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Opened 15 months ago
Closed 15 months ago
#15685 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00005380 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open C:/Users/yulab/Desktop/DS1/DS1_TR.cxs
Opened long_full_spike_230505_reconstruction.mrc as #2, grid size 288,288,288,
pixel 1.06, shown at level 0.00465, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc as #3, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc as #4, grid size
288,288,288, pixel 1.06, shown at level 0.0226, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at level 0.00084, step 1, values float32
Opened long_full_spike_230505_reconstruction.mrc gaussian as #7, grid size
288,288,288, pixel 1.06, shown at level 0.00297, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc gaussian as #8, grid size
288,288,288, pixel 1.06, shown at level 0.00291, step 1, values float32
Opened empty_spike_230505_reconstruction.mrc as #15, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 2, values float32
Opened empty_spike_230505_reconstruction.mrc gaussian as #16, grid size
288,288,288, pixel 1.06, shown at level 0.00281, step 1, values float32
opened ChimeraX session
> hide #!7 models
> open C:/Users/yulab/Desktop/DS1/all_VP2_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP5+8_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP6_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP7_DS1_sub.pdb
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP2_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 277 277 GLU P
2 LYS P 17 1 16
Start residue of secondary structure not found: HELIX 278 278 TYR P 24 ASN P
26 1 3
Start residue of secondary structure not found: HELIX 279 279 SER P 28 MET P
41 1 14
Start residue of secondary structure not found: HELIX 280 280 ALA P 75 MET P
100 1 26
Start residue of secondary structure not found: HELIX 281 281 GLU P 114 LEU P
119 1 6
3018 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP5+8_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
3470 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP6_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
1790 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP7_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
2127 messages similar to the above omitted
Chain information for all_VP2_DS1_sub.pdb #5
---
Chain | Description
1 | No description available
2 | No description available
Chain information for all_VP5+8_DS1_sub.pdb #9
---
Chain | Description
A B | No description available
C | No description available
Chain information for all_VP6_DS1_sub.pdb #10
---
Chain | Description
N O P T U V Z | No description available
Q R S | No description available
W X Y | No description available
Chain information for all_VP7_DS1_sub.pdb #11
---
Chain | Description
3 | No description available
A C G I | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
> lighting simple
> hide #5,10#!9,11 atoms
> show #5,10#!9,11 cartoons
> hide #5 models
> hide #!9 models
> hide #10 models
> hide #!11 models
> open C:/Users/yulab/Desktop/DS1/DS1_NTR_C_long_spike_reconstruction.mrc
> C:/Users/yulab/Desktop/DS1/DS1_NTR_C_others_spike_reconstruction.mrc
> C:/Users/yulab/Desktop/DS1/DS1_NTR_C_short_spike_reconstruction.mrc
Opened DS1_NTR_C_long_spike_reconstruction.mrc as #13.1, grid size
300,300,300, pixel 1.06, shown at level 0.0193, step 2, values float32
Opened DS1_NTR_C_others_spike_reconstruction.mrc as #13.2, grid size
300,300,300, pixel 1.06, shown at level 0.0177, step 2, values float32
Opened DS1_NTR_C_short_spike_reconstruction.mrc as #13.3, grid size
300,300,300, pixel 1.06, shown at level 0.0189, step 2, values float32
> hide #!13 models
> hide #!13.1 models
> hide #!13.2 models
> hide #!13.3 models
> show #!13.3 models
> show #!1 models
> hide #!1 models
> hide #!13.3 models
> show #!11 models
> color #11 magenta transparency 0
> color #11 #ff007f transparency 0
> color #11 cyan transparency 0
> color #11 #ffff7f transparency 0
> color #11 #aaaaff transparency 0
> color #11 #ffaa00 transparency 0
> color #11 #ff007f transparency 0
Drag select of 36 residues
> select up
822 atoms, 840 bonds, 116 residues, 1 model selected
> select up
6564 atoms, 6712 bonds, 896 residues, 1 model selected
> color sel cyan
> select #11
134588 atoms, 137391 bonds, 13 pseudobonds, 17165 residues, 2 models selected
> select clear
> hide #!11 models
> show #10 models
> color #10 #aaaaff transparency 0
> color #9 #ffaa00 transparency 0
> show #!9 models
> hide #10 models
> select #9
46989 atoms, 47943 bonds, 18 pseudobonds, 5892 residues, 2 models selected
> hide #!13 models
> ~select #9
Nothing selected
> hide #!9 models
> show #!9 models
> show #!9 cartoons
> show #10 models
> hide #!9 models
> hide #10 models
> show #!9 models
> show #10 models
> ui tool show "Side View"
> show #!11 models
> hide #!11 models
> hide #10 models
> hide #!9 models
> color #14 #ffaa00 transparency 0
> show #!14 models
> hide #!14 models
> show #!13.3 models
> save "C:/Users/yulab/Desktop/session 1-2024.7.cxs"
> color #13.3 #ff007f models transparency 0
> volume gaussian #13.3 sDev 3
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #17, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #17
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #17, minimum -0.002965,
maximum 0.008636, mean 6.088e-05, SD 0.001877, RMS 0.001878
> measure mapstats #17
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #17, minimum -0.002965,
maximum 0.008636, mean 6.088e-05, SD 0.001877, RMS 0.001878
> volume #17 level 0.001878
> volume gausssian #17 sd 1
Expected a density maps specifier or a keyword
> close #17
> show #!13.3 models
> volume gausssian #13.3 sd 1
Expected a density maps specifier or a keyword
> volume gaussian #13.3 sDev 1
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #17, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> volume gaussian #13.3 sDev 2
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #18, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!17 models
> hide #!18 models
> show #!17 models
> close #18
> measure mapstats #17
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #17, minimum -0.008048,
maximum 0.02086, mean 6.261e-05, SD 0.002563, RMS 0.002564
> volume #17 level 0.002564
> lighting simple
> show #!8 models
> ui mousemode right "rotate selected models"
> select #8
2 models selected
> view matrix models
> #8,0.85007,-0.52665,-0.0039021,103.47,0.52645,0.84949,0.03483,-61.325,-0.015028,-0.031662,0.99939,7.1808
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.85007,-0.52665,-0.0039021,119.83,0.52645,0.84949,0.03483,-85.407,-0.015028,-0.031662,0.99939,8.4681
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.83969,-0.543,0.0087036,122.42,0.5407,0.8374,0.080076,-91.043,-0.05077,-0.062533,0.99675,18.919
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.83969,-0.543,0.0087036,130.82,0.5407,0.8374,0.080076,-91.737,-0.05077,-0.062533,0.99675,9.887
> view matrix models
> #8,0.83969,-0.543,0.0087036,124.1,0.5407,0.8374,0.080076,-92.528,-0.05077,-0.062533,0.99675,9.5969
> view matrix models
> #8,0.83969,-0.543,0.0087036,128.63,0.5407,0.8374,0.080076,-95.91,-0.05077,-0.062533,0.99675,5.8634
> view matrix models
> #8,0.83969,-0.543,0.0087036,125.09,0.5407,0.8374,0.080076,-99.246,-0.05077,-0.062533,0.99675,7.0681
> view matrix models
> #8,0.83969,-0.543,0.0087036,-0.71254,0.5407,0.8374,0.080076,43.976,-0.05077,-0.062533,0.99675,2.2524
> view matrix models
> #8,0.83969,-0.543,0.0087036,123.93,0.5407,0.8374,0.080076,-93.261,-0.05077,-0.062533,0.99675,-1.359
> view matrix models
> #8,0.83969,-0.543,0.0087036,122.37,0.5407,0.8374,0.080076,-96.703,-0.05077,-0.062533,0.99675,1.2521
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.83812,-0.54549,0.0026628,123.69,0.54449,0.83687,0.0564,-94.423,-0.032994,-0.04582,0.9984,-4.1929
> view matrix models
> #8,0.83127,-0.55562,0.0168,124.62,0.55541,0.83143,0.015925,-90.508,-0.022816,-0.0039074,0.99973,-12.28
> view matrix models
> #8,0.87093,-0.48769,-0.060317,117.29,0.48879,0.87239,0.0041501,-85.221,0.050596,-0.033097,0.99817,-18.829
> view matrix models
> #8,0.86767,-0.49707,-0.0082722,113.1,0.49709,0.8677,0.00068758,-85.364,0.006836,-0.0047086,0.99997,-16.7
> view matrix models
> #8,0.85325,-0.52127,-0.015466,119.83,0.51946,0.85216,-0.063069,-78.925,0.046055,0.045779,0.99789,-30.114
> view matrix models
> #8,0.86763,-0.49585,-0.036748,116.27,0.49208,0.86692,-0.079474,-75.077,0.071265,0.050871,0.99616,-34.525
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.86763,-0.49585,-0.036748,113.03,0.49208,0.86692,-0.079474,-47.33,0.071265,0.050871,0.99616,-19.154
> view matrix models
> #8,0.86763,-0.49585,-0.036748,123.17,0.49208,0.86692,-0.079474,-57.415,0.071265,0.050871,0.99616,-20.525
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.86926,-0.49202,0.048026,112.39,0.4939,0.86019,-0.127,-51.093,0.021177,0.13412,0.99074,-24.938
> view matrix models
> #8,0.86786,-0.49665,0.012926,117.43,0.4944,0.8608,-0.12079,-51.991,0.048862,0.11122,0.99259,-25.884
> view matrix models
> #8,0.87145,-0.4903,0.013269,115.87,0.48791,0.86381,-0.12562,-50.893,0.05013,0.11595,0.99199,-26.726
> view matrix models
> #8,0.9349,-0.34901,0.064504,78.691,0.3543,0.90695,-0.22786,-25.124,0.021026,0.23588,0.97155,-38.158
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.9349,-0.34901,0.064504,68.402,0.3543,0.90695,-0.22786,-16.814,0.021026,0.23588,0.97155,-34.413
> view matrix models
> #8,0.9349,-0.34901,0.064504,72.103,0.3543,0.90695,-0.22786,-17.56,0.021026,0.23588,0.97155,-41.58
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.96991,-0.24133,-0.032263,61.73,0.22482,0.93856,-0.26183,1.3241,0.093468,0.2467,0.96458,-53.437
> view matrix models
> #8,0.97704,-0.20845,-0.044061,57.022,0.20322,0.9739,-0.10109,-19.624,0.063982,0.089813,0.9939,-28.502
> view matrix models
> #8,0.98218,-0.18136,-0.049387,52.74,0.18286,0.98275,0.027749,-32.986,0.043502,-0.036285,0.99839,-6.7122
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.98218,-0.18136,-0.049387,55.362,0.18286,0.98275,0.027749,-58.99,0.043502,-0.036285,0.99839,-9.3012
> view matrix models
> #8,0.98218,-0.18136,-0.049387,55.665,0.18286,0.98275,0.027749,-55.487,0.043502,-0.036285,0.99839,-13.061
> ui tool show "Fit in Map"
> hide #!13 models
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2327732 points
correlation = 0.6132, correlation about mean = 0.2136, overlap = 61.74
steps = 220, shift = 13.5, angle = 11.2 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) relative
to short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.94330562 0.33153171 -0.01616230 -47.80050159
-0.32988872 0.94179122 0.06482846 74.55968761
0.03671421 -0.05582129 0.99776553 14.23745777
Axis -0.17889666 -0.07840406 -0.98073890
Axis point 191.06140785 182.92840156 0.00000000
Rotation angle (degrees) 19.70668838
Shift along axis -11.25766096
> view matrix models
> #8,0.98218,-0.18136,-0.049387,54.677,0.18286,0.98275,0.027749,-56.191,0.043502,-0.036285,0.99839,-12.666
> view matrix models
> #8,0.98218,-0.18136,-0.049387,55.367,0.18286,0.98275,0.027749,-56.608,0.043502,-0.036285,0.99839,-12.698
> view matrix models
> #8,0.98218,-0.18136,-0.049387,55.896,0.18286,0.98275,0.027749,-56.588,0.043502,-0.036285,0.99839,-13.708
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2327732 points
correlation = 0.6132, correlation about mean = 0.2136, overlap = 61.74
steps = 68, shift = 1.3, angle = 0.00258 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) relative
to short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.94330613 0.33152937 -0.01618109 -47.79907229
-0.32988683 0.94179469 0.06478759 74.55684696
0.03671826 -0.05577661 0.99776788 14.23380962
Axis -0.17877449 -0.07843998 -0.98075830
Axis point 191.05437090 182.92257418 0.00000000
Rotation angle (degrees) 19.70615091
Shift along axis -11.26291025
> hide #!8 models
> ~select #8
Nothing selected
> show #!14 models
> select #14
6389 atoms, 6536 bonds, 3 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.98895,0.13719,-0.056225,4.3598,-0.13943,0.9895,-0.038106,2.5312,0.050407,0.045524,0.99769,35.983
> view matrix models
> #14,0.98895,0.13719,-0.056225,7.1942,-0.13943,0.9895,-0.038106,2.1067,0.050407,0.045524,0.99769,27.257
> view matrix models
> #14,0.98895,0.13719,-0.056225,0.90233,-0.13943,0.9895,-0.038106,-3.4835,0.050407,0.045524,0.99769,26.325
> view matrix models
> #14,0.98895,0.13719,-0.056225,2.0432,-0.13943,0.9895,-0.038106,-3.0306,0.050407,0.045524,0.99769,24.323
Fit molecule wt_sub_VP5CT.pdb (#14) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) using 6389 atoms
average map value = 0.007936, steps = 76
shifted from previous position = 1.83
rotated from previous position = 11.6 degrees
atoms outside contour = 587, contour level = 0.002564
Position of wt_sub_VP5CT.pdb (#14) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) coordinates:
Matrix rotation and translation
0.97876004 -0.20487052 -0.00754054 55.22328801
0.20257034 0.97211837 -0.11811493 -34.29111638
0.03152856 0.11407868 0.99297130 18.54345442
Axis 0.49341696 -0.08302277 0.86582153
Axis point 169.74558733 140.80366832 -0.00000000
Rotation angle (degrees) 13.60880516
Shift along axis 46.15037265
> hide #!14 models
> ~select #14
Nothing selected
> color #17 #ff007f models transparency 0
> show #10 models
Fit molecule all_VP6_DS1_sub.pdb (#10) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) using 177623 atoms
average map value = 0.002805, steps = 344
shifted from previous position = 39
rotated from previous position = 11.3 degrees
atoms outside contour = 117770, contour level = 0.002564
Position of all_VP6_DS1_sub.pdb (#10) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) coordinates:
Matrix rotation and translation
0.94131758 -0.33558694 0.03609191 70.11596237
0.33712883 0.93999065 -0.05255224 -54.29794975
-0.01629022 0.06163597 0.99796575 -19.49512610
Axis 0.16685745 0.07654335 0.98300545
Axis point 190.70484863 181.36558709 0.00000000
Rotation angle (degrees) 20.00931802
Shift along axis -11.62059144
> hide #10 models
> color #5 #ffff7f transparency 0
> show #5 models
Fit molecule all_VP2_DS1_sub.pdb (#5) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) using 51920 atoms
average map value = 0.002309, steps = 180
shifted from previous position = 18.2
rotated from previous position = 7.56 degrees
atoms outside contour = 37490, contour level = 0.002564
Position of all_VP2_DS1_sub.pdb (#5) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) coordinates:
Matrix rotation and translation
0.98051129 -0.08864679 0.17532643 -8.16051665
0.09094379 0.99584300 -0.00509407 -14.83919525
-0.17414602 0.02093964 0.98449718 38.34149758
Axis 0.06611256 0.88748479 0.45607003
Axis point 203.98739165 0.00000000 70.64364046
Rotation angle (degrees) 11.35511001
Shift along axis 3.77733514
> color zone #17 near #5,10,14 distance 5
> color zone #17 near #5,10,14 distance 6
> hide #5 models
> lighting soft
> lighting simple
> lighting soft
> show #5 models
> select #5
51920 atoms, 52864 bonds, 6348 residues, 1 model selected
> view matrix models
> #5,0.99305,0.068034,0.096081,-9.4057,-0.073597,0.99574,0.055592,-1.3423,-0.091889,-0.062277,0.99382,55.662
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99623,-0.027574,0.082275,4.4522,0.028409,0.99956,-0.0089991,-17.592,-0.08199,0.011302,0.99657,43.099
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99623,-0.027574,0.082275,5.5747,0.028409,0.99956,-0.0089991,-24.732,-0.08199,0.011302,0.99657,11.742
> view matrix models
> #5,0.99623,-0.027574,0.082275,6.5493,0.028409,0.99956,-0.0089991,-26.232,-0.08199,0.011302,0.99657,6.7631
Fit molecule all_VP2_DS1_sub.pdb (#5) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) using 51920 atoms
average map value = 0.00224, steps = 452
shifted from previous position = 26.7
rotated from previous position = 14.4 degrees
atoms outside contour = 36400, contour level = 0.002564
Position of all_VP2_DS1_sub.pdb (#5) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) coordinates:
Matrix rotation and translation
0.95964191 -0.27667745 0.05036866 44.50660950
0.26800351 0.95400895 0.13431696 -46.14744395
-0.08521462 -0.11539720 0.98965749 51.76643797
Axis -0.40647351 0.22069639 0.88660723
Axis point 213.40575678 155.61982973 0.00000000
Rotation angle (degrees) 17.88885458
Shift along axis 17.62116619
> view matrix models
> #5,0.99356,-0.11319,-0.0053704,19.168,0.11175,0.97083,0.21214,-39.663,-0.018799,-0.21138,0.97722,34.887
> color zone #17 near #5,10,14 distance 6
> view matrix models
> #5,0.99356,-0.11319,-0.0053704,16.987,0.11175,0.97083,0.21214,-40,-0.018799,-0.21138,0.97722,28.544
> color zone #17 near #5,10,14 distance 6
> ~select #5
Nothing selected
> hide #5 models
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> save "C:/Users/yulab/Desktop/2024.7.23图/DS1-NTR-C-short spike(1)
> -2024.7.22.png" width 1133 height 834 supersample 3 transparentBackground
> true
> save "C:/Users/yulab/Desktop/session 2-2024.7.22.cxs"
> hide #!17 models
> show #!13.2 models
> volume gaussian #13.2 sDev 1
Opened DS1_NTR_C_others_spike_reconstruction.mrc gaussian as #18, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> color #18 #ff007f models transparency 0
> measure mapstats #18
Map DS1_NTR_C_others_spike_reconstruction.mrc gaussian #18, minimum -0.007177,
maximum 0.02053, mean 6.839e-05, SD 0.002456, RMS 0.002456
> volume #18 level 0.002456
> lighting simple
> hide #!13 models
> show #10 models
> select #10
177623 atoms, 181534 bonds, 22241 residues, 1 model selected
> ~select #10
Nothing selected
> hide #10 models
> show #!16 models
> select #16
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #16,1,0,0,-106.26,0,1,0,113.61,0,0,1,-13.881
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.92526,-0.37537,0.054773,238.87,0.37723,-0.89527,0.23703,322.48,-0.039938,0.23998,0.96996,-41.518
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.92526,-0.37537,0.054773,332.39,0.37723,-0.89527,0.23703,199.22,-0.039938,0.23998,0.96996,-26.371
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.92401,-0.36072,0.12684,323.2,0.38089,-0.89744,0.22254,200.35,0.033553,0.25394,0.96664,-39.375
> view matrix models
> #16,-0.72826,-0.66881,0.14948,338.18,0.68515,-0.70583,0.17994,128.85,-0.014843,0.23346,0.97225,-29.415
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.72826,-0.66881,0.14948,352.42,0.68515,-0.70583,0.17994,140.57,-0.014843,0.23346,0.97225,-31.434
> view matrix models
> #16,-0.72826,-0.66881,0.14948,361.13,0.68515,-0.70583,0.17994,147.26,-0.014843,0.23346,0.97225,-60.152
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.70345,-0.69292,0.15818,360.21,0.71068,-0.6827,0.16989,140.79,-0.0097281,0.23192,0.97269,-60.737
> view matrix models
> #16,-0.71411,-0.68093,0.16243,359.61,0.69341,-0.71989,0.030628,162.16,0.096075,0.1345,0.98625,-63.286
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.71411,-0.68093,0.16243,357.72,0.69341,-0.71989,0.030628,155.99,0.096075,0.1345,0.98625,-50.025
> view matrix models
> #16,-0.71411,-0.68093,0.16243,358,0.69341,-0.71989,0.030628,156.93,0.096075,0.1345,0.98625,-33.859
Fit map DS1_NTR_C_others_spike_reconstruction.mrc gaussian in map
empty_spike_230505_reconstruction.mrc gaussian using 2302533 points
correlation = 0.9823, correlation about mean = 0.9249, overlap = 120.9
steps = 176, shift = 14.3, angle = 9.37 degrees
Position of DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) relative
to empty_spike_230505_reconstruction.mrc gaussian (#16) coordinates:
Matrix rotation and translation
-0.76287057 0.64655077 0.00078575 171.53501680
-0.64643597 -0.76275694 0.01795592 380.69180111
0.01220875 0.01319010 0.99983848 7.71372779
Axis -0.00368573 -0.00883418 -0.99995419
Axis point 155.54487590 158.86396943 0.00000000
Rotation angle (degrees) 139.72004016
Shift along axis -11.70870508
> view matrix models
> #16,-0.71411,-0.68093,0.16243,325.64,0.69341,-0.71989,0.030628,-50.403,0.096075,0.1345,0.98625,-39.098
> view matrix models
> #16,-0.71411,-0.68093,0.16243,322.94,0.69341,-0.71989,0.030628,-110.64,0.096075,0.1345,0.98625,-40.972
> ~select #16
Nothing selected
> hide #!16 models
> show #10 models
> select #10
177623 atoms, 181534 bonds, 22241 residues, 1 model selected
> view matrix models
> #10,0.98111,-0.18701,-0.049511,52.398,0.18866,0.98155,0.031035,-56.187,0.042793,-0.03979,0.99829,-18.82
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.97166,-0.21632,0.095297,47.157,0.21495,0.97632,0.02452,-59.044,-0.098344,-0.003341,0.99515,-1.803
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.97166,-0.21632,0.095297,37.329,0.21495,0.97632,0.02452,-51.258,-0.098344,-0.003341,0.99515,-1.4087
> view matrix models
> #10,0.97166,-0.21632,0.095297,42.312,0.21495,0.97632,0.02452,-41.798,-0.098344,-0.003341,0.99515,20.301
Fit molecule all_VP6_DS1_sub.pdb (#10) to map
DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) using 177623 atoms
average map value = 0.002757, steps = 204
shifted from previous position = 15.1
rotated from previous position = 7.08 degrees
atoms outside contour = 116820, contour level = 0.002456
Position of all_VP6_DS1_sub.pdb (#10) relative to
DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) coordinates:
Matrix rotation and translation
0.94137430 -0.33545721 0.03581746 70.11996810
0.33698068 0.94004963 -0.05244719 -54.28364204
-0.01607640 0.06144223 0.99798116 -19.52134176
Axis 0.16650848 0.07586979 0.98311683
Axis point 190.75248955 181.46648830 0.00000000
Rotation angle (degrees) 19.99833713
Shift along axis -11.63467861
> ~select #10
Nothing selected
> show #5 models
> select #5
51920 atoms, 52864 bonds, 6348 residues, 1 model selected
> view matrix models
> #5,0.99356,-0.11319,-0.0053704,9.4846,0.11175,0.97083,0.21214,-14.909,-0.018799,-0.21138,0.97722,50.039
Fit molecule all_VP2_DS1_sub.pdb (#5) to map
DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) using 51920 atoms
average map value = 0.002139, steps = 184
shifted from previous position = 23.6
rotated from previous position = 4.86 degrees
atoms outside contour = 36596, contour level = 0.002456
Position of all_VP2_DS1_sub.pdb (#5) relative to
DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) coordinates:
Matrix rotation and translation
0.97084006 -0.15935805 -0.17909378 30.26220993
0.20278518 0.94435644 0.25897700 -36.03533098
0.12785830 -0.28774281 0.94913452 41.17398645
Axis -0.75507027 -0.42392901 0.50015306
Axis point 0.00000000 95.98689081 138.45626346
Rotation angle (degrees) 21.22506545
Shift along axis 13.01962273
> view matrix models
> #5,0.98941,-0.14384,-0.01926,7.1637,0.14328,0.94714,0.28706,-13.496,-0.023048,-0.28678,0.95772,50.019
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.69234,-0.61336,0.38008,342.53,0.49025,-0.78634,-0.37594,195.7,0.52945,-0.073943,0.84511,-69.07
> view matrix models
> #5,0.83761,-0.4122,-0.35846,74.991,0.34132,0.90726,-0.24573,-33.733,0.42651,0.083475,0.90062,-76.561
> view matrix models
> #5,0.656,-0.69054,0.30464,138.57,0.75441,0.58766,-0.29243,-51.947,0.022909,0.42166,0.90646,-62.207
> view matrix models
> #5,0.61624,-0.78149,0.097629,160.65,0.78246,0.59345,-0.1886,-58.396,0.089454,0.19262,0.97719,-39.546
> view matrix models
> #5,0.47087,-0.86462,0.17527,195.51,0.87564,0.43387,-0.21215,-49.352,0.10739,0.25337,0.96139,-51.294
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.47087,-0.86462,0.17527,193.17,0.87564,0.43387,-0.21215,-52.757,0.10739,0.25337,0.96139,-55.651
> color zone #18 near #5,10 distance 5
> color zone #18 near #5,10 distance 3
> color zone #18 near #5,10 distance 5
> color zone #18 near #5,10 distance 6
> hide #10 models
> select clear
> hide #5 models
> lighting soft
> lighting simple
> lighting soft
> save "C:/Users/yulab/Desktop/session 3-2024.7.22.cxs"
> save "C:/Users/yulab/Desktop/中期图-2024.7.22/DS1-NTR-C-other
> spike(1)-2024.7.22.png" width 1133 height 833 supersample 3
> transparentBackground true
> lighting simple
> show #10 models
> hide #10 models
> show #!7 models
> select #7
3 models selected
> lighting simple
> ~select #7
Nothing selected
> hide #!7 models
> show #!16 models
> hide #!16 models
> hide #!18 models
> show #!13.2 models
> hide #!13.2 models
> hide #!13 models
> show #!18 models
> show #!13.2 models
> hide #!13.2 models
> show #!8 models
> hide #!8 models
> show #!16 models
> hide #!18 models
> show #!17 models
> hide #!16 models
> hide #!17 models
> hide #!13 models
> show #10 models
> show #!11 models
> open C:/Users/yulab/Desktop/DS1/all_VP2_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP5+8_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP6_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP7_DS1_sub.pdb
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP2_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 277 277 GLU P
2 LYS P 17 1 16
Start residue of secondary structure not found: HELIX 278 278 TYR P 24 ASN P
26 1 3
Start residue of secondary structure not found: HELIX 279 279 SER P 28 MET P
41 1 14
Start residue of secondary structure not found: HELIX 280 280 ALA P 75 MET P
100 1 26
Start residue of secondary structure not found: HELIX 281 281 GLU P 114 LEU P
119 1 6
3018 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP5+8_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
3470 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP6_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
1790 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP7_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
2127 messages similar to the above omitted
Chain information for all_VP2_DS1_sub.pdb #19
---
Chain | Description
1 | No description available
2 | No description available
Chain information for all_VP5+8_DS1_sub.pdb #20
---
Chain | Description
A B | No description available
C | No description available
Chain information for all_VP6_DS1_sub.pdb #21
---
Chain | Description
N O P T U V Z | No description available
Q R S | No description available
W X Y | No description available
Chain information for all_VP7_DS1_sub.pdb #22
---
Chain | Description
3 | No description available
A C G I | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
> hide #10,19,21#!11,20,22 atoms
> show #10,19,21#!11,20,22 cartoons
> hide #10 models
> hide #!11 models
> show #!6 models
> show #!7 models
> hide #!6 models
> lighting soft
> hide #19 models
> hide #!20 models
> hide #21 models
> hide #!22 models
> show #!13.1 models
> hide #!7 models
> hide #!13.1 models
> show #!2 models
> hide #!2 models
> show #!17 models
> show #!8 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> select #17
2 models selected
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.56195,0.76777,0.30781,99.788,-0.6625,-0.64057,0.38829,314.58,0.49529,0.014274,0.86861,-68.948
> view matrix models
> #17,-0.67121,0.73935,0.053328,150.16,-0.73471,-0.67309,0.084584,365.25,0.098432,0.017593,0.99499,-20.69
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.67121,0.73935,0.053328,159.29,-0.73471,-0.67309,0.084584,349.66,0.098432,0.017593,0.99499,-20.541
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2327732 points
correlation = 0.9804, correlation about mean = 0.9225, overlap = 131
steps = 128, shift = 4.73, angle = 7.06 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) relative
to short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
-0.76295156 0.64645517 0.00079553 171.56089352
-0.64633921 -0.76283691 0.01804085 380.69185933
0.01226947 0.01325011 0.99983694 7.69192724
Axis -0.00370555 -0.00887489 -0.99995375
Axis point 155.54416810 158.86533475 0.00000000
Rotation angle (degrees) 139.72724187
Shift along axis -11.70589662
> lighting soft
> ~select #17
Nothing selected
> volume #17 level 0.00438
> hide #!17 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> close #10#9,11
> hide #!7 models
> hide #!13 models
> save "C:/Users/yulab/Desktop/session 4-2024.7.25.cxs"
> show #!17 models
> hide #!17 models
> show #!13.1 models
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!13 models
> volume gaussian #13.1 sDev 3
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!9 models
> measure mapstats #10
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #10, minimum -0.00343,
maximum 0.008499, mean 6.071e-05, SD 0.001891, RMS 0.001892
> volume #10 level 0.001892
> lighting simple
> close #10
> show #!9 models
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.009071,
maximum 0.02186, mean 6.198e-05, SD 0.002588, RMS 0.002589
> volume #9 level 0.002589
> volume gaussian #9 sDev 3
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #10
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #10, minimum -0.003382,
maximum 0.00813, mean 6.036e-05, SD 0.001871, RMS 0.001872
> volume #10 level 0.001872
> close #10
> show #!9 models
> show #!18 models
> hide #!18 models
> hide #!9 models
> show #!6 models
> hide #!6 models
> show #!8 models
> measure mapstats #8
Map short_better_spike_230505_reconstruction.mrc gaussian #8, minimum
-0.008516, maximum 0.02307, mean 5.695e-05, SD 0.002914, RMS 0.002914
> hide #!8 models
> show #!7 models
> measure mapstats #7
Map long_full_spike_230505_reconstruction.mrc gaussian #7, minimum -0.009334,
maximum 0.02329, mean 6.021e-05, SD 0.002964, RMS 0.002965
> hide #!7 models
> close #9
> show #!13.1 models
> measure mapstats #13.1
Map DS1_NTR_C_long_spike_reconstruction.mrc #13.1, step 2, minimum -0.03056,
maximum 0.05107, mean 6.433e-05, SD 0.005103, RMS 0.005103
> volume #13.1 level 0.005103
> volume gaussian #13.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!13 models
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> volume #9 level 0.002243
> show #!2 models
> hide #!2 models
> show #!7 models
> lighting simple
> hide #!7 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!9 models
> hide #!9 models
> close #9
> show #!13.1 models
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!13 models
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.009071,
maximum 0.02186, mean 6.198e-05, SD 0.002588, RMS 0.002589
> volume #9 level 0.002589
> hide #!9 models
> show #!7 models
> hide #!7 models
> close #9
> show #!13.1 models
> volume gaussian #13.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> hide #!13 models
> volume #9 level 0.002243
> color #9 #ff007f models transparency 0
> volume #9 level 0.002101
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!2 models
> measure mapstats #2
Map long_full_spike_230505_reconstruction.mrc #2, minimum -0.01726, maximum
0.05362, mean 5.97e-05, SD 0.004433, RMS 0.004434
> volume gaussian #2 sDev 1.5
Opened long_full_spike_230505_reconstruction.mrc gaussian as #10, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> measure mapstats #10
Map long_full_spike_230505_reconstruction.mrc gaussian #10, minimum -0.005654,
maximum 0.01589, mean 6.052e-05, SD 0.002548, RMS 0.002549
> volume #10 level 0.002549
> hide #!10 models
> show #!7 models
> show #!10 models
> select #10
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,20.985,0,1,0,54.766,0,0,1,5.9414
> volume #10 level 0.002319
> volume #10 level 0.002434
> volume #10 level 0.002578
> volume #10 level 0.002722
> volume #10 level 0.002981
> hide #!7 models
> close #10
> show #!9 models
> hide #!9 models
> close #9
> show #!13.3 models
> hide #!13.3 models
> show #!13.1 models
> volume gaussian #13.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> volume #9 level 0.002243
> volume #9 level 0.002527
> volume #9 level 0.002583
> volume #9 level 0.002754
> volume #9 level 0.00264
> volume #9 level 0.002243
> close #9
> show #!13.1 models
> volume gaussian #13.1 sDev 1.3
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.006865,
maximum 0.01703, mean 6.177e-05, SD 0.002347, RMS 0.002348
> volume #9 level 0.002348
> close #9
> show #!13.1 models
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.009071,
maximum 0.02186, mean 6.198e-05, SD 0.002588, RMS 0.002589
> volume #9 level 0.002589
> volume #9 level 0.003085
> close #9
> hide #!7 models
> show #!13.1 models
> volume gaussian #13.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> volume #9 level 0.002243
> volume #9 level 0.002271
> volume #9 level 0.002356
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!9 models
> volume #9 level 0.00243
> lighting soft
> lighting simple
> hide #!9 models
> show #!2 models
> hide #!2 models
> show #!7 models
> lighting soft
> hide #!7 models
> hide #!13 models
> show #!9 models
> volume #9 level 0.002629
> lighting simple
> volume #9 level 0.002827
> volume #9 level 0.002884
> volume #9 level 0.002856
> volume #9 level 0.002941
> volume #9 level 0.003054
> volume #9 level 0.002912
> hide #!9 models
> show #!13.1 models
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #11, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!10 models
> hide #!11 models
> show #!11 models
> show #!10 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> close #11
> show #!10 models
> measure mapstats #10
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #10, minimum -0.009071,
maximum 0.02186, mean 6.198e-05, SD 0.002588, RMS 0.002589
> volume #10 level 0.002589
> volume #10 level 0.003375
> volume #10 level 0.00292
> volume #10 level 0.003003
> hide #!10 models
> show #!9 models
> volume #10 level 0.003044
> hide #!10 models
> volume #9 level 0.004416
> volume #9 level 0.002243
> volume #10 level 0.00354
> volume #10 level 0.003954
> volume #10 level 0.00354
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!9 models
> hide #!13 models
> hide #!10 models
> show #!9 models
> volume #9 level 0.002442
> color #9 #ff007f models transparency 0
> color #19 #ffff7f transparency 0
> color #20 #ffaa00 transparency 0
> color #21 #aaaaff transparency 0
> color #22 #ff007f transparency 0
> hide #!9 models
> show #!22 models
Drag select of 38 residues
Drag select of 43 residues
> select up
708 atoms, 724 bonds, 99 residues, 1 model selected
> select up
6564 atoms, 6712 bonds, 896 residues, 1 model selected
> color sel cyan
> hide #!22 models
> select #22
134588 atoms, 137391 bonds, 13 pseudobonds, 17165 residues, 2 models selected
> ~select #22
Nothing selected
> show #!9 models
> volume #9 level 0.002669
> volume #9 level 0.002442
> show #!7 models
> lighting simple
> lighting soft
> lighting simple
> volume #9 level 0.001732
> volume #9 level 0.001874
> volume #9 level 0.00213
> volume #9 level 0.002215
> volume #9 level 0.002385
> volume #9 level 0.002527
> select #9
2 models selected
> lighting simple
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,43.72,0,1,0,63.396,0,0,1,13.798
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.89844,-0.062288,0.43466,296.7,-0.002853,-0.98904,-0.14763,400.42,0.43909,-0.13388,0.88841,-19.615
> view matrix models
> #9,-0.91234,-0.0034031,0.40942,292.9,-0.037352,-0.9951,-0.091506,399.35,0.40772,-0.098777,0.90775,-22.817
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.91234,-0.0034031,0.40942,288.58,-0.037352,-0.9951,-0.091506,399.35,0.40772,-0.098777,0.90775,-32.331
> view matrix models
> #9,-0.91234,-0.0034031,0.40942,309.99,-0.037352,-0.9951,-0.091506,401.51,0.40772,-0.098777,0.90775,6.1498
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.87986,-0.19825,0.43191,332.86,0.15091,-0.97835,-0.14166,375.68,0.45064,-0.059458,0.89072,-4.6446
> view matrix models
> #9,-0.96122,-0.21995,0.16634,384.76,0.16318,-0.93991,-0.2999,388.79,0.22231,-0.26113,0.93936,57.199
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.96122,-0.21995,0.16634,307.45,0.16318,-0.93991,-0.2999,349.68,0.22231,-0.26113,0.93936,43.488
> view matrix models
> #9,-0.96122,-0.21995,0.16634,380.96,0.16318,-0.93991,-0.2999,403.55,0.22231,-0.26113,0.93936,34.507
> view matrix models
> #9,-0.96122,-0.21995,0.16634,381.96,0.16318,-0.93991,-0.2999,409.85,0.22231,-0.26113,0.93936,32.445
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.95244,-0.30471,0.0021292,416.04,0.29354,-0.91937,-0.26191,380.81,0.081765,-0.24883,0.96509,49.342
> view matrix models
> #9,-0.95924,-0.27698,0.055967,405.5,0.27577,-0.9608,-0.028455,358.99,0.061655,-0.011861,0.99803,10.381
> view matrix models
> #9,-0.5567,0.8305,-0.018998,175.26,-0.82503,-0.55541,-0.10415,479.21,-0.097052,-0.042308,0.99438,40.9
> view matrix models
> #9,-0.56056,0.82548,0.066024,165.29,-0.82558,-0.55084,-0.12242,481.01,-0.064688,-0.12313,0.99028,49.188
> view matrix models
> #9,-0.56118,0.82263,0.09145,162.44,-0.82587,-0.54918,-0.12779,481.51,-0.054898,-0.14724,0.98758,51.836
> view matrix models
> #9,-0.59534,0.80011,0.073425,173.86,-0.80188,-0.58592,-0.11702,482.11,-0.050607,-0.12854,0.99041,47.798
> view matrix models
> #9,-0.58505,0.80568,0.092679,168.77,-0.81099,-0.58168,-0.062843,475.63,0.0032781,-0.11193,0.99371,36.16
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.58505,0.80568,0.092679,130.22,-0.81099,-0.58168,-0.062843,374.32,0.0032781,-0.11193,0.99371,19.778
> view matrix models
> #9,-0.58505,0.80568,0.092679,125,-0.81099,-0.58168,-0.062843,380.1,0.0032781,-0.11193,0.99371,5.2713
> view matrix models
> #9,-0.58505,0.80568,0.092679,104.66,-0.81099,-0.58168,-0.062843,374.27,0.0032781,-0.11193,0.99371,15.125
> view matrix models
> #9,-0.58505,0.80568,0.092679,97.694,-0.81099,-0.58168,-0.062843,399.91,0.0032781,-0.11193,0.99371,26.632
> view matrix models
> #9,-0.58505,0.80568,0.092679,90.44,-0.81099,-0.58168,-0.062843,371.78,0.0032781,-0.11193,0.99371,27.287
> view matrix models
> #9,-0.58505,0.80568,0.092679,89.593,-0.81099,-0.58168,-0.062843,399.57,0.0032781,-0.11193,0.99371,36.592
> view matrix models
> #9,-0.58505,0.80568,0.092679,98.072,-0.81099,-0.58168,-0.062843,398.35,0.0032781,-0.11193,0.99371,37.952
Fit map DS1_NTR_C_long_spike_reconstruction.mrc gaussian in map
long_full_spike_230505_reconstruction.mrc gaussian using 2710167 points
correlation = 0.9517, correlation about mean = 0.8579, overlap = 109.2
steps = 244, shift = 19.3, angle = 15.6 degrees
Position of DS1_NTR_C_long_spike_reconstruction.mrc gaussian (#9) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76287030 0.64655109 0.00077330 171.53152575
-0.64643797 -0.76275816 0.01783070 380.69357438
0.01211830 0.01310262 0.99984072 7.71169534
Axis -0.00365654 -0.00877385 -0.99995482
Axis point 155.54381176 158.86562713 0.00000000
Rotation angle (degrees) 139.71998356
Shift along axis -11.67870565
> ~select #9
Nothing selected
> hide #!7 models
> show #19 models
> show #!20 models
> show #21 models
> show #!22 models
> hide #!22 models
> color zone #9 near #19-21 distance 3
> hide #19 models
> hide #!20 models
> hide #21 models
> undo
> hide #21 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!7 models
> select #9
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.76287,0.64655,0.0007733,148.04,-0.64644,-0.76276,0.017831,280.61,0.012118,0.013103,0.99984,-1.7344
> view matrix models
> #9,-0.76287,0.64655,0.0007733,163.34,-0.64644,-0.76276,0.017831,378.69,0.012118,0.013103,0.99984,9.9129
> view matrix models
> #9,-0.76287,0.64655,0.0007733,168.77,-0.64644,-0.76276,0.017831,380.66,0.012118,0.013103,0.99984,13.013
Fit map DS1_NTR_C_long_spike_reconstruction.mrc gaussian in map
long_full_spike_230505_reconstruction.mrc gaussian using 2710167 points
correlation = 0.9517, correlation about mean = 0.8578, overlap = 109.2
steps = 72, shift = 5.98, angle = 0.00666 degrees
Position of DS1_NTR_C_long_spike_reconstruction.mrc gaussian (#9) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76294544 0.64646242 0.00077488 171.56141207
-0.64634927 -0.76283327 0.01783355 380.69276441
0.01211982 0.01310518 0.99984067 7.70607456
Axis -0.00365726 -0.00877501 -0.99995481
Axis point 155.54607252 158.86541448 0.00000000
Rotation angle (degrees) 139.72664358
Shift along axis -11.67375328
> hide #!7 models
> color zone #9 near #19-21 distance 2
> color zone #9 near #19-21 distance 4
> color zone #9 near #19-21 distance 5
> show #!7 models
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.76295,0.64646,0.00077488,139.81,-0.64635,-0.76283,0.017834,325.48,0.01212,0.013105,0.99984,2.5638
> view matrix models
> #9,-0.76295,0.64646,0.00077488,138.24,-0.64635,-0.76283,0.017834,306.38,0.01212,0.013105,0.99984,6.6514
> view matrix models
> #9,-0.76295,0.64646,0.00077488,115.61,-0.64635,-0.76283,0.017834,252.16,0.01212,0.013105,0.99984,9.4588
> view matrix models
> #9,-0.76295,0.64646,0.00077488,183.03,-0.64635,-0.76283,0.017834,367.52,0.01212,0.013105,0.99984,1.5735
> view matrix models
> #9,-0.76295,0.64646,0.00077488,172.14,-0.64635,-0.76283,0.017834,381.01,0.01212,0.013105,0.99984,1.1846
> view matrix models
> #9,-0.76295,0.64646,0.00077488,173.78,-0.64635,-0.76283,0.017834,378,0.01212,0.013105,0.99984,3.21
> view matrix models
> #9,-0.76295,0.64646,0.00077488,171.33,-0.64635,-0.76283,0.017834,377.7,0.01212,0.013105,0.99984,3.3809
> view matrix models
> #9,-0.76295,0.64646,0.00077488,173.06,-0.64635,-0.76283,0.017834,377.86,0.01212,0.013105,0.99984,7.232
> view matrix models
> #9,-0.76295,0.64646,0.00077488,172.61,-0.64635,-0.76283,0.017834,377.88,0.01212,0.013105,0.99984,7.4313
> view matrix models
> #9,-0.76295,0.64646,0.00077488,172.43,-0.64635,-0.76283,0.017834,379.38,0.01212,0.013105,0.99984,7.0262
> view matrix models
> #9,-0.76295,0.64646,0.00077488,169.28,-0.64635,-0.76283,0.017834,371.66,0.01212,0.013105,0.99984,3.4371
> hide #!7 models
> ui tool show "Side View"
> color zone #9 near #19-21 distance 5
> lighting soft
> lighting simple
> select #9
3 models selected
> hide #!9 models
> show #!9 models
> color zone #9 near #19-21 distance 5
> ~select #9
Nothing selected
> color zone #9 near #19-21 distance 5
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> show #!7 models
> select #9
3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.76295,0.64646,0.00077488,171.99,-0.64635,-0.76283,0.017834,379.07,0.01212,0.013105,0.99984,9.1529
> lighting simple
> view matrix models
> #9,-0.76295,0.64646,0.00077488,142.27,-0.64635,-0.76283,0.017834,351.15,0.01212,0.013105,0.99984,9.6988
> view matrix models
> #9,-0.76295,0.64646,0.00077488,172.57,-0.64635,-0.76283,0.017834,379.46,0.01212,0.013105,0.99984,6.5396
Fit map DS1_NTR_C_long_spike_reconstruction.mrc gaussian in map
long_full_spike_230505_reconstruction.mrc gaussian using 2710167 points
correlation = 0.9518, correlation about mean = 0.8583, overlap = 109.2
steps = 56, shift = 1.99, angle = 0.00204 degrees
Position of DS1_NTR_C_long_spike_reconstruction.mrc gaussian (#9) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76296775 0.64643609 0.00077787 171.56500444
-0.64632300 -0.76285572 0.01782507 380.69833753
0.01211617 0.01309720 0.99984082 7.73400902
Axis -0.00365703 -0.00877023 -0.99995485
Axis point 155.54508055 158.86913542 0.00000000
Rotation angle (degrees) 139.72862075
Shift along axis -11.69988868
> hide #!7 models
> color zone #9 near #19-21 distance 3
> lighting soft
> lighting simple
> color zone #9 near #19-21 distance 5
> lighting soft
> lighting simple
> lighting soft
> ~select #9
Nothing selected
> lighting simple
> lighting soft
> save "C:/Users/yulab/Desktop/session 5-2024.7.25.cxs" includeMaps true
> lighting simple
> lighting soft
> hide #!9 models
> show #!7 models
> view list
Named views: 1, 2
> view name 3
> view name 4
> view list
Named views: 1, 2, 3, 4
> view 3
> view 4
> view 3
> view 4
> hide #!7 models
> show #!9 models
> hide #!9 models
> show #!8 models
> view 3
> view 4
> show #!9 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!4 models
> hide #!7 models
> volume #4 level 0.01099
> show #!8 models
> hide #!8 models
> volume #4 level 0.00759
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!9 models
> view 3
> view 4
> view 3
> view 4
> hide #!9 models
> show #!7 models
> view 3
> hide #!7 models
> show #!9 models
> hide #!9 models
> show #!6 models
> lighting simple
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!4 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!16 models
> hide #!16 models
> hide #!7 models
> show #!2 models
> show #!7 models
> hide #!2 models
> hide #!7 models
> show #!4 models
> show #!8 models
> hide #!8 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!15 models
> show #!16 models
> hide #!16 models
> hide #!15 models
> close #8
> close #16
> show #!4 models
> measure mapstats #4
Map short_better_spike_230505_reconstruction.mrc #4, minimum -0.01891, maximum
0.05379, mean 5.669e-05, SD 0.00453, RMS 0.00453
> volume gaussian #4 sDev 1.5
Opened short_better_spike_230505_reconstruction.mrc gaussian as #8, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> measure mapstats #8
Map short_better_spike_230505_reconstruction.mrc gaussian #8, minimum
-0.005468, maximum 0.01566, mean 5.71e-05, SD 0.002483, RMS 0.002484
> volume #8 level 0.002484
> show #!4 models
> hide #!4 models
> color #8 #ff007f models transparency 0
> hide #!8 models
> show #!15 models
> volume gaussian #15 sDev 1.5
Opened empty_spike_230505_reconstruction.mrc gaussian as #11, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> measure mapstats #11
Map empty_spike_230505_reconstruction.mrc gaussian #11, minimum -0.006069,
maximum 0.01536, mean 6.648e-05, SD 0.002436, RMS 0.002437
> volume #11 level 0.002437
> color #11 #ff007f models transparency 0
> hide #!11 models
> show #!11 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #!10 models
> close #10
> show #!18 models
> hide #!18 models
> close #17
> show #!18 models
> hide #!18 models
> color #18 white models transparency 0
> show #!13.3 models
> volume gaussian #13.3 sDev 1
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!13 models
> volume gaussian #13.3 sDev 1.5
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #16, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!10 models
> hide #!16 models
> show #!10 models
> measure mapstats #10
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #10, minimum -0.008048,
maximum 0.02086, mean 6.261e-05, SD 0.002563, RMS 0.002564
> volume #10 level 0.002564
> hide #!10 models
> show #!16 models
> measure mapstats #16
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #16, minimum -0.004597,
maximum 0.0151, mean 6.214e-05, SD 0.00223, RMS 0.002231
> volume #16 level 0.002231
> show #!10 models
> hide #!10 models
> close #10
> hide #!16 models
> show #!16 models
> show #!13.3 models
> hide #!16 models
> show #!16 models
> hide #!13.3 models
> hide #!16 models
> show #!18 models
> hide #!18 models
> show #!13.2 models
> hide #!13.2 models
> hide #!13 models
> show #!18 models
> hide #!18 models
> close #18
> show #!13.2 models
> volume gaussian #13.2 sDev 1.5
Opened DS1_NTR_C_others_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!13 models
> measure mapstats #10
Map DS1_NTR_C_others_spike_reconstruction.mrc gaussian #10, minimum -0.00432,
maximum 0.01484, mean 6.779e-05, SD 0.002155, RMS 0.002156
> volume #10 level 0.002156
> show #!13.2 models
> hide #!10 models
> hide #!13 models
> hide #!13.2 models
> show #!10 models
> color #10 #ff007f models transparency 0
> hide #!10 models
> color #7 #ff007f models transparency 0
> show #!22 models
> hide #!22 models
> show #!7 models
> show #19 models
> show #!20 models
> show #21 models
> show #!22 models
> lighting simple
> color zone #19-22 distance 3
Missing required "near" argument
> color zone #7 near #19-22
> color zone #7 near #19-22 distance 3
> color zone #7 near #19-22 distance 5
> hide #19 models
> hide #!20 models
> hide #21 models
> hide #!22 models
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> view name 5
> lighting simple
> lighting soft
> view name 6
> hide #!7 models
> show #!8 models
> lighting simple
> show #!4 models
> hide #!4 models
> color #14 #ff007f transparency 0
> show #!14 models
> show #19 models
> show #!20 models
> show #21 models
> hide #!20 models
> show #!22 models
> hide #!8 models
> hide #19 models
> hide #21 models
> hide #!22 models
> hide #!14 models
> show #!8 models
> color #14 #ffff7f transparency 0
> show #!14 models
> select #14
6389 atoms, 6536 bonds, 3 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.99309,-0.057292,-0.10241,32.373,0.054758,0.99812,-0.027386,-4.9018,0.10379,0.021589,0.99436,20.867
> view matrix models
> #14,0.99309,-0.057292,-0.10241,33.989,0.054758,0.99812,-0.027386,-10.748,0.10379,0.021589,0.99436,23.833
> view matrix models
> #14,0.99309,-0.057292,-0.10241,31.128,0.054758,0.99812,-0.027386,-1.4789,0.10379,0.021589,0.99436,22.935
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.98086,0.16787,-0.098698,-7.0349,-0.1693,0.98555,-0.006189,28.843,0.096232,0.02278,0.9951,23.673
Fit molecule wt_sub_VP5CT.pdb (#14) to map
short_better_spike_230505_reconstruction.mrc gaussian (#8) using 6389 atoms
average map value = 0.004978, steps = 108
shifted from previous position = 12.9
rotated from previous position = 3.5 degrees
atoms outside contour = 1166, contour level = 0.002484
Position of wt_sub_VP5CT.pdb (#14) relative to
short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.98906041 0.13641514 -0.05612863 -10.57730771
-0.13865721 0.98960392 -0.03818710 26.77050919
0.05033581 0.04555199 0.99769300 38.60398872
Axis 0.27310980 -0.34722708 -0.89713120
Axis point 76.58346957 -10.05091396 0.00000000
Rotation angle (degrees) 8.81860048
Shift along axis -46.81705492
> show #19 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #21 models
> show #!22 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color zone #8 near #14,19,21,22 distance 5
> ~select #14
Nothing selected
> hide #!14 models
> hide #19 models
> hide #21 models
> hide #!22 models
> view list
Named views: 1, 2, 3, 4, 5, 6
> view 5
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> view name 7
> hide #!8 models
> show #!6 models
> lighting simple
> hide #!6 models
> show #!15 models
> hide #!15 models
> show #!11 models
> show #!15 models
> hide #!11 models
> show #!11 models
> hide #!15 models
> show #!22 models
> show #21 models
> show #19 models
> hide #!11 models
> show #!11 models
> color zone #11 near #19,21,22 distance 5
> hide #19 models
> hide #21 models
> hide #!22 models
> view list
Named views: 1, 2, 3, 4, 5, 6, 7
> view 5
> lighting soft
> lighting simple
> view 6
> view 7
> view 6
> lighting soft
> color zone #11 near #19,21,22 distance 5
> view 6
> view 7
> lighting simple
> lighting soft
> view 7
> save "C:/Users/yulab/Desktop/中期图-2024.7.22/DS1-TR-empty spike-2024.7.26.png"
> width 1133 height 833 supersample 3 transparentBackground true
> hide #!11 models
> show #!7 models
> view 7
> save "C:/Users/yulab/Desktop/中期图-2024.7.22/DS1-TR-long spike-2024.7.26.png"
> width 1133 height 833 supersample 3 transparentBackground true
> hide #!7 models
> show #!8 models
> view 7
> color #14 #ffaa00 transparency 0
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!8 models
> lighting simple
> color zone #8 near #14,19,21,22 distance 5
> show #!14 models
> show #19 models
> show #21 models
> show #!22 models
> hide #!8 models
> hide #!22 models
> hide #21 models
> hide #19 models
> show #!8 models
> select #14
6389 atoms, 6536 bonds, 3 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.99309,-0.057292,-0.10241,-15.912,0.054758,0.99812,-0.027386,-63.077,0.10379,0.021589,0.99436,25.593
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!4 models
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!4 models
> view matrix models
> #14,0.99309,-0.057292,-0.10241,-14.507,0.054758,0.99812,-0.027386,-63.096,0.10379,0.021589,0.99436,25.729
> view matrix models
> #14,0.99309,-0.057292,-0.10241,27.497,0.054758,0.99812,-0.027386,-7.3349,0.10379,0.021589,0.99436,8.8637
> view matrix models
> #14,0.99309,-0.057292,-0.10241,17.989,0.054758,0.99812,-0.027386,-56.958,0.10379,0.021589,0.99436,18.206
> view matrix models
> #14,0.99309,-0.057292,-0.10241,12.351,0.054758,0.99812,-0.027386,-54.166,0.10379,0.021589,0.99436,14.787
> view matrix models
> #14,0.99309,-0.057292,-0.10241,34.109,0.054758,0.99812,-0.027386,-8.2668,0.10379,0.021589,0.99436,13.522
> view matrix models
> #14,0.99309,-0.057292,-0.10241,35.483,0.054758,0.99812,-0.027386,-13.364,0.10379,0.021589,0.99436,18.83
> view matrix models
> #14,0.99309,-0.057292,-0.10241,25.487,0.054758,0.99812,-0.027386,-10.767,0.10379,0.021589,0.99436,19.724
> view matrix models
> #14,0.99309,-0.057292,-0.10241,31.098,0.054758,0.99812,-0.027386,-11.584,0.10379,0.021589,0.99436,24.86
> view matrix models
> #14,0.99309,-0.057292,-0.10241,29.818,0.054758,0.99812,-0.027386,-8.5654,0.10379,0.021589,0.99436,24.685
> view matrix models
> #14,0.99309,-0.057292,-0.10241,30.579,0.054758,0.99812,-0.027386,-9.0646,0.10379,0.021589,0.99436,24.73
> view matrix models
> #14,0.99309,-0.057292,-0.10241,33.336,0.054758,0.99812,-0.027386,-10.724,0.10379,0.021589,0.99436,28.246
> view matrix models
> #14,0.99309,-0.057292,-0.10241,31.673,0.054758,0.99812,-0.027386,-8.4143,0.10379,0.021589,0.99436,27.809
Fit molecule wt_sub_VP5CT.pdb (#14) to map
short_better_spike_230505_reconstruction.mrc gaussian (#8) using 6389 atoms
average map value = 0.004978, steps = 88
shifted from previous position = 9.79
rotated from previous position = 11.5 degrees
atoms outside contour = 1164, contour level = 0.002484
Position of wt_sub_VP5CT.pdb (#14) relative to
short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.98907694 0.13643325 -0.05579222 -10.63001450
-0.13865131 0.98961140 -0.03801450 26.75125527
0.05002618 0.04533493 0.99771846 38.69121223
Axis 0.27212206 -0.34547954 -0.89810549
Axis point 76.82664615 -9.44658414 0.00000000
Rotation angle (degrees) 8.80935156
Shift along axis -46.88346295
> show #19 models
> show #!20 models
> show #21 models
> show #!22 models
> hide #!20 models
> color zone #8 near #14,19,21,22 distance 5
> hide #!14 models
> ~select #14
Nothing selected
> hide #19 models
> hide #21 models
> hide #!22 models
> view list
Named views: 1, 2, 3, 4, 5, 6, 7
> view 7
> lighting soft
> save "C:/Users/yulab/Desktop/中期图-2024.7.22/DS1-TR-short spike-2024.7.26.png"
> width 1133 height 833 supersample 3
> hide #!8 models
> show #!16 models
> hide #!16 models
> show #!9 models
> lighting simple
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #19 models
> show #!20 models
> show #21 models
> color zone #9 near #19-21 distance 5
> hide #19 models
> hide #!20 models
> hide #21 models
> view list
Named views: 1, 2, 3, 4, 5, 6, 7
> view 7
> lighting soft
> view 7
> hide #!9 models
> show #!13.3 models
> hide #!13.3 models
> show #!16 models
> lighting simple
> color #16 #ff007f models transparency 0
> show #!8 models
> hide #!13 models
> select #16
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #16,1,0,0,-42.027,0,1,0,-115.07,0,0,1,4.1051
> view matrix models #16,1,0,0,-13.833,0,1,0,22.795,0,0,1,21.837
> view matrix models #16,1,0,0,-9.9317,0,1,0,24.51,0,0,1,23.368
> view matrix models #16,1,0,0,-10.381,0,1,0,28.147,0,0,1,21.384
> view matrix models #16,1,0,0,-9.4,0,1,0,28.096,0,0,1,21.429
> view matrix models #16,1,0,0,-10.792,0,1,0,27.142,0,0,1,21.971
> view matrix models #16,1,0,0,-14.536,0,1,0,32.608,0,0,1,22.865
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.4719,0.75878,0.44896,47.884,-0.68854,-0.63522,0.34987,362.87,0.55066,-0.14402,0.82221,-21.643
> view matrix models
> #16,-0.50752,0.83791,0.20083,68.738,-0.77924,-0.54581,0.30802,367.72,0.36771,-0.00016429,0.92994,-27.586
> view matrix models
> #16,-0.23429,0.97025,0.060972,20.003,-0.96388,-0.24001,0.11546,369.91,0.12666,-0.031719,0.99144,8.7817
> view matrix models
> #16,-0.18655,0.91957,0.3458,-11.412,-0.95625,-0.2507,0.1508,366.44,0.22537,-0.30254,0.92611,43.543
> view matrix models
> #16,-0.18192,0.98284,0.030402,13.116,-0.97632,-0.18422,0.11342,363.23,0.11707,-0.0090496,0.99308,6.5102
> view matrix models
> #16,-0.28769,0.95139,0.10996,25.987,-0.93772,-0.30316,0.16963,369.74,0.19472,-0.054314,0.97935,2.9354
> view matrix models
> #16,-0.39269,0.91102,0.12586,47.287,-0.91808,-0.39637,0.004623,399.94,0.054098,-0.11373,0.99204,33.276
> view matrix models
> #16,-0.52099,0.85218,0.048594,85.657,-0.84753,-0.52323,0.089007,399.49,0.10128,0.0051873,0.99484,6.5528
> view matrix models
> #16,-0.56106,0.82603,0.053805,95.59,-0.82637,-0.56271,0.021872,409.94,0.048344,-0.032191,0.99831,20.509
> view matrix models
> #16,-0.78982,0.6085,0.076912,163.91,-0.60935,-0.79277,0.014622,412.94,0.069871,-0.035318,0.99693,17.747
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.78982,0.6085,0.076912,182.08,-0.60935,-0.79277,0.014622,376.18,0.069871,-0.035318,0.99693,14.981
> view matrix models
> #16,-0.78982,0.6085,0.076912,180.78,-0.60935,-0.79277,0.014622,376.48,0.069871,-0.035318,0.99693,-7.3533
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2828369 points
correlation = 0.9835, correlation about mean = 0.9163, overlap = 94.12
steps = 144, shift = 15.4, angle = 5.12 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#16) relative
to short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
-0.76288043 0.64653909 0.00079922 171.53676990
-0.64642566 -0.76276864 0.01782838 380.68867235
0.01213636 0.01308428 0.99984073 7.70781632
Axis -0.00366899 -0.00876793 -0.99995483
Axis point 155.54379261 158.86305349 0.00000000
Rotation angle (degrees) 139.72089652
Shift along axis -11.67468857
> ~select #16
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #19 models
> hide #19 models
> color zone #16 near #14,19,21 distance 5
> show #!11 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> select #16
3 models selected
> view matrix models
> #16,-0.76288,0.64654,0.00079922,261.32,-0.64643,-0.76277,0.017828,344.12,0.012136,0.013084,0.99984,2.7434
> view matrix models
> #16,-0.76288,0.64654,0.00079922,175.29,-0.64643,-0.76277,0.017828,381.65,0.012136,0.013084,0.99984,-4.6062
> hide #!11 models
> show #!8 models
> view matrix models
> #16,-0.76288,0.64654,0.00079922,172.13,-0.64643,-0.76277,0.017828,381.05,0.012136,0.013084,0.99984,-4.7531
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2828369 points
correlation = 0.9834, correlation about mean = 0.9158, overlap = 94.11
steps = 104, shift = 12.5, angle = 0.0076 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#16) relative
to short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
-0.76296505 0.64643923 0.00080213 171.56553204
-0.64632552 -0.76285299 0.01784977 380.68268887
0.01215070 0.01310031 0.99984035 7.68049013
Axis -0.00367371 -0.00877813 -0.99995472
Axis point 155.54299133 158.86123203 0.00000000
Rotation angle (degrees) 139.72840148
Shift along axis -11.65210598
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!14 models
> select #14
6389 atoms, 6536 bonds, 3 pseudobonds, 799 residues, 2 models selected
> view matrix models
> #14,0.99309,-0.057292,-0.10241,32.64,0.054758,0.99812,-0.027386,-1.2158,0.10379,0.021589,0.99436,20.932
> view matrix models
> #14,0.99309,-0.057292,-0.10241,27.222,0.054758,0.99812,-0.027386,-5.1407,0.10379,0.021589,0.99436,21.562
Fit molecule wt_sub_VP5CT.pdb (#14) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#16) using 6389 atoms
average map value = 0.006089, steps = 112
shifted from previous position = 14
rotated from previous position = 11.4 degrees
atoms outside contour = 597, contour level = 0.002231
Position of wt_sub_VP5CT.pdb (#14) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#16) coordinates:
Matrix rotation and translation
-0.66592496 -0.74153000 0.08171426 367.82753482
0.74440897 -0.66768162 0.00752079 152.94445442
0.04898222 0.06583711 0.99662743 23.88131877
Axis 0.03920575 0.02200558 0.99898882
Axis point 149.52795213 157.90664437 0.00000000
Rotation angle (degrees) 131.95059587
Shift along axis 41.64375618
> hide #!16 models
> show #19 models
> show #!20 models
> hide #!20 models
> show #21 models
> show #!22 models
> hide #19 models
> hide #21 models
> hide #!22 models
> show #!16 models
> show #19 models
> show #21 models
> show #!22 models
> hide #!22 models
> color zone #16 near #14,19,21 distance 5
> view list
Named views: 1, 2, 3, 4, 5, 6, 7
> view 7
> hide #21 models
> hide #19 models
> hide #!14 models
> ~select #14
Nothing selected
> view 7
> lighting soft
> lighting simple
> view 7
> lighting soft
> lighting simple
> hide #!16 models
> show #!8 models
> view 7
> hide #!8 models
> show #!16 models
> lighting soft
> lighting simple
> lighting soft
> view name 8
> view 7
> view list
Named views: 1, 2, 3, 4, 5, 6, 7, 8
> view 8
> lighting simple
> lighting soft
> lighting simple
> view 8
> lighting soft
> lighting simple
> hide #!16 models
> show #!8 models
> view 8
> lighting simple
> lighting soft
> lighting simple
> show #!13.3 models
> hide #!13.3 models
> show #!16 models
> select #16
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #16,1,0,0,55.342,0,1,0,60.701,0,0,1,3.505
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.32299,0.91553,0.23976,92.632,-0.94629,-0.30846,-0.096919,429.89,-0.014778,-0.25818,0.96598,50.748
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.32299,0.91553,0.23976,38.406,-0.94629,-0.30846,-0.096919,391.9,-0.014778,-0.25818,0.96598,50.251
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.73535,0.63486,0.2371,148.78,-0.6752,-0.71629,-0.17616,422.68,0.058,-0.28963,0.95538,44.899
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 536.23
OpenGL renderer: NVIDIA GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 10SWCTO1WW
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 8,466,862,080
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 15 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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