted from previous position = 3.55
rotated from previous position = 24 degrees
atoms outside contour = 359, contour level = 0.13476
Position of AaRseP_298to393.pdb (#6) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.59808323 0.77676637 0.19730800 119.90920633
-0.80054303 0.59063578 0.10139148 128.18833049
-0.03777968 -0.21859409 0.97508426 105.44724871
Axis -0.19673038 0.14453429 -0.96974584
Axis point 193.37667619 -27.13162000 0.00000000
Rotation angle (degrees) 54.41559489
Shift along axis -107.31920428
> save
> /Users/asahi/Documents/servalcat関連/P113_W1/J223_open/P113_J223_fit_240214.pdb
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J224_close/P113_J224_240214_1.pdb
P113_J224_240214_1.pdb title:
\--- [more info...]
Chain information for P113_J224_240214_1.pdb #8
---
Chain | Description
A | No description available
H | No description available
L | No description available
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J224_close/diffmap_normalized_fofc.mrc
Opened diffmap_normalized_fofc.mrc as #9, grid size 90,92,120, pixel 1.35,
shown at level 1.99, step 1, values float32
> select subtract #6
Nothing selected
> color #8 #929292ff
> color #8 #5e5e5eff
> color #9 #00fdffff models
> color #9 #73fdffff models
> color #9 #76d6ffff models
> color #9 #73fdffff models
> color #9 #ff8ad8ff models
> color #9 #ff7e79ff models
> color #9 #ffd479ff models
> volume #9 level 2.047
> close #1
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J223_open/cryosparc_P113_J223_009_volume_map.mrc
Opened cryosparc_P113_J223_009_volume_map.mrc as #1, grid size 180,180,180,
pixel 1.35, shown at level 0.094, step 1, values float32
> select add #2
3347 atoms, 3428 bonds, 1 pseudobond, 434 residues, 2 models selected
> select add #3
4254 atoms, 4365 bonds, 1 pseudobond, 546 residues, 3 models selected
> select add #4
5003 atoms, 5125 bonds, 1 pseudobond, 641 residues, 4 models selected
> select add #5
5702 atoms, 5835 bonds, 1 pseudobond, 731 residues, 5 models selected
> select add #6
6421 atoms, 6569 bonds, 1 pseudobond, 827 residues, 6 models selected
> select add #7
6732 atoms, 6887 bonds, 1 pseudobond, 863 residues, 7 models selected
> view matrix models
> #2,0.94755,-0.2707,-0.1699,-47.722,-0.16725,-0.87299,0.45816,2.2659,-0.27235,-0.40571,-0.87248,42.759,#3,0.98466,-0.039639,-0.16995,-12.854,-0.0063134,0.96513,-0.26168,22.914,0.1744,0.25874,0.95007,-39.224,#4,0.89317,0.3232,-0.31271,-20.079,-0.40749,0.8758,-0.2587,18.113,0.19025,0.35849,0.91394,-40.27,#5,0.77825,0.46143,-0.42593,-20.061,-0.55556,0.82211,-0.12446,12.932,0.29273,0.33349,0.89615,-38.776,#6,0.98529,-0.16665,-0.03786,-14.767,0.163,0.98297,-0.084911,24.36,0.051366,0.077491,0.99567,-39.285,#7,0.9786,-0.016904,-0.20508,-13.928,-0.033296,0.97048,-0.23887,24.224,0.20307,0.24059,0.94915,-40.214
> view matrix models
> #2,0.94755,-0.2707,-0.1699,-21.431,-0.16725,-0.87299,0.45816,50.079,-0.27235,-0.40571,-0.87248,184.35,#3,0.98466,-0.039639,-0.16995,13.437,-0.0063134,0.96513,-0.26168,70.728,0.1744,0.25874,0.95007,102.37,#4,0.89317,0.3232,-0.31271,6.2112,-0.40749,0.8758,-0.2587,65.926,0.19025,0.35849,0.91394,101.32,#5,0.77825,0.46143,-0.42593,6.2293,-0.55556,0.82211,-0.12446,60.746,0.29273,0.33349,0.89615,102.82,#6,0.98529,-0.16665,-0.03786,11.524,0.163,0.98297,-0.084911,72.174,0.051366,0.077491,0.99567,102.31,#7,0.9786,-0.016904,-0.20508,12.363,-0.033296,0.97048,-0.23887,72.037,0.20307,0.24059,0.94915,101.38
> view matrix models
> #2,0.94755,-0.2707,-0.1699,25.543,-0.16725,-0.87299,0.45816,86.601,-0.27235,-0.40571,-0.87248,184.28,#3,0.98466,-0.039639,-0.16995,60.411,-0.0063134,0.96513,-0.26168,107.25,0.1744,0.25874,0.95007,102.29,#4,0.89317,0.3232,-0.31271,53.186,-0.40749,0.8758,-0.2587,102.45,0.19025,0.35849,0.91394,101.25,#5,0.77825,0.46143,-0.42593,53.204,-0.55556,0.82211,-0.12446,97.267,0.29273,0.33349,0.89615,102.74,#6,0.98529,-0.16665,-0.03786,58.498,0.163,0.98297,-0.084911,108.7,0.051366,0.077491,0.99567,102.23,#7,0.9786,-0.016904,-0.20508,59.337,-0.033296,0.97048,-0.23887,108.56,0.20307,0.24059,0.94915,101.3
> view matrix models
> #2,0.94755,-0.2707,-0.1699,26.126,-0.16725,-0.87299,0.45816,86.568,-0.27235,-0.40571,-0.87248,183.96,#3,0.98466,-0.039639,-0.16995,60.994,-0.0063134,0.96513,-0.26168,107.22,0.1744,0.25874,0.95007,101.98,#4,0.89317,0.3232,-0.31271,53.769,-0.40749,0.8758,-0.2587,102.42,0.19025,0.35849,0.91394,100.93,#5,0.77825,0.46143,-0.42593,53.787,-0.55556,0.82211,-0.12446,97.235,0.29273,0.33349,0.89615,102.42,#6,0.98529,-0.16665,-0.03786,59.081,0.163,0.98297,-0.084911,108.66,0.051366,0.077491,0.99567,101.91,#7,0.9786,-0.016904,-0.20508,59.92,-0.033296,0.97048,-0.23887,108.53,0.20307,0.24059,0.94915,100.99
> hide #!8 models
> hide #!9 models
> view matrix models
> #2,0.94755,-0.2707,-0.1699,43.394,-0.16725,-0.87299,0.45816,107.56,-0.27235,-0.40571,-0.87248,205.6,#3,0.98466,-0.039639,-0.16995,78.261,-0.0063134,0.96513,-0.26168,128.21,0.1744,0.25874,0.95007,123.62,#4,0.89317,0.3232,-0.31271,71.036,-0.40749,0.8758,-0.2587,123.41,0.19025,0.35849,0.91394,122.57,#5,0.77825,0.46143,-0.42593,71.054,-0.55556,0.82211,-0.12446,118.23,0.29273,0.33349,0.89615,124.06,#6,0.98529,-0.16665,-0.03786,76.348,0.163,0.98297,-0.084911,129.65,0.051366,0.077491,0.99567,123.55,#7,0.9786,-0.016904,-0.20508,77.188,-0.033296,0.97048,-0.23887,129.52,0.20307,0.24059,0.94915,122.63
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.23861,-0.76856,-0.59361,100.43,-0.72388,-0.54824,0.41884,135.78,-0.64735,0.32976,-0.68716,212.03,#3,0.6579,0.52322,0.54168,63.799,-0.59488,0.80211,-0.052264,126.46,-0.46183,-0.28785,0.83896,128.75,#4,0.47702,0.76155,0.43874,57.409,-0.85591,0.51594,0.035031,127,-0.19969,-0.39223,0.89793,134.69,#5,0.44074,0.7971,0.41276,56.701,-0.89761,0.38796,0.20924,122.97,0.0066539,-0.46272,0.88648,138.2,#6,0.62494,0.32306,0.71069,63.248,-0.46791,0.88372,0.0097351,128.77,-0.62491,-0.33862,0.70344,129.12,#7,0.66689,0.52342,0.53036,62.938,-0.611,0.79152,-0.012872,128.1,-0.42653,-0.31547,0.84767,128.1
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.23861,-0.76856,-0.59361,104.69,-0.72388,-0.54824,0.41884,143.52,-0.64735,0.32976,-0.68716,212.92,#3,0.6579,0.52322,0.54168,68.059,-0.59488,0.80211,-0.052264,134.21,-0.46183,-0.28785,0.83896,129.64,#4,0.47702,0.76155,0.43874,61.67,-0.85591,0.51594,0.035031,134.75,-0.19969,-0.39223,0.89793,135.58,#5,0.44074,0.7971,0.41276,60.961,-0.89761,0.38796,0.20924,130.72,0.0066539,-0.46272,0.88648,139.09,#6,0.62494,0.32306,0.71069,67.508,-0.46791,0.88372,0.0097351,136.51,-0.62491,-0.33862,0.70344,130.01,#7,0.66689,0.52342,0.53036,67.198,-0.611,0.79152,-0.012872,135.84,-0.42653,-0.31547,0.84767,128.99
> view matrix models
> #2,0.23861,-0.76856,-0.59361,131.21,-0.72388,-0.54824,0.41884,133.67,-0.64735,0.32976,-0.68716,184.85,#3,0.6579,0.52322,0.54168,94.583,-0.59488,0.80211,-0.052264,124.35,-0.46183,-0.28785,0.83896,101.57,#4,0.47702,0.76155,0.43874,88.194,-0.85591,0.51594,0.035031,124.89,-0.19969,-0.39223,0.89793,107.5,#5,0.44074,0.7971,0.41276,87.486,-0.89761,0.38796,0.20924,120.86,0.0066539,-0.46272,0.88648,111.01,#6,0.62494,0.32306,0.71069,94.033,-0.46791,0.88372,0.0097351,126.66,-0.62491,-0.33862,0.70344,101.94,#7,0.66689,0.52342,0.53036,93.722,-0.611,0.79152,-0.012872,125.99,-0.42653,-0.31547,0.84767,100.91
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.19627,-0.97212,0.12828,119.74,-0.90523,0.22992,0.35734,142.91,-0.37688,-0.045986,-0.92512,183.94,#3,0.10718,0.9922,0.063699,113.55,-0.99402,0.10827,-0.013873,124.07,-0.020662,-0.061831,0.99787,94.665,#4,-0.26977,0.9618,0.046457,108.28,-0.95271,-0.2736,0.1322,130.77,0.13986,-0.0085979,0.99013,96.588,#5,-0.38093,0.91058,0.16043,103.91,-0.87319,-0.41134,0.26141,129.93,0.30403,-0.040507,0.9518,99.633,#6,0.22508,0.94104,0.25254,114.78,-0.95577,0.26361,-0.13042,126.12,-0.1893,-0.21202,0.95876,94.504,#7,0.091109,0.99239,0.08289,114.39,-0.99572,0.089465,0.02334,125.43,0.015747,-0.084662,0.99629,93.528
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.19627,-0.97212,0.12828,123.48,-0.90523,0.22992,0.35734,150.37,-0.37688,-0.045986,-0.92512,193.92,#3,0.10718,0.9922,0.063699,117.28,-0.99402,0.10827,-0.013873,131.54,-0.020662,-0.061831,0.99787,104.64,#4,-0.26977,0.9618,0.046457,112.02,-0.95271,-0.2736,0.1322,138.24,0.13986,-0.0085979,0.99013,106.56,#5,-0.38093,0.91058,0.16043,107.65,-0.87319,-0.41134,0.26141,137.39,0.30403,-0.040507,0.9518,109.61,#6,0.22508,0.94104,0.25254,118.52,-0.95577,0.26361,-0.13042,133.59,-0.1893,-0.21202,0.95876,104.48,#7,0.091109,0.99239,0.08289,118.12,-0.99572,0.089465,0.02334,132.9,0.015747,-0.084662,0.99629,103.5
> view matrix models
> #2,-0.19627,-0.97212,0.12828,119.18,-0.90523,0.22992,0.35734,146.79,-0.37688,-0.045986,-0.92512,193.24,#3,0.10718,0.9922,0.063699,112.98,-0.99402,0.10827,-0.013873,127.95,-0.020662,-0.061831,0.99787,103.96,#4,-0.26977,0.9618,0.046457,107.72,-0.95271,-0.2736,0.1322,134.66,0.13986,-0.0085979,0.99013,105.89,#5,-0.38093,0.91058,0.16043,103.35,-0.87319,-0.41134,0.26141,133.81,0.30403,-0.040507,0.9518,108.93,#6,0.22508,0.94104,0.25254,114.21,-0.95577,0.26361,-0.13042,130.01,-0.1893,-0.21202,0.95876,103.8,#7,0.091109,0.99239,0.08289,113.82,-0.99572,0.089465,0.02334,129.31,0.015747,-0.084662,0.99629,102.83
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.0094258,-0.9945,0.10435,110.83,-0.96264,0.037266,0.26821,154.91,-0.27062,-0.097923,-0.95769,189.76,#3,0.28797,0.95747,0.01794,112.41,-0.95227,0.28432,0.1111,125.29,0.10127,-0.049076,0.99365,103.26,#4,-0.097335,0.99493,-0.025333,105.92,-0.96436,-0.087991,0.24954,131.06,0.24604,0.048718,0.96803,104.23,#5,-0.22879,0.97132,0.064777,101.64,-0.88901,-0.23559,0.39262,129.76,0.39662,0.032241,0.91742,107.24,#6,0.40473,0.88593,0.22654,113.25,-0.91193,0.40937,0.028287,127.5,-0.06768,-0.21804,0.97359,102.88,#7,0.27077,0.96217,0.030057,113.04,-0.95282,0.26343,0.15082,126.64,0.1372,-0.069478,0.9881,101.99
> transparency #1.1 50
> volume #1 level 0.1207
> select subtract #2
3385 atoms, 3459 bonds, 429 residues, 5 models selected
> select subtract #3
2478 atoms, 2522 bonds, 317 residues, 4 models selected
> select subtract #4
1729 atoms, 1762 bonds, 222 residues, 3 models selected
> select subtract #5
1030 atoms, 1052 bonds, 132 residues, 2 models selected
> select subtract #6
311 atoms, 318 bonds, 36 residues, 1 model selected
> select subtract #7
Nothing selected
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> fitmap #2 inMap #1
Fit molecule 4A9_Fab_210811.pdb (#2) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 3347 atoms
average map value = 0.1758, steps = 96
shifted from previous position = 9.01
rotated from previous position = 13 degrees
atoms outside contour = 942, contour level = 0.12071
Position of 4A9_Fab_210811.pdb (#2) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.20938445 -0.97605576 0.05893470 109.92748417
-0.94692939 -0.18736562 0.26118738 156.46915572
-0.24389112 -0.11049557 -0.96348734 191.51701511
Axis -0.77383579 0.63047672 0.06064047
Axis point 0.00000000 137.97530375 88.99641558
Rotation angle (degrees) 166.10423927
Shift along axis 25.19801967
> show #3 models
> hide #!2 models
> fitmap #3 inMap #1
Fit molecule AaRseP_1to112.pdb (#3) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 907 atoms
average map value = 0.1438, steps = 108
shifted from previous position = 10.5
rotated from previous position = 12.9 degrees
atoms outside contour = 343, contour level = 0.12071
Position of AaRseP_1to112.pdb (#3) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.48947494 0.87167994 -0.02425616 119.57834731
-0.86220977 0.48794266 0.13603774 125.83010573
0.13041699 -0.04567317 0.99040667 105.86259380
Axis -0.10382097 -0.08837288 -0.99066212
Axis point 152.21916427 -32.73578411 0.00000000
Rotation angle (degrees) 61.05877685
Shift along axis -128.40877107
> show #4 models
> hide #3 models
> fitmap #4 inMap #1
Fit molecule AaRseP_113to207.pdb (#4) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 749 atoms
average map value = 0.1896, steps = 84
shifted from previous position = 4.6
rotated from previous position = 12.9 degrees
atoms outside contour = 188, contour level = 0.12071
Position of AaRseP_113to207.pdb (#4) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.11426652 0.98868374 -0.09719890 111.93947350
-0.95569937 0.13611200 0.26098320 130.07660374
0.27125979 0.06307128 0.96043747 106.58886698
Axis -0.09951033 -0.18526142 -0.97763792
Axis point 109.80878374 -0.81135711 0.00000000
Rotation angle (degrees) 83.94932662
Shift along axis -139.44262831
> show #5 models
> hide #4 models
> fitmap #5 inMap #1
Fit molecule AaRseP_208to297.pdb (#5) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 699 atoms
average map value = 0.1489, steps = 64
shifted from previous position = 3.21
rotated from previous position = 13 degrees
atoms outside contour = 223, contour level = 0.12071
Position of AaRseP_208to297.pdb (#5) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.03293041 0.99863454 -0.04055419 108.01814556
-0.90783461 -0.01291554 0.41912946 127.91531633
0.41803337 0.05061860 0.90702032 109.60555483
Axis -0.18470092 -0.22984817 -0.95553932
Axis point 88.56678240 11.94104439 0.00000000
Rotation angle (degrees) 93.98026206
Shift along axis -154.08456957
> hide #5 models
> show #6 models
> fitmap #6 inMap #1
Fit molecule AaRseP_298to393.pdb (#6) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 719 atoms
average map value = 0.1179, steps = 72
shifted from previous position = 2.56
rotated from previous position = 13.6 degrees
atoms outside contour = 392, contour level = 0.12071
Position of AaRseP_298to393.pdb (#6) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.24088083 0.92223922 0.30240906 115.19638648
-0.94156063 0.29764205 -0.15771109 126.07660919
-0.23545701 -0.24674688 0.94004041 101.72030741
Axis -0.04584982 0.27697922 -0.95978138
Axis point 151.52142916 3.19199362 0.00000000
Rotation angle (degrees) 76.15585348
Shift along axis -67.99039031
> volume #1 level 0.1235
> volume #1 level 0.1558
> ui mousemode right "translate selected models"
> select add #6
719 atoms, 734 bonds, 96 residues, 1 model selected
> view matrix models
> #6,0.24088,0.92224,0.30241,117.33,-0.94156,0.29764,-0.15771,125.73,-0.23546,-0.24675,0.94004,104.12
> view matrix models
> #6,0.24088,0.92224,0.30241,116.36,-0.94156,0.29764,-0.15771,129.58,-0.23546,-0.24675,0.94004,106.67
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.38216,0.92335,-0.037067,113.51,-0.90643,0.38236,0.17942,130.74,0.17984,-0.034969,0.98307,102.9
> fitmap #6 inMap #1
Fit molecule AaRseP_298to393.pdb (#6) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 719 atoms
average map value = 0.1394, steps = 92
shifted from previous position = 6.3
rotated from previous position = 21 degrees
atoms outside contour = 443, contour level = 0.15584
Position of AaRseP_298to393.pdb (#6) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.59792219 0.77694371 0.19709775 119.90918134
-0.80065608 0.59055135 0.10098984 128.18207329
-0.03793292 -0.21819157 0.97516846 105.44787773
Axis -0.19622205 0.14448900 -0.96985557
Axis point 193.35432861 -27.17771529 0.00000000
Rotation angle (degrees) 54.42127570
Shift along axis -107.27713879
> show #7 models
> select subtract #6
Nothing selected
> hide #6 models
> fitmap #7 inMap #1
Fit molecule AaRseP_394to429.pdb (#7) to map
cryosparc_P113_J223_009_volume_map.mrc (#1) using 311 atoms
average map value = 0.1193, steps = 92
shifted from previous position = 12.6
rotated from previous position = 12.7 degrees
atoms outside contour = 269, contour level = 0.15584
Position of AaRseP_394to429.pdb (#7) relative to
cryosparc_P113_J223_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.46854534 0.88310246 -0.02439911 120.01530465
-0.86828920 0.46542740 0.17161352 127.28250397
0.16290834 -0.05922323 0.98486216 104.68118155
Axis -0.12994339 -0.10543973 -0.98589917
Axis point 147.55514276 -27.64707829 0.00000000
Rotation angle (degrees) 62.65047690
Shift along axis -132.22091801
> volume #1 level 0.1305
> show #6 models
> show #5 models
> show #4 models
> show #3 models
> show #!2 models
> save
> /Users/asahi/Documents/servalcat関連/P113_W1/J224_close/P113_J223_fit_240214.pdb
> save
> /Users/asahi/Documents/servalcat関連/P113_W1/J223_open/P113_J223_fit_240214.pdb
> models #2-7
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #!2 models
> hide #3 models
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J223_open/P113_J223_fit_240214-coot-0.pdb
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event
if self.handle_drag_and_drop(event):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 563, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1918, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open
return pdb.open_pdb(session, data, file_name, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/pdb.py", line 78, in open_pdb
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 0:
invalid start byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 0:
invalid start byte
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
See log for complete Python traceback.
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J223_open/P113_J223_fit_240214-coot-0.pdb
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event
if self.handle_drag_and_drop(event):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 563, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1918, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open
return pdb.open_pdb(session, data, file_name, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/pdb.py", line 78, in open_pdb
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 0:
invalid start byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 0:
invalid start byte
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
See log for complete Python traceback.
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J223_open/P113_J223_fit_240214.pdb
Summary of feedback from opening
/Users/asahi/Documents/servalcat関連/P113_W1/J223_open/P113_J223_fit_240214.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
3380 messages similar to the above omitted
Chain information for P113_J223_fit_240214.pdb #10
---
Chain | Description
A | No description available
H | No description available
L | No description available
> isolde start
> set selectionWidth 4
> 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 84 residues in model #10 to IUPAC-IUB
standards.
Chain information for P113_J223_fit_240214.pdb
---
Chain | Description
10.2/A | No description available
10.2/H | No description available
10.2/L | No description available
ISOLDE: created disulfide bonds between the following residues:
H226-L214; H24-H100; H151-H206; L23-L88; L134-L194
> clipper associate #1 toModel #10
Opened cryosparc_P113_J223_009_volume_map.mrc as #10.1.1.1, grid size
180,180,180, pixel 1.35, shown at step 1, values float32
> isolde sim start #10.2/H-L,A
Sim termination reason: None
ISOLDE: stopped sim
> addh #10.2
Summary of feedback from adding hydrogens to P113_J223_fit_240214.pdb #10.2
---
notes | No usable SEQRES records for P113_J223_fit_240214.pdb (#10.2) chain A;
guessing termini instead
No usable SEQRES records for P113_J223_fit_240214.pdb (#10.2) chain H;
guessing termini instead
No usable SEQRES records for P113_J223_fit_240214.pdb (#10.2) chain L;
guessing termini instead
Chain-initial residues that are actual N termini: P113_J223_fit_240214.pdb
#10.2/A MET 1, P113_J223_fit_240214.pdb #10.2/H GLU 3,
P113_J223_fit_240214.pdb #10.2/L ASP 1
Chain-initial residues that are not actual N termini: P113_J223_fit_240214.pdb
#10.2/H THR 143
Chain-final residues that are actual C termini: P113_J223_fit_240214.pdb
#10.2/H CYS 226, P113_J223_fit_240214.pdb #10.2/L CYS 214
Chain-final residues that are not actual C termini: P113_J223_fit_240214.pdb
#10.2/A ARG 429, P113_J223_fit_240214.pdb #10.2/H GLY 138
746 hydrogen bonds
Adding 'H' to P113_J223_fit_240214.pdb #10.2/H THR 143
P113_J223_fit_240214.pdb #10.2/A ARG 429 is not terminus, removing H atom from
'C'
6826 hydrogens added
> isolde sim start #10.2/H-L,A
ISOLDE: started sim
> volume #10.1.1.1 level 0.1203
> volume #10.1.1.1 level 0.1399
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 23 residues in model #10.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save
> /Users/asahi/Documents/servalcat関連/P113_W1/J223_open/P113_J223_fit_240214_isolde0.pdb
> models #10
> hide #!10 models
> hide #!10.1 models
> hide #!10.2 models
> hide #10.3 models
> select add #10.2
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 15 models selected
> select add #10.2
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 15 models selected
> select add #10
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 22 models selected
> select add #10.2
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 22 models selected
> open /Users/asahi/Downloads/cryosparc_P113_J128_007_volume_map.mrc
Opened cryosparc_P113_J128_007_volume_map.mrc as #1, grid size 180,180,180,
pixel 1.35, shown at level 0.0907, step 1, values float32
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/4A9_Fab_210811.pdb
Chain information for 4A9_Fab_210811.pdb #11
---
Chain | Description
H | No description available
L | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_1to112.pdb
Chain information for AaRseP_1to112.pdb #12
---
Chain | Description
A | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_113to207.pdb
Chain information for AaRseP_113to207.pdb #13
---
Chain | Description
A | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_208to297.pdb
Chain information for AaRseP_208to297.pdb #14
---
Chain | Description
A | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_298to393.pdb
Chain information for AaRseP_298to393.pdb #15
---
Chain | Description
A | No description available
> open
> /Users/asahi/Documents/servalcat関連/230822_AaRseP_AF2_model/AaRseP_394to429.pdb
Chain information for AaRseP_394to429.pdb #16
---
Chain | Description
A | No description available
> transparency #1.1 50
> select add #11
16905 atoms, 17150 bonds, 2 pseudobonds, 1297 residues, 24 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #10,1,0,0,49.721,0,1,0,15.226,0,0,1,166.19,#11,1,0,0,49.721,0,1,0,15.226,0,0,1,166.19
> select subtract #11
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 22 models selected
> select add #12
14465 atoms, 14659 bonds, 1 pseudobond, 975 residues, 23 models selected
> select add #13
15214 atoms, 15419 bonds, 1 pseudobond, 1070 residues, 24 models selected
> select add #14
15913 atoms, 16129 bonds, 1 pseudobond, 1160 residues, 25 models selected
> select add #15
16632 atoms, 16863 bonds, 1 pseudobond, 1256 residues, 26 models selected
> select add #16
16943 atoms, 17181 bonds, 1 pseudobond, 1292 residues, 27 models selected
> view matrix models
> #10,1,0,0,96.702,0,1,0,39.618,0,0,1,321.99,#12,1,0,0,46.982,0,1,0,24.392,0,0,1,155.79,#13,1,0,0,46.982,0,1,0,24.392,0,0,1,155.79,#14,1,0,0,46.982,0,1,0,24.392,0,0,1,155.79,#15,1,0,0,46.982,0,1,0,24.392,0,0,1,155.79,#16,1,0,0,46.982,0,1,0,24.392,0,0,1,155.79
> select add #11
20290 atoms, 20609 bonds, 2 pseudobonds, 1726 residues, 29 models selected
> view matrix models
> #10,1,0,0,118.02,0,1,0,108.5,0,0,1,314.67,#11,1,0,0,71.042,0,1,0,84.112,0,0,1,158.88,#12,1,0,0,68.303,0,1,0,93.279,0,0,1,148.48,#13,1,0,0,68.303,0,1,0,93.279,0,0,1,148.48,#14,1,0,0,68.303,0,1,0,93.279,0,0,1,148.48,#15,1,0,0,68.303,0,1,0,93.279,0,0,1,148.48,#16,1,0,0,68.303,0,1,0,93.279,0,0,1,148.48
> view matrix models
> #10,1,0,0,116.77,0,1,0,96.969,0,0,1,300.86,#11,1,0,0,69.785,0,1,0,72.577,0,0,1,145.06,#12,1,0,0,67.045,0,1,0,81.744,0,0,1,134.67,#13,1,0,0,67.045,0,1,0,81.744,0,0,1,134.67,#14,1,0,0,67.045,0,1,0,81.744,0,0,1,134.67,#15,1,0,0,67.045,0,1,0,81.744,0,0,1,134.67,#16,1,0,0,67.045,0,1,0,81.744,0,0,1,134.67
> select subtract #12
19383 atoms, 19672 bonds, 2 pseudobonds, 1614 residues, 28 models selected
> select subtract #13
18634 atoms, 18912 bonds, 2 pseudobonds, 1519 residues, 27 models selected
> select subtract #14
17935 atoms, 18202 bonds, 2 pseudobonds, 1429 residues, 26 models selected
> select subtract #15
17216 atoms, 17468 bonds, 2 pseudobonds, 1333 residues, 25 models selected
> select subtract #16
16905 atoms, 17150 bonds, 2 pseudobonds, 1297 residues, 24 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.95929,-0.21134,0.18736,136.33,-0.26823,-0.88945,0.37005,96.926,0.088438,-0.40524,-0.90992,34.182,#11,0.95929,-0.21134,0.18736,67.225,-0.26823,-0.88945,0.37005,73.572,0.088438,-0.40524,-0.90992,181.67
> view matrix models
> #10,0.99372,-0.094088,0.060483,122.4,-0.10994,-0.9212,0.37324,96.518,0.020599,-0.37755,-0.92576,32.787,#11,0.99372,-0.094088,0.060483,68.587,-0.10994,-0.9212,0.37324,66.004,0.020599,-0.37755,-0.92576,185.26
> view matrix models
> #10,0.58134,-0.7765,-0.2431,63.777,-0.75852,-0.6253,0.18342,78.854,-0.29444,0.077764,-0.9525,41.17,#11,0.58134,-0.7765,-0.2431,93.279,-0.75852,-0.6253,0.18342,101.17,-0.29444,0.077764,-0.9525,201.5
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.58134,-0.7765,-0.2431,43.193,-0.75852,-0.6253,0.18342,103.1,-0.29444,0.077764,-0.9525,41.31,#11,0.58134,-0.7765,-0.2431,72.695,-0.75852,-0.6253,0.18342,125.42,-0.29444,0.077764,-0.9525,201.64
> view matrix models
> #10,0.58134,-0.7765,-0.2431,61.661,-0.75852,-0.6253,0.18342,105.35,-0.29444,0.077764,-0.9525,42.391,#11,0.58134,-0.7765,-0.2431,91.163,-0.75852,-0.6253,0.18342,127.67,-0.29444,0.077764,-0.9525,202.72
> view matrix models
> #10,0.58134,-0.7765,-0.2431,71.818,-0.75852,-0.6253,0.18342,129.88,-0.29444,0.077764,-0.9525,29.854,#11,0.58134,-0.7765,-0.2431,101.32,-0.75852,-0.6253,0.18342,152.2,-0.29444,0.077764,-0.9525,190.19
> fitmap #11 inMap #1
Fit molecule 4A9_Fab_210811.pdb (#11) to map
cryosparc_P113_J128_007_volume_map.mrc (#1) using 3347 atoms
average map value = 0.1808, steps = 180
shifted from previous position = 4.95
rotated from previous position = 28.9 degrees
atoms outside contour = 534, contour level = 0.090668
Position of 4A9_Fab_210811.pdb (#11) relative to
cryosparc_P113_J128_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.30561743 -0.94280081 0.13313388 103.93077764
-0.92635132 -0.26208364 0.27052799 155.54281718
-0.22016179 -0.20600681 -0.95346210 190.22658148
Axis -0.80300099 0.59533275 0.02771875
Axis point 0.00000000 134.23772588 83.01829874
Rotation angle (degrees) 162.73922453
Shift along axis 14.41605987
> select subtract #11
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 22 models selected
> select add #12
14465 atoms, 14659 bonds, 1 pseudobond, 975 residues, 23 models selected
> select add #13
15214 atoms, 15419 bonds, 1 pseudobond, 1070 residues, 24 models selected
> select add #14
15913 atoms, 16129 bonds, 1 pseudobond, 1160 residues, 25 models selected
> select add #15
16632 atoms, 16863 bonds, 1 pseudobond, 1256 residues, 26 models selected
> select add #16
16943 atoms, 17181 bonds, 1 pseudobond, 1292 residues, 27 models selected
> view matrix models
> #10,0.58134,-0.7765,-0.2431,89.81,-0.75852,-0.6253,0.18342,180.14,-0.29444,0.077764,-0.9525,3.4919,#12,1,0,0,85.038,0,1,0,132,0,0,1,108.3,#13,1,0,0,85.038,0,1,0,132,0,0,1,108.3,#14,1,0,0,85.038,0,1,0,132,0,0,1,108.3,#15,1,0,0,85.038,0,1,0,132,0,0,1,108.3,#16,1,0,0,85.038,0,1,0,132,0,0,1,108.3
> view matrix models
> #10,0.58134,-0.7765,-0.2431,106.44,-0.75852,-0.6253,0.18342,165.42,-0.29444,0.077764,-0.9525,6.8751,#12,1,0,0,101.67,0,1,0,117.28,0,0,1,111.69,#13,1,0,0,101.67,0,1,0,117.28,0,0,1,111.69,#14,1,0,0,101.67,0,1,0,117.28,0,0,1,111.69,#15,1,0,0,101.67,0,1,0,117.28,0,0,1,111.69,#16,1,0,0,101.67,0,1,0,117.28,0,0,1,111.69
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.51928,-0.80471,0.28773,164.47,-0.83921,0.54378,0.0062676,97.388,-0.1615,-0.23821,-0.95769,19.572,#12,0.25304,0.94985,-0.18374,98.275,-0.91163,0.29768,0.28341,117.11,0.32389,0.095791,0.94123,112.07,#13,0.25304,0.94985,-0.18374,98.275,-0.91163,0.29768,0.28341,117.11,0.32389,0.095791,0.94123,112.07,#14,0.25304,0.94985,-0.18374,98.275,-0.91163,0.29768,0.28341,117.11,0.32389,0.095791,0.94123,112.07,#15,0.25304,0.94985,-0.18374,98.275,-0.91163,0.29768,0.28341,117.11,0.32389,0.095791,0.94123,112.07,#16,0.25304,0.94985,-0.18374,98.275,-0.91163,0.29768,0.28341,117.11,0.32389,0.095791,0.94123,112.07
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.51928,-0.80471,0.28773,183.45,-0.83921,0.54378,0.0062676,98.147,-0.1615,-0.23821,-0.95769,20.369,#12,0.25304,0.94985,-0.18374,117.25,-0.91163,0.29768,0.28341,117.87,0.32389,0.095791,0.94123,112.87,#13,0.25304,0.94985,-0.18374,117.25,-0.91163,0.29768,0.28341,117.87,0.32389,0.095791,0.94123,112.87,#14,0.25304,0.94985,-0.18374,117.25,-0.91163,0.29768,0.28341,117.87,0.32389,0.095791,0.94123,112.87,#15,0.25304,0.94985,-0.18374,117.25,-0.91163,0.29768,0.28341,117.87,0.32389,0.095791,0.94123,112.87,#16,0.25304,0.94985,-0.18374,117.25,-0.91163,0.29768,0.28341,117.87,0.32389,0.095791,0.94123,112.87
> view matrix models
> #10,-0.51928,-0.80471,0.28773,187.8,-0.83921,0.54378,0.0062676,105.21,-0.1615,-0.23821,-0.95769,16.181,#12,0.25304,0.94985,-0.18374,121.61,-0.91163,0.29768,0.28341,124.93,0.32389,0.095791,0.94123,108.68,#13,0.25304,0.94985,-0.18374,121.61,-0.91163,0.29768,0.28341,124.93,0.32389,0.095791,0.94123,108.68,#14,0.25304,0.94985,-0.18374,121.61,-0.91163,0.29768,0.28341,124.93,0.32389,0.095791,0.94123,108.68,#15,0.25304,0.94985,-0.18374,121.61,-0.91163,0.29768,0.28341,124.93,0.32389,0.095791,0.94123,108.68,#16,0.25304,0.94985,-0.18374,121.61,-0.91163,0.29768,0.28341,124.93,0.32389,0.095791,0.94123,108.68
> view matrix models
> #10,-0.51928,-0.80471,0.28773,188.12,-0.83921,0.54378,0.0062676,106.24,-0.1615,-0.23821,-0.95769,11.263,#12,0.25304,0.94985,-0.18374,121.93,-0.91163,0.29768,0.28341,125.96,0.32389,0.095791,0.94123,103.76,#13,0.25304,0.94985,-0.18374,121.93,-0.91163,0.29768,0.28341,125.96,0.32389,0.095791,0.94123,103.76,#14,0.25304,0.94985,-0.18374,121.93,-0.91163,0.29768,0.28341,125.96,0.32389,0.095791,0.94123,103.76,#15,0.25304,0.94985,-0.18374,121.93,-0.91163,0.29768,0.28341,125.96,0.32389,0.095791,0.94123,103.76,#16,0.25304,0.94985,-0.18374,121.93,-0.91163,0.29768,0.28341,125.96,0.32389,0.095791,0.94123,103.76
> view matrix models
> #10,-0.51928,-0.80471,0.28773,184.22,-0.83921,0.54378,0.0062676,108.98,-0.1615,-0.23821,-0.95769,13.856,#12,0.25304,0.94985,-0.18374,118.02,-0.91163,0.29768,0.28341,128.7,0.32389,0.095791,0.94123,106.35,#13,0.25304,0.94985,-0.18374,118.02,-0.91163,0.29768,0.28341,128.7,0.32389,0.095791,0.94123,106.35,#14,0.25304,0.94985,-0.18374,118.02,-0.91163,0.29768,0.28341,128.7,0.32389,0.095791,0.94123,106.35,#15,0.25304,0.94985,-0.18374,118.02,-0.91163,0.29768,0.28341,128.7,0.32389,0.095791,0.94123,106.35,#16,0.25304,0.94985,-0.18374,118.02,-0.91163,0.29768,0.28341,128.7,0.32389,0.095791,0.94123,106.35
> select subtract #16
16632 atoms, 16863 bonds, 1 pseudobond, 1256 residues, 26 models selected
> select subtract #15
15913 atoms, 16129 bonds, 1 pseudobond, 1160 residues, 25 models selected
> select subtract #13
15164 atoms, 15369 bonds, 1 pseudobond, 1065 residues, 24 models selected
> select subtract #12
14257 atoms, 14432 bonds, 1 pseudobond, 953 residues, 23 models selected
> select add #13
15006 atoms, 15192 bonds, 1 pseudobond, 1048 residues, 24 models selected
> select subtract #13
14257 atoms, 14432 bonds, 1 pseudobond, 953 residues, 23 models selected
> fitmap #14 inMap #1
Fit molecule AaRseP_208to297.pdb (#14) to map
cryosparc_P113_J128_007_volume_map.mrc (#1) using 699 atoms
average map value = 0.141, steps = 92
shifted from previous position = 4.18
rotated from previous position = 18 degrees
atoms outside contour = 144, contour level = 0.090668
Position of AaRseP_208to297.pdb (#14) relative to
cryosparc_P113_J128_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02577181 0.99221899 -0.12180838 110.67435391
-0.89809238 0.03053502 0.43874559 127.22342229
0.43905113 0.12070245 0.89031737 109.78449838
Axis -0.15924084 -0.28081643 -0.94645892
Axis point 87.73795110 4.40071376 0.00000000
Rotation angle (degrees) 93.00710026
Shift along axis -157.25682239
> select add #13
15006 atoms, 15192 bonds, 1 pseudobond, 1048 residues, 24 models selected
> select subtract #14
14307 atoms, 14482 bonds, 1 pseudobond, 958 residues, 23 models selected
> fitmap #13 inMap #1
Fit molecule AaRseP_113to207.pdb (#13) to map
cryosparc_P113_J128_007_volume_map.mrc (#1) using 749 atoms
average map value = 0.1989, steps = 84
shifted from previous position = 1.94
rotated from previous position = 6.05 degrees
atoms outside contour = 106, contour level = 0.090668
Position of AaRseP_113to207.pdb (#13) relative to
cryosparc_P113_J128_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.16066962 0.96680347 -0.19868652 115.75307356
-0.94350412 0.20954933 0.25668863 129.72493931
0.28980208 0.14621948 0.94585127 106.31945514
Axis -0.05593751 -0.24735266 -0.96730949
Axis point 112.23877418 -14.10599928 0.00000000
Rotation angle (degrees) 80.90713495
Shift along axis -141.40656571
> volume #1 level 0.1104
> select add #16
14618 atoms, 14800 bonds, 1 pseudobond, 994 residues, 24 models selected
> select subtract #13
13869 atoms, 14040 bonds, 1 pseudobond, 899 residues, 23 models selected
> fitmap #16 inMap #1
Fit molecule AaRseP_394to429.pdb (#16) to map
cryosparc_P113_J128_007_volume_map.mrc (#1) using 311 atoms
average map value = 0.1138, steps = 156
shifted from previous position = 5.78
rotated from previous position = 11.3 degrees
atoms outside contour = 143, contour level = 0.11045
Position of AaRseP_394to429.pdb (#16) relative to
cryosparc_P113_J128_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.38885289 0.91453129 -0.11147171 118.27214406
-0.90303748 0.40231614 0.15054911 127.53082305
0.18252874 0.04212168 0.98229783 104.44471839
Axis -0.05878791 -0.15940314 -0.98546163
Axis point 137.48605072 -29.07859194 0.00000000
Rotation angle (degrees) 67.24860392
Shift along axis -130.20804841
> volume #1 level 0.1272
> select add #15
14588 atoms, 14774 bonds, 1 pseudobond, 995 residues, 24 models selected
> select subtract #16
14277 atoms, 14456 bonds, 1 pseudobond, 959 residues, 23 models selected
> fitmap #15 inMap #1
Fit molecule AaRseP_298to393.pdb (#15) to map
cryosparc_P113_J128_007_volume_map.mrc (#1) using 719 atoms
average map value = 0.136, steps = 120
shifted from previous position = 2.6
rotated from previous position = 12.3 degrees
atoms outside contour = 347, contour level = 0.12719
Position of AaRseP_298to393.pdb (#15) relative to
cryosparc_P113_J128_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.34673114 0.92884419 -0.13048368 118.49566591
-0.92865121 0.35950561 0.09144753 127.14244542
0.13185012 0.08946612 0.98722407 105.50851503
Axis -0.00105623 -0.13984202 -0.99017326
Axis point 138.96535056 -29.69784614 0.00000000
Rotation angle (degrees) 69.71253779
Shift along axis -122.37672567
> select subtract #15
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 22 models selected
> select add #12
14465 atoms, 14659 bonds, 1 pseudobond, 975 residues, 23 models selected
> fitmap #12 inMap #1
Fit molecule AaRseP_1to112.pdb (#12) to map
cryosparc_P113_J128_007_volume_map.mrc (#1) using 907 atoms
average map value = 0.1394, steps = 68
shifted from previous position = 3.39
rotated from previous position = 12.6 degrees
atoms outside contour = 385, contour level = 0.12719
Position of AaRseP_1to112.pdb (#12) relative to
cryosparc_P113_J128_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.38299795 0.91956994 -0.08777064 119.26997338
-0.91121679 0.39169072 0.12752385 126.42159780
0.15164605 0.03113671 0.98794432 105.71263049
Axis -0.05213246 -0.12949219 -0.99020906
Axis point 139.80245068 -28.68393239 0.00000000
Rotation angle (degrees) 67.58474660
Shift along axis -127.26605096
> select subtract #12
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 22 models selected
> save /Users/asahi/Documents/servalcat関連/P113_W1/P113_J128_fit_240214.pdb
> models #11-16
> color #1 #d6d6d6ff models
> color #1 silver models
> color #1 darkgrey models
> hide #!11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> volume #1 level 0.0861
> select add #10
13558 atoms, 13722 bonds, 1 pseudobond, 863 residues, 22 models selected
> surface dust #1 size 13.5
> color #1 silver models
> color #1 darkgrey models
> lighting full
> lighting shadows false
> save /Users/asahi/Desktop/wtre_128_1.png width 936 height 955 supersample 3
> transparentBackground true
> color #1 silver models
> color #1 #d6d6d6ff models
> color #1 silver models
> save /Users/asahi/Desktop/wtre_128_2.png width 936 height 955 supersample 3
> transparentBackground true
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J128_all/P113_J128_fit_240214-coot-0.pdb
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 563, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1918, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open
return pdb.open_pdb(session, data, file_name, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/pdb.py", line 78, in open_pdb
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 0:
invalid start byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 0:
invalid start byte
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
See log for complete Python traceback.
> open
> /Users/asahi/Documents/servalcat関連/P113_W1/J128_all/P113_J128_fit_240214-coot-0.pdb
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 563, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1918, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open
return pdb.open_pdb(session, data, file_name, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/pdb.py", line 78, in open_pdb
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 0:
invalid start byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 0:
invalid start byte
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,1
Model Number: Z1300005BJ/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 8日 23時間 41分
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 21 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Non-ASCII PDB |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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