Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#10120 closed defect (can't reproduce)

Crash setting volume level

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18363
ChimeraX Version: 1.4rc202205110644 (2022-05-11 06:44:50 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Current thread 0x00004a04 (most recent call first):
  File "C:\Users\zhangshuhao\software\ChimeraX 1.4rc202205110644\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Users\zhangshuhao\software\ChimeraX 1.4rc202205110644\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Users\zhangshuhao\software\ChimeraX 1.4rc202205110644\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Users\zhangshuhao\software\ChimeraX 1.4rc202205110644\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Users\zhangshuhao\software\ChimeraX 1.4rc202205110644\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open C:/Users/zhangshuhao/Desktop/J247_model/gnn_output_round_3/output.cif

Summary of feedback from opening
C:/Users/zhangshuhao/Desktop/J247_model/gnn_output_round_3/output.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for output.cif #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
A | No description available  
A3 AM Aj | No description available  
AA | No description available  
AB | No description available  
AC | No description available  
AD | No description available  
AE | No description available  
AF | No description available  
AG | No description available  
AH | No description available  
AI | No description available  
AJ | No description available  
AK | No description available  
AO | No description available  
AP | No description available  
AU | No description available  
AV | No description available  
AX | No description available  
AY | No description available  
Aa | No description available  
Ad | No description available  
Ag | No description available  
As | No description available  
Aw | No description available  
B | No description available  
B0 | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
B4 | No description available  
B5 | No description available  
B6 | No description available  
B7 | No description available  
B8 | No description available  
B9 | No description available  
BM | No description available  
BN | No description available  
BO | No description available  
BP | No description available  
BQ | No description available  
BR | No description available  
BS | No description available  
BT | No description available  
BU | No description available  
BV | No description available  
BW | No description available  
BX | No description available  
BY | No description available  
BZ | No description available  
Ba | No description available  
Bb | No description available  
Bc | No description available  
Bd | No description available  
Be | No description available  
Bf | No description available  
Bg | No description available  
Bh | No description available  
Bi | No description available  
Bj | No description available  
Bk | No description available  
Bl | No description available  
Bm | No description available  
Bn | No description available  
Bo | No description available  
Bp | No description available  
Bq | No description available  
Br | No description available  
Bs | No description available  
Bt | No description available  
Bu | No description available  
Bv | No description available  
Bw | No description available  
Bx | No description available  
By | No description available  
Bz | No description available  
CA | No description available  
CB | No description available  
CC | No description available  
CD | No description available  
CE | No description available  
CF | No description available  
CG | No description available  
CH | No description available  
CI | No description available  
CJ | No description available  
CK | No description available  
CL | No description available  
CM | No description available  
CN | No description available  
CO | No description available  
CP | No description available  
CQ | No description available  
CR | No description available  
CS | No description available  
CT | No description available  
CU | No description available  
CV | No description available  
CW | No description available  
CX | No description available  
CY | No description available  
CZ | No description available  
Ca | No description available  
Cb | No description available  
Cc | No description available  
Cd | No description available  
Ce | No description available  
Cf | No description available  
Cg | No description available  
Ch | No description available  
Ci | No description available  
Cj | No description available  
Ck | No description available  
Cl | No description available  
Cm | No description available  
Cn | No description available  
Co | No description available  
Cp | No description available  
Cq | No description available  
Cr | No description available  
Cs | No description available  
Ct | No description available  
Cu | No description available  
Cv | No description available  
Cw | No description available  
Cx | No description available  
Cy | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
N | No description available  
R | No description available  
U | No description available  
W | No description available  
X | No description available  
Z | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> show cartoons

> hide atoms

> hide #1 models

> close

> open
> C:/Users/zhangshuhao/Downloads/cryosparc_P17_J1344_class_00_00121_volume_sharp.mrc

Opened cryosparc_P17_J1344_class_00_00121_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.16, shown at level 0.13, step 1, values float32  

> lighting soft

> volume #1 level 0.5458

> open C:/Users/zhangshuhao/Desktop/model_angelo_new/model_angelo_new.cif

Summary of feedback from opening
C:/Users/zhangshuhao/Desktop/model_angelo_new/model_angelo_new.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model_angelo_new.cif #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
AA | No description available  
AB | No description available  
AC | No description available  
AD | No description available  
AE | No description available  
AF | No description available  
AG | No description available  
AH | No description available  
AI | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
O | No description available  
R | No description available  
T | No description available  
X | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> show cartoons

> hide atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /5

Alignment identifier is 2/5  

> ui tool show "Show Sequence Viewer"

> sequence chain /0

Alignment identifier is 2/0  

> select /5:64

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

> select /5:1-64

503 atoms, 514 bonds, 64 residues, 1 model selected  

> select /x:87

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

> select up

61 atoms, 61 bonds, 8 residues, 1 model selected  

> select up

1095 atoms, 1121 bonds, 138 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /x

Alignment identifier is 2/x  

> select /x:138

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /x:1-138

1095 atoms, 1121 bonds, 138 residues, 1 model selected  

> open C:/Users/zhangshuhao/Downloads/AF-Q9HCC0-F1-model_v4.pdb

AF-Q9HCC0-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for methylcrotonoyl-coa carboxylase β chain,
mitochondrial (Q9HCC0) [more info...]  
  
Chain information for AF-Q9HCC0-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | methylcrotonoyl-coa carboxylase β chain, mitochondrial | MCCB_HUMAN  
  

> mmaker #3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker model_angelo_new.cif, chain u (#2) with AF-Q9HCC0-F1-model_v4.pdb,
chain A (#3), sequence alignment score = 865.4  
RMSD between 199 pruned atom pairs is 0.478 angstroms; (across all 213 pairs:
1.716)  
  

> color #2 #55ffff transparency 0

> color #3 #b2b2b2 transparency 0

> color #2 #b2b2b2 transparency 0

> color #3 #ff55ff transparency 0

> select add #2

25947 atoms, 26411 bonds, 3348 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #2

25947 atoms, 26411 bonds, 3348 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select #2/9:107

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

> select up

74 atoms, 73 bonds, 10 residues, 1 model selected  

> select up

1059 atoms, 1072 bonds, 138 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/9

Alignment identifier is 2/9  

> select #2/9:138

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/9:1-138

1059 atoms, 1072 bonds, 138 residues, 1 model selected  

> open C:/Users/zhangshuhao/Downloads/AF-Q96RQ3-F1-model_v4.pdb

AF-Q96RQ3-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for methylcrotonoyl-coa carboxylase subunit
α, mitochondrial (Q96RQ3) [more info...]  
  
Chain information for AF-Q96RQ3-F1-model_v4.pdb #4  
---  
Chain | Description | UniProt  
A | methylcrotonoyl-coa carboxylase subunit α, mitochondrial | MCCA_HUMAN  
  

> mmaker #4 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker model_angelo_new.cif, chain 9 (#2) with AF-Q96RQ3-F1-model_v4.pdb,
chain A (#4), sequence alignment score = 457.6  
RMSD between 126 pruned atom pairs is 0.721 angstroms; (across all 138 pairs:
1.244)  
  

> select add #2

25947 atoms, 26411 bonds, 3348 residues, 1 model selected  

> select subtract #2

Nothing selected  

> close #1

> close #2

> close

> open C:/Users/zhangshuhao/Downloads/emd_34564.map.gz

File reader requires uncompressed file;
'C:/Users/zhangshuhao/Downloads/emd_34564.map.gz' is compressed  

> open C:/Users/zhangshuhao/Downloads/emd_34564.map/emd_34564.map

Opened emd_34564.map as #1, grid size 512,512,512, pixel 0.73, shown at level
0.0781, step 2, values float32  

> volume #1 level 0.09121

> volume #1 level 0.1017

> volume #1 level 0.1226

> volume #1 level 0.1383

> volume #1 level 0.08859

> volume #1 step 1

> volume #1 level 0.1061

> volume #1 level 0.1177

> volume #1 level 0.1818

> volume #1 level 0.1177

> volume #1 level 0.1002

> open C:/Users/zhangshuhao/Downloads/emd_34580.map/emd_34580.map

Opened emd_34580.map as #2, grid size 512,512,512, pixel 0.73, shown at level
2.75, step 2, values float32  

> open C:/Users/zhangshuhao/Downloads/emd_34581.map/emd_34581.map

Opened emd_34581.map as #3, grid size 512,512,512, pixel 0.73, shown at level
2.96, step 2, values float32  

> open C:/Users/zhangshuhao/Downloads/emd_34582.map/emd_34582.map

Opened emd_34582.map as #4, grid size 512,512,512, pixel 0.73, shown at level
2.88, step 2, values float32  

> open C:/Users/zhangshuhao/Downloads/emd_34583.map/emd_34583.map

Opened emd_34583.map as #5, grid size 512,512,512, pixel 0.73, shown at level
3.11, step 2, values float32  

> volume #2 level 3.748

> volume #1 level 0.1183

> volume #2 level 6.081

> volume #3 level 5.637

> fitmap #2 inMap #3

Fit map emd_34580.map in map emd_34581.map using 50561 points  
correlation = 0.5885, correlation about mean = 0.2133, overlap = 2.63e+06  
steps = 548, shift = 4.87, angle = 19 degrees  
  
Position of emd_34580.map (#2) relative to emd_34581.map (#3) coordinates:  
Matrix rotation and translation  
0.94526579 -0.31676488 0.07831094 58.22144775  
0.31719883 0.94833199 0.00716469 -49.34137252  
-0.07653429 0.01806760 0.99690324 14.57946671  
Axis 0.01670455 0.23724116 0.97130716  
Axis point 182.87946865 152.01944700 0.00000000  
Rotation angle (degrees) 19.04712008  
Shift along axis 3.42789950  
  

> volume #4 level 5.983

> select add #4

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.99723,-0.0025761,-0.074401,14.889,0.0053917,0.99928,0.037667,-8.0487,0.074251,-0.037964,0.99652,-8.8308

> view matrix models
> #4,0.99988,0.00088464,0.015378,-2.9889,-0.00076426,0.99997,-0.0078321,1.6279,-0.015385,0.0078194,0.99985,1.9998

> view matrix models
> #4,0.99993,0.00067184,0.011864,-2.3086,-0.0006002,0.99998,-0.0060409,1.257,-0.011868,0.0060334,0.99991,1.5376

> view matrix models
> #4,-0.96793,-0.23926,-0.076545,461.68,0.2183,-0.95191,0.21497,221.65,-0.1243,0.19136,0.97362,0.68319

> view matrix models
> #4,-0.9955,-0.072838,0.060534,415.6,0.079355,-0.99038,0.11333,275.64,0.051698,0.11762,0.99171,-27.731

> view matrix models
> #4,-0.9945,-0.078677,0.069109,414.71,0.076649,-0.99656,-0.03153,304.25,0.071352,-0.026059,0.99711,-10.213

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.9945,-0.078677,0.069109,409.98,0.076649,-0.99656,-0.03153,385.38,0.071352,-0.026059,0.99711,-11.39

> view matrix models
> #4,-0.9945,-0.078677,0.069109,371.25,0.076649,-0.99656,-0.03153,379.38,0.071352,-0.026059,0.99711,-4.8707

> view matrix models
> #4,-0.9945,-0.078677,0.069109,370.08,0.076649,-0.99656,-0.03153,371.22,0.071352,-0.026059,0.99711,-9.3985

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.  

> fitmap #4 inMap #2

Fit map emd_34582.map in map emd_34580.map using 51226 points  
correlation = 0.2367, correlation about mean = 0.04491, overlap = 7.597e+05  
steps = 108, shift = 1.96, angle = 3.07 degrees  
  
Position of emd_34582.map (#4) relative to emd_34580.map (#2) coordinates:  
Matrix rotation and translation  
-0.93881748 -0.34441493 -0.00033099 423.23964137  
0.34434739 -0.93861346 -0.02072850 308.69804899  
0.00682854 -0.01957426 0.99978509 -2.59324899  
Axis 0.00167573 -0.01039419 0.99994457  
Axis point 184.20759055 191.92919507 0.00000000  
Rotation angle (degrees) 159.85481114  
Shift along axis -5.09253384  
  

> view matrix models
> #4,-0.99597,-0.029777,0.084547,366.3,0.028813,-0.99951,-0.012599,380.98,0.084881,-0.010113,0.99634,-8.8452

> view matrix models
> #4,-0.99597,-0.029777,0.084547,361.61,0.028813,-0.99951,-0.012599,368.45,0.084881,-0.010113,0.99634,-16.82

> view matrix models
> #4,-0.99597,-0.029777,0.084547,361.73,0.028813,-0.99951,-0.012599,368.92,0.084881,-0.010113,0.99634,-16.884

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.97293,0.22819,0.036487,325.31,-0.22892,-0.97329,-0.017252,419.32,0.031576,-0.025137,0.99919,-3.9526

> view matrix models
> #4,-0.94495,0.32704,-0.010329,312.67,-0.327,-0.94501,-0.0054351,433.07,-0.011539,-0.0017582,0.99993,1.2035

> ui mousemode right "move picked models"

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.94495,0.32704,-0.010329,305.7,-0.327,-0.94501,-0.0054351,431.55,-0.011539,-0.0017582,0.99993,0.69486

> fitmap #4 inMap #2

Fit map emd_34582.map in map emd_34580.map using 51226 points  
correlation = 0.4278, correlation about mean = 0.06626, overlap = 1.872e+06  
steps = 248, shift = 4.79, angle = 5.64 degrees  
  
Position of emd_34582.map (#4) relative to emd_34580.map (#2) coordinates:  
Matrix rotation and translation  
-0.99810643 0.06123000 -0.00586961 362.15610742  
-0.06121694 -0.99812165 -0.00238106 386.58394471  
-0.00600438 -0.00201724 0.99997995 0.10386572  
Axis 0.00297129 0.00110062 -0.99999498  
Axis point 187.00080170 187.74371991 0.00000000  
Rotation angle (degrees) 176.48994081  
Shift along axis 1.39768864  
  

> select subtract #4

Nothing selected  

> select add #5

2 models selected  

> select subtract #5

Nothing selected  

> select add #5

2 models selected  

> volume #5 level 5.014

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.58446,0.78594,0.20176,-105.98,0.74033,-0.61829,0.26388,113.9,0.33214,-0.0048575,-0.94322,298.88

> view matrix models
> #5,-0.20231,0.97521,0.089645,29.995,0.95384,0.17547,0.24372,-72.804,0.22195,0.13482,-0.96569,297.86

> volume #5 level 6.012

> view matrix models
> #5,-0.60368,-0.79708,-0.015184,491.62,-0.78919,0.60018,-0.1302,156.02,0.11289,-0.066616,-0.99137,362.04

> view matrix models
> #5,-0.066911,-0.99775,-0.003738,455.45,-0.99776,0.066902,0.0024919,277.31,-0.0022363,0.0038964,-0.99999,364.98

> view matrix models
> #5,-0.029954,-0.99019,0.13647,422.59,-0.98897,0.04917,0.1397,254.56,-0.14504,-0.13078,-0.98075,411.26

> view matrix models
> #5,-0.17072,-0.9698,0.1742,431.55,-0.9712,0.19545,0.13626,220.91,-0.16619,-0.14593,-0.97524,416.59

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.17072,-0.9698,0.1742,371.43,-0.9712,0.19545,0.13626,281.51,-0.16619,-0.14593,-0.97524,418.66

> view matrix models
> #5,-0.17072,-0.9698,0.1742,386.71,-0.9712,0.19545,0.13626,288.97,-0.16619,-0.14593,-0.97524,413.68

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.59799,-0.72882,0.3335,366.81,-0.79769,0.58172,-0.15905,234.64,-0.078082,-0.36114,-0.92924,439.12

> view matrix models
> #5,-0.58548,-0.79885,-0.13801,467.21,-0.69924,0.58376,-0.41265,266.78,0.41021,-0.1451,-0.90037,316.38

> view matrix models
> #5,-0.75515,-0.59197,-0.28165,473.38,-0.61005,0.79185,-0.028671,137.9,0.24,0.15017,-0.95909,287.8

> view matrix models
> #5,-0.94595,-0.32351,0.022874,386.54,-0.32077,0.92288,-0.21307,101.72,0.047822,-0.20889,-0.97677,396.69

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.94595,-0.32351,0.022874,419.67,-0.32077,0.92288,-0.21307,120.39,0.047822,-0.20889,-0.97677,399.21

> view matrix models
> #5,-0.94595,-0.32351,0.022874,417.15,-0.32077,0.92288,-0.21307,121.67,0.047822,-0.20889,-0.97677,402.7

> fitmap #5 inMap #2

Fit map emd_34583.map in map emd_34580.map using 58197 points  
correlation = 0.3843, correlation about mean = 0.1148, overlap = 1.442e+06  
steps = 424, shift = 2.97, angle = 15.9 degrees  
  
Position of emd_34583.map (#5) relative to emd_34580.map (#2) coordinates:  
Matrix rotation and translation  
-0.96540017 -0.25503684 0.05439408 401.25925051  
-0.25999310 0.95746053 -0.12519155 84.96434674  
-0.02015173 -0.13500202 -0.99064038 403.52440497  
Axis -0.13019576 0.98930416 -0.06577501  
Axis point 210.06696506 0.00000000 200.75847477  
Rotation angle (degrees) 177.84082019  
Shift along axis 5.27150622  
  

> view matrix models
> #5,-0.83178,-0.55494,0.013495,451.1,-0.55293,0.82613,-0.10857,152.43,0.049099,-0.097766,-0.994,383.44

> fitmap #5 inMap #2

Fit map emd_34583.map in map emd_34580.map using 58197 points  
correlation = 0.5311, correlation about mean = 0.2112, overlap = 2.449e+06  
steps = 2000, shift = 9.89, angle = 8.65 degrees  
  
Position of emd_34583.map (#5) relative to emd_34580.map (#2) coordinates:  
Matrix rotation and translation  
-0.96675742 -0.25553851 -0.00895262 413.27601692  
-0.25563028 0.96670850 0.01130637 52.65847058  
0.00576536 0.01321908 -0.99989600 368.10864964  
Axis 0.12887106 -0.99164208 -0.00618314  
Axis point 209.37099693 0.00000000 184.66365778  
Rotation angle (degrees) 179.57480337  
Shift along axis -1.23510537  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.77572,-0.6272,-0.069788,466.48,-0.62597,0.77877,-0.041014,165.51,0.080073,0.01187,-0.99672,358.61

> fitmap #5 inMap #2

Fit map emd_34583.map in map emd_34580.map using 58197 points  
correlation = 0.5611, correlation about mean = 0.2138, overlap = 2.684e+06  
steps = 196, shift = 2.66, angle = 5.31 degrees  
  
Position of emd_34583.map (#5) relative to emd_34580.map (#2) coordinates:  
Matrix rotation and translation  
-0.96462536 -0.26290563 0.01945612 411.05186038  
-0.26323449 0.96458463 -0.01685502 57.69825598  
-0.01433580 -0.02138030 -0.99966863 378.15895948  
Axis -0.13272505 0.99110596 -0.00964532  
Axis point 211.01550544 0.00000000 187.59310829  
Rotation angle (degrees) 179.02319832  
Shift along axis -1.01925351  
  

> volume #5 level 6.919

> select subtract #5

Nothing selected  

> hide #!2 models

> fitmap #4 inMap #5

Fit map emd_34582.map in map emd_34583.map using 51226 points  
correlation = 0.8161, correlation about mean = 0.3499, overlap = 4.06e+06  
steps = 204, shift = 1.79, angle = 5.55 degrees  
  
Position of emd_34582.map (#4) relative to emd_34583.map (#5) coordinates:  
Matrix rotation and translation  
0.99400037 0.10937651 -0.00025241 -19.56802750  
0.10937080 -0.99396736 -0.00818139 354.36770119  
-0.00114574 0.00810470 -0.99996651 371.64365325  
Axis 0.99849894 0.05476991 -0.00035004  
Axis point 0.00000000 176.96165894 186.54201656  
Rotation angle (degrees) 179.53273125  
Shift along axis -0.26005986  
  

> show #!3 models

> show #!2 models

> open
> C:/Users/zhangshuhao/Downloads/cryosparc_P46_J1567_006_volume_map_sharp.mrc

Opened cryosparc_P46_J1567_006_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.62, shown at level 0.247, step 1, values float32  

> volume #6 level 0.4473

> volume #6 level 0.4655

> select add #6

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,-27.905,0,1,0,-20.379,0,0,1,-21.871

> volume #6 level 0.32

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.92036,0.38869,0.043124,-99.422,-0.38873,0.92132,-0.0078079,76.405,-0.042766,-0.0095777,0.99904,-11.015

> view matrix models
> #6,0.99688,-0.018089,0.076814,-39.388,0.017342,0.9998,0.010376,-26.004,-0.076986,-0.0090113,0.99699,-3.7364

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.99688,-0.018089,0.076814,-32.69,0.017342,0.9998,0.010376,-21.508,-0.076986,-0.0090113,0.99699,-9.4418

> view matrix models
> #6,0.99688,-0.018089,0.076814,-27.484,0.017342,0.9998,0.010376,-31.236,-0.076986,-0.0090113,0.99699,-8.8618

> fitmap #6 inMap #5

Fit map cryosparc_P46_J1567_006_volume_map_sharp.mrc in map emd_34583.map
using 110833 points  
correlation = 0.3732, correlation about mean = 0.04987, overlap = 2.183e+05  
steps = 564, shift = 6.82, angle = 17.2 degrees  
  
Position of cryosparc_P46_J1567_006_volume_map_sharp.mrc (#6) relative to
emd_34583.map (#5) coordinates:  
Matrix rotation and translation  
-0.96310369 -0.26911126 -0.00322848 443.75912654  
-0.26889589 0.96269534 -0.03021069 50.59732413  
0.01123808 -0.02822790 -0.99953834 403.13705040  
Axis 0.13577584 -0.99062981 0.01474802  
Axis point 224.60457130 0.00000000 202.75885920  
Rotation angle (degrees) 179.58163999  
Shift along axis 16.07402396  
  

> volume #6 level 0.7384

> fitmap #6 inMap #5

Fit map cryosparc_P46_J1567_006_volume_map_sharp.mrc in map emd_34583.map
using 37392 points  
correlation = 0.411, correlation about mean = 0.03673, overlap = 1.48e+05  
steps = 52, shift = 0.31, angle = 0.648 degrees  
  
Position of cryosparc_P46_J1567_006_volume_map_sharp.mrc (#6) relative to
emd_34583.map (#5) coordinates:  
Matrix rotation and translation  
-0.96559011 -0.26005447 0.00272386 441.69907286  
-0.26002665 0.96519246 -0.02810080 47.92076540  
0.00467869 -0.02784213 -0.99960138 404.51081178  
Axis 0.13116684 -0.99125990 0.01410892  
Axis point 223.91951718 0.00000000 202.70575755  
Rotation angle (degrees) 179.94350460  
Shift along axis 16.14155144  
  

> select subtract #6

Nothing selected  

> volume #6 level 0.5383


===== Log before crash end =====

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4rc202205110644 (2022-05-11)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.13547 Core Profile Forward-Compatible Context 25.20.15032.2001
OpenGL renderer: Radeon 520
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: LENOVO
Model: 30BFA3H4CW
OS: Microsoft Windows 10 IoT 企业版 (Build 18363)
Memory: 68,255,723,520
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Xeon(R) W-2123 CPU @ 3.60GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4rc202205110644
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.2.0
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash setting volume level

comment:2 by Tom Goddard, 2 years ago

Resolution: → can't reproduce
Status: assigned → closed

Probable graphics driver crash.

comment:3 by Tom Goddard, 2 years ago

ATI driver from 2019.

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