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Opened 9 months ago
Closed 9 months ago
#16967 closed defect (duplicate)
MemoryError opening mmCIF file
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:\\\Users\\\maav501\\\Desktop\\\MA_PV586_ModelBuild\\\MA_SI\\\working\\\SI_map_v3p0_gemmi.cif
Summary of feedback from opening
C:\\\Users\\\maav501\\\Desktop\\\MA_PV586_ModelBuild\\\MA_SI\\\working\\\SI_map_v3p0_gemmi.cif
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for SI_map_v3p0_gemmi.cif #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
AA | No description available
B | No description available
BB | No description available
C | No description available
CC | No description available
D | No description available
DD | No description available
E | No description available
EE | No description available
F | No description available
FF | No description available
G | No description available
GG | No description available
H | No description available
HH | No description available
I | No description available
II | No description available
J | No description available
JJ | No description available
K | No description available
KK | No description available
L | No description available
LL | No description available
M | No description available
MM | 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
a | 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
j | No description available
r | No description available
s | No description available
t | No description available
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open
> C:/Users/maav501/Desktop/MA_PV586_ModelBuild/MA_SII/Petrychenko_48S2/8pj2_48S2.cif
8pj2_48S2.cif title:
Structure of human 48S translation initiation complex in AUG recognition state
after eIF5-induced GTP hydrolysis by eIF2 (48S-2) [more info...]
Chain information for 8pj2_48S2.cif #2
---
Chain | Description | UniProt
1 | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814
2 | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325
3 | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218
4 | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357
5 | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564
6 | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374
7 | mRNA |
8 | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352
9 | 60S ribosomal protein L41 | RL41_HUMAN 1-25
A | 18S rRNA |
B | 40S ribosomal protein S11 | RS11_HUMAN 1-158
C | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263
D | 40S ribosomal protein S9 | RS9_HUMAN 1-194
E | 40S ribosomal protein S23 | RS23_HUMAN 1-143
F | 40S ribosomal protein S30 | RS30_HUMAN 75-133
G | 40S ribosomal protein S7 | RS7_HUMAN 1-194
H | 40S ribosomal protein S27 | RS27_HUMAN 1-84
I | 40S ribosomal protein S13 | RS13_HUMAN 1-151
J | 40S ribosomal protein S15a | RS15A_HUMAN 1-130
K | 40S ribosomal protein S21 | RS21_HUMAN 1-83
L | 40S ribosomal protein S2 | RS2_HUMAN 1-293
M | 40S ribosomal protein S17 | RS17_HUMAN 1-135
N | 40S ribosomal protein SA | RSSA_HUMAN 1-295
O | 40S ribosomal protein S3a | RS3A_HUMAN 1-264
P | 40S ribosomal protein S14 | RS14_HUMAN 1-151
Q | 40S ribosomal protein S26 | RS26_HUMAN 1-115
R | 40S ribosomal protein S8 | RS8_HUMAN 1-208
S | 40S ribosomal protein S6 | RS6_HUMAN 1-249
T | 40S ribosomal protein S24 | RS24_HUMAN 1-133
V | 40S ribosomal protein S5 | RS5_HUMAN 1-204
Y | 40S ribosomal protein S16 | RS16_HUMAN 1-146
Z | 40S ribosomal protein S3 | RS3_HUMAN 1-243
a | 40S ribosomal protein S10 | RS10_HUMAN 1-165
b | 40S ribosomal protein S15 | RS15_HUMAN 1-145
c | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317
d | 40S ribosomal protein S19 | RS19_HUMAN 1-145
e | 40S ribosomal protein S25 | RS25_HUMAN 1-125
f | 40S ribosomal protein S18 | RS18_HUMAN 1-152
h | 40S ribosomal protein S20 | RS20_HUMAN 1-119
i | 40S ribosomal protein S29 | RS29_HUMAN 1-56
k | Ubiquitin | RS27A_HUMAN 1-156
m | 40S ribosomal protein S12 | RS12_HUMAN 1-132
n | 40S ribosomal protein S28 | RS28_HUMAN 1-69
o | Eukaryotic translation initiation factor 3 subunit G | EIF3G_HUMAN 1-320
q | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN 1-144
r | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 0-314
t | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
u | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1382
v | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445
w | Initiator Met-tRNA-i |
x | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548
y | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913
z | Eukaryotic translation initiation factor 5 | IF5_HUMAN 1-430
Non-standard residues in 8pj2_48S2.cif #2
---
5MC — 5-methylcytidine-5'-monophosphate
5MU — 5-methyluridine 5'-monophosphate
6MZ — N6-methyladenosine-5'-monophosphate
A2M — 2'-O-methyladenosine 5'-(dihydrogen phosphate)
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
JMH — 3-Methylcytidine- 5'-monophosphate
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
OMC — O2'-methylycytidine-5'-monophosphate
OMG — O2'-methylguanosine-5'-monophosphate
OMU — O2'-methyluridine 5'-monophosphate
UR3 — 3-methyluridine-5'-monophoshate
ZN — zinc ion
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #2/k:84-151
554 atoms, 566 bonds, 68 residues, 1 model selected
> hide #!1 models
> select #2/k:84-151
554 atoms, 566 bonds, 68 residues, 1 model selected
> sequence chain #2/k
Alignment identifier is 2/k
> show #!1 models
> select add #1
114089 atoms, 119732 bonds, 25 pseudobonds, 12209 residues, 3 models selected
> select add #2
232234 atoms, 243716 bonds, 1844 pseudobonds, 24794 residues, 6 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.94205,-0.31762,0.108,48.857,0.18361,0.75757,0.6264,-121.64,-0.28077,-0.57027,0.77198,211.44,#2,0.94205,-0.31762,0.108,48.857,0.18361,0.75757,0.6264,-121.64,-0.28077,-0.57027,0.77198,211.44
> view matrix models
> #1,0.46526,-0.58689,0.66264,91.703,-0.33631,0.57526,0.74564,2.0989,-0.8188,-0.56977,0.07027,470.56,#2,0.46526,-0.58689,0.66264,91.703,-0.33631,0.57526,0.74564,2.0989,-0.8188,-0.56977,0.07027,470.56
> select subtract #1
118699 atoms, 124550 bonds, 1819 pseudobonds, 12653 residues, 4 models
selected
> view matrix models
> #2,-0.24748,-0.91175,0.32781,395,-0.96674,0.25492,-0.020814,368.46,-0.06459,-0.32206,-0.94451,435.17
> view matrix models
> #2,0.25795,-0.88953,-0.3771,405.63,-0.1042,0.36242,-0.92617,314.53,0.96052,0.2782,0.00079301,-118.4
> view matrix models
> #2,-0.16708,-0.1043,0.98041,83.195,-0.14054,-0.98172,-0.12839,444.25,0.97587,-0.15924,0.14937,-61.165
> open C:/Users/maav501/Desktop/MA_PV586_ModelBuild/MA_SII/SII_1p6.mrc
Opened SII_1p6.mrc as #3, grid size 240,240,240, pixel 1.67, shown at level
0.049, step 1, values float32
> volume #3 level 0.01725
> hide #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.16708,-0.1043,0.98041,13.544,-0.14054,-0.98172,-0.12839,466.74,0.97587,-0.15924,0.14937,11.012
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.70301,0.39969,0.58824,115.28,-0.70773,-0.47462,-0.52332,575.9,0.070021,-0.78421,0.61653,266.68
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.70301,0.39969,0.58824,145.18,-0.70773,-0.47462,-0.52332,531.52,0.070021,-0.78421,0.61653,228.29
> fit#2 inmap #3
Unknown command: fit#2 inmap #3
> fitmap #2 inMap #3
Fit molecule 8pj2_48S2.cif (#2) to map SII_1p6.mrc (#3) using 118699 atoms
average map value = 0.04433, steps = 176
shifted from previous position = 27.2
rotated from previous position = 16.9 degrees
atoms outside contour = 11732, contour level = 0.017246
Position of 8pj2_48S2.cif (#2) relative to SII_1p6.mrc (#3) coordinates:
Matrix rotation and translation
-0.58743127 0.21139911 0.78117534 106.04770396
-0.76219997 -0.46893899 -0.44625936 548.37466927
0.27198475 -0.85755853 0.43659782 239.37600198
Axis -0.35058667 0.43402819 -0.82988464
Axis point 109.35750855 315.92709787 0.00000000
Rotation angle (degrees) 144.08481643
Shift along axis 2.17668864
> hide #!3 models
> show #!1 models
> select add #1
232234 atoms, 243716 bonds, 1844 pseudobonds, 24794 residues, 6 models
selected
> select subtract #2
113535 atoms, 119166 bonds, 25 pseudobonds, 12141 residues, 2 models selected
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.91121,0.078161,-0.40445,112.43,-0.14219,0.98117,-0.13075,77.633,0.38662,0.17665,0.90517,-74
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.91121,0.078161,-0.40445,79.401,-0.14219,0.98117,-0.13075,63.34,0.38662,0.17665,0.90517,-81.075
> select ~sel & ##selected
Nothing selected
> fitmap #1 inMap #3
Fit molecule SI_map_v3p0_gemmi.cif (#1) to map SII_1p6.mrc (#3) using 113535
atoms
average map value = 0.04503, steps = 256
shifted from previous position = 9.79
rotated from previous position = 25.4 degrees
atoms outside contour = 11196, contour level = 0.017246
Position of SI_map_v3p0_gemmi.cif (#1) relative to SII_1p6.mrc (#3)
coordinates:
Matrix rotation and translation
0.99881660 -0.03946277 -0.02842696 14.36727943
0.03965209 0.99919476 0.00612684 -7.50482297
0.02816229 -0.00724677 0.99957710 -3.87209559
Axis -0.13620787 -0.57635135 0.80577077
Axis point 207.40503025 355.25808348 0.00000000
Rotation angle (degrees) 2.81393345
Shift along axis -0.75154310
> hide #!3 models
> select /1:1-3
65 atoms, 72 bonds, 3 residues, 1 model selected
> view matrix models
> #1,0.99882,-0.039463,-0.028427,28.721,0.039652,0.99919,0.0061268,35.537,0.028162,-0.0072468,0.99958,22.568
> undo
> select add #1
113535 atoms, 119166 bonds, 25 pseudobonds, 12141 residues, 2 models selected
> select subtract #1
Nothing selected
> set bgColor white
> lighting soft
> select #2/1:170-764
3258 atoms, 3279 bonds, 1 pseudobond, 588 residues, 2 models selected
> select /1:1-3
65 atoms, 72 bonds, 3 residues, 1 model selected
> hide #!2 models
> select #1/1
65 atoms, 72 bonds, 3 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> select add #1
113535 atoms, 119166 bonds, 25 pseudobonds, 12141 residues, 2 models selected
> hide #!1 models
> show #!1 models
> select subtract #1
Nothing selected
> hide #!1 atoms
> show #!1 cartoons
> select #1/1
65 atoms, 72 bonds, 3 residues, 1 model selected
> set bgColor black
> select :MG
87 atoms, 87 residues, 1 model selected
> select :MG
87 atoms, 87 residues, 1 model selected
> select :MG
87 atoms, 87 residues, 1 model selected
> select :MG
87 atoms, 87 residues, 1 model selected
> hide #!1 models
> show #!2 models
> select :MG
87 atoms, 87 residues, 1 model selected
> select :MG
87 atoms, 87 residues, 1 model selected
> style sel sphere
Changed 87 atom styles
> hide sel cartoons
> show sel cartoons
> select /2:1-1869
36854 atoms, 41033 bonds, 11 pseudobonds, 1960 residues, 4 models selected
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select /2:1-1869
36854 atoms, 41033 bonds, 11 pseudobonds, 1960 residues, 4 models selected
> select /2:1-1869
36854 atoms, 41033 bonds, 11 pseudobonds, 1960 residues, 4 models selected
> select /3:1-74
1925 atoms, 2110 bonds, 146 residues, 2 models selected
> select /4:5-112
991 atoms, 1000 bonds, 132 residues, 2 models selected
> view matrix models
> #1,0.99882,-0.039463,-0.028427,-49.567,0.039652,0.99919,0.0061268,20.193,0.028162,-0.0072468,0.99958,-27.25,#2,-0.58743,0.2114,0.78118,42.113,-0.7622,-0.46894,-0.44626,576.07,0.27198,-0.85756,0.4366,216
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select #2/5:45-564
4347 atoms, 4458 bonds, 520 residues, 1 model selected
> select /AA:2-216
1057 atoms, 1055 bonds, 1 pseudobond, 213 residues, 2 models selected
> view matrix models
> #1,0.99882,-0.039463,-0.028427,-71.554,0.039652,0.99919,0.0061268,57.171,0.028162,-0.0072468,0.99958,-78.879
> view matrix models
> #1,0.99882,-0.039463,-0.028427,-44.798,0.039652,0.99919,0.0061268,62.277,0.028162,-0.0072468,0.99958,-73.77
> show #!2 models
> fitmap #2 inMap #3
Fit molecule 8pj2_48S2.cif (#2) to map SII_1p6.mrc (#3) using 118699 atoms
average map value = 0.04433, steps = 328
shifted from previous position = 73.5
rotated from previous position = 0.00728 degrees
atoms outside contour = 11729, contour level = 0.017246
Position of 8pj2_48S2.cif (#2) relative to SII_1p6.mrc (#3) coordinates:
Matrix rotation and translation
-0.58739780 0.21143101 0.78119188 106.03942151
-0.76225992 -0.46882843 -0.44627312 548.37307541
0.27188899 -0.85761111 0.43655417 239.40102181
Axis -0.35057836 0.43407264 -0.82986491
Axis point 109.36491442 315.93804342 0.00000000
Rotation angle (degrees) 144.07991436
Shift along axis 2.18811430
> select /B:2-207
2790 atoms, 2847 bonds, 1 pseudobond, 348 residues, 3 models selected
> show #!3 models
> hide #!3 models
> fitmap #1 inMap #3
Fit molecule SI_map_v3p0_gemmi.cif (#1) to map SII_1p6.mrc (#3) using 113535
atoms
average map value = 0.04503, steps = 404
shifted from previous position = 115
rotated from previous position = 0.00828 degrees
atoms outside contour = 11196, contour level = 0.017246
Position of SI_map_v3p0_gemmi.cif (#1) relative to SII_1p6.mrc (#3)
coordinates:
Matrix rotation and translation
0.99881814 -0.03943681 -0.02840870 14.36089567
0.03962997 0.99919476 0.00626854 -7.52679096
0.02813861 -0.00738696 0.99957674 -3.84277619
Axis -0.13911303 -0.57606563 0.80547871
Axis point 208.15066825 355.24080609 0.00000000
Rotation angle (degrees) 2.81324231
Shift along axis -0.75713655
> select /BB:89-357
1272 atoms, 1269 bonds, 2 pseudobonds, 257 residues, 2 models selected
> hide #!1 models
> show #!1 models
> select /C:21-233
3413 atoms, 3472 bonds, 426 residues, 2 models selected
> select /CC:45-564
4347 atoms, 4458 bonds, 520 residues, 1 model selected
> select /D:59-276
2672 atoms, 2722 bonds, 338 residues, 2 models selected
> view matrix models
> #1,0.99882,-0.039437,-0.028409,28.934,0.03963,0.99919,0.0062685,21.687,0.028139,-0.007387,0.99958,-2.7889,#2,-0.5874,0.21143,0.78119,120.61,-0.76226,-0.46883,-0.44627,577.59,0.27189,-0.85761,0.43655,240.45
> select /D:59-276
2672 atoms, 2722 bonds, 338 residues, 2 models selected
> select /DD:8-369
2196 atoms, 2212 bonds, 362 residues, 1 model selected
> hide #!2 models
> select /DD:8-369
2196 atoms, 2212 bonds, 362 residues, 1 model selected
> show #!2 models
> select /E:2-259
3137 atoms, 3197 bonds, 398 residues, 2 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> select add #2
120749 atoms, 126642 bonds, 1819 pseudobonds, 12911 residues, 5 models
selected
> select subtract #2
2050 atoms, 2092 bonds, 258 residues, 1 model selected
> select /EE:1-62
1325 atoms, 1479 bonds, 62 residues, 1 model selected
> select /F:3-227
2216 atoms, 2250 bonds, 284 residues, 2 models selected
> select add #2
120447 atoms, 126326 bonds, 1819 pseudobonds, 12878 residues, 5 models
selected
> select subtract #2
1748 atoms, 1776 bonds, 225 residues, 1 model selected
> select /FF:29-352
1574 atoms, 1572 bonds, 1 pseudobond, 317 residues, 2 models selected
> select /FF:29-352
1574 atoms, 1572 bonds, 1 pseudobond, 317 residues, 2 models selected
> select /FF:29-352
1574 atoms, 1572 bonds, 1 pseudobond, 317 residues, 2 models selected
> hide #!2 models
> show #!2 models
> select /G:1-226
3261 atoms, 3305 bonds, 2 pseudobonds, 403 residues, 3 models selected
> hide #!2 models
> select add #2
120530 atoms, 126404 bonds, 1819 pseudobonds, 12879 residues, 5 models
selected
> select subtract #2
1831 atoms, 1854 bonds, 226 residues, 1 model selected
> select /G:1-226
3261 atoms, 3305 bonds, 2 pseudobonds, 403 residues, 3 models selected
> show #!2 models
> select add #2
120530 atoms, 126404 bonds, 1819 pseudobonds, 12879 residues, 5 models
selected
> select subtract #2
1831 atoms, 1854 bonds, 226 residues, 1 model selected
> select /GG:18-422
2740 atoms, 2778 bonds, 405 residues, 1 model selected
> select /H:8-192
2078 atoms, 2113 bonds, 260 residues, 2 models selected
> view matrix models
> #1,0.99882,-0.039437,-0.028409,33.931,0.03963,0.99919,0.0062685,10.457,0.028139,-0.007387,0.99958,-6.5995,#2,-0.5874,0.21143,0.78119,125.61,-0.76226,-0.46883,-0.44627,566.36,0.27189,-0.85761,0.43655,236.64
> select /HH:317-875
4361 atoms, 4436 bonds, 1 pseudobond, 543 residues, 2 models selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> fitmap #1 inMap #3
Fit molecule SI_map_v3p0_gemmi.cif (#1) to map SII_1p6.mrc (#3) using 113535
atoms
average map value = 0.04503, steps = 144
shifted from previous position = 26.7
rotated from previous position = 0.00539 degrees
atoms outside contour = 11202, contour level = 0.017246
Position of SI_map_v3p0_gemmi.cif (#1) relative to SII_1p6.mrc (#3)
coordinates:
Matrix rotation and translation
0.99881951 -0.03941515 -0.02839059 14.35108343
0.03961071 0.99919495 0.00635893 -7.55289428
0.02811709 -0.00747599 0.99957668 -3.82185494
Axis -0.14098484 -0.57584173 0.80531334
Axis point 208.82564313 355.15720600 0.00000000
Rotation angle (degrees) 2.81236312
Shift along axis -0.75180428
> fitmap #2 inMap #3
Fit molecule 8pj2_48S2.cif (#2) to map SII_1p6.mrc (#3) using 118699 atoms
average map value = 0.04433, steps = 144
shifted from previous position = 26.7
rotated from previous position = 0.00638 degrees
atoms outside contour = 11748, contour level = 0.017246
Position of 8pj2_48S2.cif (#2) relative to SII_1p6.mrc (#3) coordinates:
Matrix rotation and translation
-0.58738455 0.21140440 0.78120903 106.02997872
-0.76223423 -0.46891814 -0.44622276 548.38669219
0.27198963 -0.85756863 0.43657494 239.38373841
Axis -0.35060804 0.43402993 -0.82987471
Axis point 109.35337877 315.93756392 0.00000000
Rotation angle (degrees) 144.08263386
Shift along axis 2.18276354
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #3 level 0.01833
> hide #!3 models
> select /I:2-206
2890 atoms, 2943 bonds, 355 residues, 2 models selected
> show #!2 models
> select /II:170-764
3258 atoms, 3279 bonds, 1 pseudobond, 588 residues, 2 models selected
> select /J:2-181
2533 atoms, 2575 bonds, 309 residues, 2 models selected
> select /JJ:1-312
1493 atoms, 1491 bonds, 1 pseudobond, 304 residues, 2 models selected
> select /K:16-204
1990 atoms, 2014 bonds, 255 residues, 2 models selected
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> select /K:16-204
1990 atoms, 2014 bonds, 255 residues, 2 models selected
> view matrix models
> #1,0.99882,-0.039415,-0.028391,-4.5588,0.039611,0.99919,0.0063589,-8.6454,0.028117,-0.007476,0.99958,26.608,#2,-0.58738,0.2114,0.78121,87.12,-0.76223,-0.46892,-0.44622,547.29,0.27199,-0.85757,0.43657,269.81
> view matrix models
> #1,0.99882,-0.039415,-0.028391,-0.064212,0.039611,0.99919,0.0063589,-4.2936,0.028117,-0.007476,0.99958,24.798,#2,-0.58738,0.2114,0.78121,91.615,-0.76223,-0.46892,-0.44622,551.65,0.27199,-0.85757,0.43657,268
> show #!2 models
> select /K:16-204
1990 atoms, 2014 bonds, 255 residues, 2 models selected
> select /K:16-204
1990 atoms, 2014 bonds, 255 residues, 2 models selected
> select /JJ:1-312
1493 atoms, 1491 bonds, 1 pseudobond, 304 residues, 2 models selected
> select /K:16-204
1990 atoms, 2014 bonds, 255 residues, 2 models selected
> select /KK:238-314
616 atoms, 628 bonds, 77 residues, 1 model selected
> select #1/KK
616 atoms, 628 bonds, 77 residues, 1 model selected
> hide #!2 models
> view matrix models
> #1,0.99882,-0.039415,-0.028391,-15.158,0.039611,0.99919,0.0063589,-39.708,0.028117,-0.007476,0.99958,63.795
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> fir #1 inmap #3
Unknown command: fir #1 inmap #3
> fitmap #1 inMap #3
Fit molecule SI_map_v3p0_gemmi.cif (#1) to map SII_1p6.mrc (#3) using 113535
atoms
average map value = 0.04503, steps = 260
shifted from previous position = 80.5
rotated from previous position = 0.0117 degrees
atoms outside contour = 12287, contour level = 0.018332
Position of SI_map_v3p0_gemmi.cif (#1) relative to SII_1p6.mrc (#3)
coordinates:
Matrix rotation and translation
0.99881628 -0.03948451 -0.02840785 14.37523973
0.03967481 0.99919362 0.00616640 -7.51429019
0.02814147 -0.00728618 0.99957740 -3.87466254
Axis -0.13697918 -0.57580626 0.80602969
Axis point 207.72492055 355.19003939 0.00000000
Rotation angle (degrees) 2.81461070
Shift along axis -0.76542623
> fitmap #2 inMap #3
Fit molecule 8pj2_48S2.cif (#2) to map SII_1p6.mrc (#3) using 118699 atoms
average map value = 0.04433, steps = 152
shifted from previous position = 32.2
rotated from previous position = 0.00574 degrees
atoms outside contour = 12883, contour level = 0.018332
Position of 8pj2_48S2.cif (#2) relative to SII_1p6.mrc (#3) coordinates:
Matrix rotation and translation
-0.58739780 0.21139371 0.78120197 106.03281459
-0.76225029 -0.46883753 -0.44628003 548.35937603
0.27191601 -0.85761533 0.43652904 239.41423424
Axis -0.35059018 0.43407569 -0.82985831
Axis point 109.35063826 315.93860567 0.00000000
Rotation angle (degrees) 144.08158537
Shift along axis 2.17551656
> print #2/o
Unknown command: print #2/o
> info #2/o
1 models
#2, 8pj2_48S2.cif, shown
118699 atoms, 124550 bonds, 12653 residues, 53 chains
(1,2,3,4,5,6,7,8,9,A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,V,Y,Z,a,b,c,d,e,f,h,i,k,m,n,o,q,r,t,u,v,w,x,y,z)
1656 hydrogen bonds, 142 metal coordination bonds, 21 missing structure
> info #2 o
Expected a keyword
> info #2 #o
Expected a keyword
> info #2/o attribute
Expected a keyword
> info #2/o description
Expected a keyword
> info cahins #2/o
Expected a models specifier or a keyword
> info chains #2/o
chain id #2/o chain_id o
> info chains #2/
Expected a keyword
> info chains #2
chain id #2/1 chain_id 1
chain id #2/2 chain_id 2
chain id #2/3 chain_id 3
chain id #2/4 chain_id 4
chain id #2/5 chain_id 5
chain id #2/6 chain_id 6
chain id #2/7 chain_id 7
chain id #2/8 chain_id 8
chain id #2/9 chain_id 9
chain id #2/A chain_id A
chain id #2/B chain_id B
chain id #2/C chain_id C
chain id #2/D chain_id D
chain id #2/E chain_id E
chain id #2/F chain_id F
chain id #2/G chain_id G
chain id #2/H chain_id H
chain id #2/I chain_id I
chain id #2/J chain_id J
chain id #2/K chain_id K
chain id #2/L chain_id L
chain id #2/M chain_id M
chain id #2/N chain_id N
chain id #2/O chain_id O
chain id #2/P chain_id P
chain id #2/Q chain_id Q
chain id #2/R chain_id R
chain id #2/S chain_id S
chain id #2/T chain_id T
chain id #2/V chain_id V
chain id #2/Y chain_id Y
chain id #2/Z chain_id Z
chain id #2/a chain_id a
chain id #2/b chain_id b
chain id #2/c chain_id c
chain id #2/d chain_id d
chain id #2/e chain_id e
chain id #2/f chain_id f
chain id #2/h chain_id h
chain id #2/i chain_id i
chain id #2/k chain_id k
chain id #2/m chain_id m
chain id #2/n chain_id n
chain id #2/o chain_id o
chain id #2/q chain_id q
chain id #2/r chain_id r
chain id #2/t chain_id t
chain id #2/u chain_id u
chain id #2/v chain_id v
chain id #2/w chain_id w
chain id #2/x chain_id x
chain id #2/y chain_id y
chain id #2/z chain_id z
> select /L:2-148
1936 atoms, 1969 bonds, 239 residues, 2 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select /D:59-276
2672 atoms, 2722 bonds, 338 residues, 2 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> select /L:2-148
1936 atoms, 1969 bonds, 239 residues, 2 models selected
> select add #2
119903 atoms, 125775 bonds, 1819 pseudobonds, 12800 residues, 5 models
selected
> select subtract #2
1204 atoms, 1225 bonds, 147 residues, 1 model selected
> select add #1
113535 atoms, 119166 bonds, 25 pseudobonds, 12141 residues, 2 models selected
> select subtract #1
Nothing selected
> select /L:2-148
1936 atoms, 1969 bonds, 239 residues, 2 models selected
> show #!2 models
> select add #1
114267 atoms, 119910 bonds, 25 pseudobonds, 12233 residues, 3 models selected
> select subtract #1
732 atoms, 744 bonds, 92 residues, 1 model selected
> select add #2
118699 atoms, 124550 bonds, 1819 pseudobonds, 12653 residues, 4 models
selected
> select subtract #2
Nothing selected
> select #1/LL
5071 atoms, 5159 bonds, 1 pseudobond, 645 residues, 2 models selected
> select #1/M
816 atoms, 840 bonds, 97 residues, 1 model selected
> select #1/M
816 atoms, 840 bonds, 97 residues, 1 model selected
> select #1/MM
2837 atoms, 2880 bonds, 2 pseudobonds, 422 residues, 2 models selected
> select #1/N
1152 atoms, 1176 bonds, 141 residues, 1 model selected
> select #1/O
929 atoms, 939 bonds, 120 residues, 1 model selected
> select #1/P
998 atoms, 1011 bonds, 134 residues, 1 model selected
> select #1/Q
1043 atoms, 1064 bonds, 127 residues, 1 model selected
> select #1/R
1109 atoms, 1126 bonds, 139 residues, 1 model selected
> hide #!2 models
> show #!2 models
> select #1/S
1066 atoms, 1080 bonds, 132 residues, 1 model selected
> select #1/T
1183 atoms, 1201 bonds, 143 residues, 1 model selected
> hide #!2 models
> show #!2 models
> select #1/U
1083 atoms, 1101 bonds, 139 residues, 1 model selected
> select #1/V
803 atoms, 813 bonds, 101 residues, 1 model selected
> select #1/W
1034 atoms, 1051 bonds, 129 residues, 1 model selected
> select #1/X
1098 atoms, 1116 bonds, 141 residues, 1 model selected
> select #1/Y
1006 atoms, 1023 bonds, 123 residues, 1 model selected
> select #1/Z
625 atoms, 631 bonds, 82 residues, 1 model selected
> select #1/a
574 atoms, 580 bonds, 72 residues, 1 model selected
> hide #!2 models
> show #!2 models
> select #1/b
640 atoms, 653 bonds, 82 residues, 1 model selected
> hide #!2 models
> show #!2 models
> select #1/c
793 atoms, 805 bonds, 100 residues, 1 model selected
> select #1/d
449 atoms, 451 bonds, 58 residues, 1 model selected
> hide #!2 models
> show #!2 models
> select #1/e
391 atoms, 393 bonds, 1 pseudobond, 51 residues, 2 models selected
> select #1/f
456 atoms, 466 bonds, 55 residues, 1 model selected
> select #1/g
530 atoms, 540 bonds, 66 residues, 1 model selected
> select #1/h
185 atoms, 186 bonds, 19 residues, 1 model selected
> hide #!2 models
> show #!2 models
> select #1/i
Nothing selected
> hide #!2 models
> select #1/j
2440 atoms, 2497 bonds, 314 residues, 1 model selected
> select #1/r
2215 atoms, 2247 bonds, 275 residues, 1 model selected
> show #!2 models
> select #1/s
1123 atoms, 1142 bonds, 138 residues, 1 model selected
> select #1/t
1750 atoms, 1745 bonds, 4 pseudobonds, 356 residues, 2 models selected
> close #1
> close #3
> open
> C:/Users/maav501/Desktop/MA_PV586_ModelBuild/MA_SIII/working/aligned_maps/pdb_extract_v12.cif
Summary of feedback from opening
C:/Users/maav501/Desktop/MA_PV586_ModelBuild/MA_SIII/working/aligned_maps/pdb_extract_v12.cif
---
warnings | Unknown polymer entity '1' on line 56
Unknown polymer entity '2' on line 1680
Unknown polymer entity '3' on line 3409
Unknown polymer entity '4' on line 5091
Unknown polymer entity '5' on line 7141
36 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for pdb_extract_v12.cif #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
EE | 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
a | 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
j | No description available
r | No description available
s | No description available
t | No description available
> open
> C:/Users/maav501/Desktop/MA_PV586_ModelBuild/MA_SIII/working/aligned_maps/1-6apix_s3_r3d_J573.mrc
Opened 1-6apix_s3_r3d_J573.mrc as #3, grid size 270,270,270, pixel 1.66, shown
at level 0.0185, step 2, values float32
> fitmap #2 inMap #3
Fit molecule 8pj2_48S2.cif (#2) to map 1-6apix_s3_r3d_J573.mrc (#3) using
118699 atoms
average map value = 0.02126, steps = 196
shifted from previous position = 38.1
rotated from previous position = 9.64 degrees
atoms outside contour = 58417, contour level = 0.01852
Position of 8pj2_48S2.cif (#2) relative to 1-6apix_s3_r3d_J573.mrc (#3)
coordinates:
Matrix rotation and translation
-0.55441817 0.06533859 0.82966942 138.36300381
-0.72715103 -0.52294180 -0.44472829 571.30611833
0.40481090 -0.84986042 0.33743946 258.12668598
Axis -0.41078299 0.43078453 -0.80354342
Axis point 98.23067293 333.36365778 0.00000000
Rotation angle (degrees) 150.45402144
Shift along axis -18.14333081
> hide #!2 models
> show #!1 cartoons
> hide #!1 atoms
> select #1/1
65 atoms, 72 bonds, 3 residues, 1 model selected
> select #1/2:1-1869
35361 atoms, 39542 bonds, 10 pseudobonds, 1656 residues, 2 models selected
> select #1/U:4-142
1083 atoms, 1101 bonds, 139 residues, 1 model selected
> show #!2 models
> hide #!3 models
> close #3
> close #2
> close #1
> open
> C:/Users/maav501/Desktop/MA_PV586_ModelBuild/MA_SII/working/aligned/SII_v1p9_gemmi.cif
Summary of feedback from opening
C:/Users/maav501/Desktop/MA_PV586_ModelBuild/MA_SII/working/aligned/SII_v1p9_gemmi.cif
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 513, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\mmcif\\__init__.py", line 54, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "src\\\mmcif.pyx", line 102, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory!
MemoryError: not enough memory!
File "src\\\mmcif.pyx", line 102, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 517.13
OpenGL renderer: NVIDIA RTX A1000 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: HP
Model: HP ZBook Power 15.6 inch G9 Mobile Workstation PC
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 34,012,098,560
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError opening mmCIF file |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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