Opened 22 months ago
Closed 22 months ago
#10445 closed defect (duplicate)
segger savePath arg allows folder
| Reported by: | 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: Linux-5.4.115-1.el8.elrepo.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /archive/processing/andre/dba_ips_ctrl/maps/unsharp_post_corrected.mrc
Opened unsharp_post_corrected.mrc as #1, grid size 480,480,480, pixel 0.85,
shown at level 0.0182, step 2, values float32
> volume #1 step 1
> open
> /archive/processing/disha/hES_wildtype/relion/Refine3D/3d_ref_shiny/run_class001.mrc
Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.85, shown at
level 0.0137, step 2, values float32
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map unsharp_post_corrected.mrc in map run_class001.mrc using 1107194
points
correlation = 0.3467, correlation about mean = 0.03433, overlap = 114.4
steps = 172, shift = 8.79, angle = 3.05 degrees
Position of unsharp_post_corrected.mrc (#1) relative to run_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99858253 0.04957284 0.01937709 -11.15880780
-0.04952448 0.99876850 -0.00296779 3.68200937
-0.01950035 0.00200395 0.99980784 8.26055496
Axis 0.04665381 0.36481801 -0.92990927
Axis point 119.35103556 222.05689934 0.00000000
Rotation angle (degrees) 3.05435623
Shift along axis -6.85890411
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.24128,0.85009,0.46812,-19.135,-0.42548,0.34088,-0.83832,386.49,-0.87221,-0.40144,0.27944,399.56
> view matrix models
> #2,0.22049,0.8816,0.41734,-109.14,-0.74785,0.42748,-0.50791,369.55,-0.62618,-0.20012,0.75356,216.05
> view matrix models
> #2,0.34952,0.85737,0.37782,-122.44,-0.61965,0.514,-0.59316,341.88,-0.70276,-0.026796,0.71092,203.17
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.34952,0.85737,0.37782,-159.95,-0.61965,0.514,-0.59316,261.43,-0.70276,-0.026796,0.71092,1.9852
> view matrix models
> #2,0.34952,0.85737,0.37782,-161.15,-0.61965,0.514,-0.59316,262.53,-0.70276,-0.026796,0.71092,1.7991
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.26338,0.85607,0.44471,-50.132,-0.96465,-0.23805,-0.11308,398.13,0.0090582,-0.45878,0.88851,-84.948
> view matrix models
> #2,-0.030411,0.99841,0.047413,-50.528,-0.81942,0.0022605,-0.57318,406.89,-0.57238,-0.056282,0.81805,-38.944
> view matrix models
> #2,-0.22522,0.96753,0.11468,-17.69,-0.69019,-0.075356,-0.7197,425.44,-0.68769,-0.24125,0.68475,49.028
> view matrix models
> #2,-0.26813,0.95538,0.12394,-8.2557,-0.65683,-0.087177,-0.74898,426.85,-0.70476,-0.28223,0.65089,67.644
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.26813,0.95538,0.12394,45.212,-0.65683,-0.087177,-0.74898,494.9,-0.70476,-0.28223,0.65089,275.18
> view matrix models
> #2,-0.26813,0.95538,0.12394,43.817,-0.65683,-0.087177,-0.74898,496.76,-0.70476,-0.28223,0.65089,275.94
> volume #1 level 0.005
> volume #1 level 0.009
> volume #2 level 0.007
> view matrix models
> #2,-0.26813,0.95538,0.12394,2.3121,-0.65683,-0.087177,-0.74898,415.42,-0.70476,-0.28223,0.65089,66.379
> view matrix models
> #2,-0.26813,0.95538,0.12394,-10.554,-0.65683,-0.087177,-0.74898,424.69,-0.70476,-0.28223,0.65089,60.015
> view matrix models
> #2,-0.26813,0.95538,0.12394,46.813,-0.65683,-0.087177,-0.74898,507.42,-0.70476,-0.28223,0.65089,261.97
> fitmap #1 inMap #2
Fit map unsharp_post_corrected.mrc in map run_class001.mrc using 3266529
points
correlation = 0.9142, correlation about mean = 0.8267, overlap = 967.6
steps = 292, shift = 20.6, angle = 11.3 degrees
Position of unsharp_post_corrected.mrc (#1) relative to run_class001.mrc (#2)
coordinates:
Matrix rotation and translation
-0.34760533 -0.70403515 -0.61927784 541.12450731
0.93601792 -0.22170677 -0.27334331 117.48745463
0.05514521 -0.67467074 0.73605597 178.15899180
Axis -0.22073346 -0.37093834 0.90204295
Axis point 250.87552903 287.67269248 0.00000000
Rotation angle (degrees) 114.62188537
Shift along axis -2.31782192
> view matrix models
> #2,-0.26813,0.95538,0.12394,53.133,-0.65683,-0.087177,-0.74898,495.25,-0.70476,-0.28223,0.65089,246.09
> view matrix models
> #2,-0.26813,0.95538,0.12394,48.677,-0.65683,-0.087177,-0.74898,505.21,-0.70476,-0.28223,0.65089,260.6
> view matrix models
> #2,-0.26813,0.95538,0.12394,49.587,-0.65683,-0.087177,-0.74898,508.37,-0.70476,-0.28223,0.65089,260.54
> select add #1
4 models selected
> select subtract #2
2 models selected
> transparency sel 50
> view matrix models
> #1,0.99429,-0.10666,-0.0038755,35.072,0.10542,0.98708,-0.12071,9.1679,0.0167,0.11961,0.99268,-35.094
> fitmap #1 inMap #2
Fit map unsharp_post_corrected.mrc in map run_class001.mrc using 3266529
points
correlation = 0.9142, correlation about mean = 0.8267, overlap = 967.6
steps = 120, shift = 4.76, angle = 0.00711 degrees
Position of unsharp_post_corrected.mrc (#1) relative to run_class001.mrc (#2)
coordinates:
Matrix rotation and translation
-0.34756804 -0.70404900 -0.61928302 541.12604054
0.93603808 -0.22175830 -0.27323243 117.47308917
0.05503787 -0.67463936 0.73609277 178.15343366
Axis -0.22077592 -0.37088004 0.90205653
Axis point 250.88641272 287.65722047 0.00000000
Rotation angle (degrees) 114.62117454
Shift along axis -2.33155649
> select clear
[Repeated 1 time(s)]
> volume #1 level 0.01
> volume #1 level 0.02
> open
> /archive/processing/andre/dba_ips_ctrl/relion/Refine3D/unsharp/run_ct24_class001.mrc
Opened run_ct24_class001.mrc as #3, grid size 480,480,480, pixel 0.85, shown
at level 0.0109, step 2, values float32
> select add #3
2 models selected
> view matrix models #3,1,0,0,-26.63,0,1,0,-10.64,0,0,1,-229.85
> view matrix models #3,1,0,0,-28.317,0,1,0,-8.0523,0,0,1,-225.86
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.69958,-0.58756,-0.40665,239.54,0.63989,0.7684,-0.0094101,-87.007,0.318,-0.25363,0.91353,-219.18
> view matrix models
> #3,-0.030985,-0.99833,0.048704,370.69,0.85211,-0.00091382,0.52337,-88.443,-0.52245,0.057717,0.85072,-100.64
> view matrix models
> #3,0.043376,-0.99421,-0.098333,386.84,0.74351,-0.033618,0.66787,-91.371,-0.66731,-0.10208,0.73775,-14.628
> view matrix models
> #3,-0.090829,-0.93781,0.33505,308.29,0.97646,-0.017766,0.21498,-43.061,-0.19566,0.34669,0.91735,-239.31
> view matrix models
> #3,-0.51627,-0.11174,0.84911,113.95,-0.0076601,0.99201,0.12589,-32.183,-0.85639,0.05849,-0.513,261.68
> view matrix models
> #3,-0.98261,-0.099497,-0.15679,422.88,0.063323,0.61419,-0.78661,228.29,0.17456,-0.78286,-0.59721,244.72
> open /archive/processing/andre/dba_ips_ctrl/maps/unsharp_correct_hand.mrc
Opened unsharp_correct_hand.mrc as #4, grid size 480,480,480, pixel 0.85,
shown at level 0.0109, step 2, values float32
> close #3
> fitmap #1 inMap #2
Fit map unsharp_post_corrected.mrc in map run_class001.mrc using 935572 points
correlation = 0.9607, correlation about mean = 0.7826, overlap = 760.3
steps = 40, shift = 0.00995, angle = 0.00806 degrees
Position of unsharp_post_corrected.mrc (#1) relative to run_class001.mrc (#2)
coordinates:
Matrix rotation and translation
-0.34758240 -0.70403173 -0.61929459 541.12376265
0.93602555 -0.22167488 -0.27334304 117.47251812
0.05516012 -0.67468479 0.73604198 178.15540511
Axis -0.22073906 -0.37095193 0.90203599
Axis point 250.87986778 287.67180925 0.00000000
Rotation angle (degrees) 114.62059896
Shift along axis -2.32122241
> fitmap #2 inMap #4
Fit map run_class001.mrc in map unsharp_correct_hand.mrc using 325028 points
correlation = 0.9425, correlation about mean = 0.7862, overlap = 63.9
steps = 204, shift = 19.3, angle = 9.25 degrees
Position of run_class001.mrc (#2) relative to unsharp_correct_hand.mrc (#4)
coordinates:
Matrix rotation and translation
-0.34762001 0.93602535 0.05492605 68.34016988
-0.70399817 -0.22186100 -0.67465864 527.23124705
-0.61931165 -0.27319268 0.73608345 236.07286046
Axis 0.22081752 0.37084961 -0.90205886
Axis point 250.89128204 287.65225473 0.00000000
Rotation angle (degrees) 114.62634237
Shift along axis -2.33740575
> hide #!1 models
> transparency #2.1#4.1 50
> select add #4
2 models selected
> transparency sel 0
> select clear
> open /yonath_group/disha/Downloads/ComplexModeler(2).cif
Summary of feedback from opening
/yonath_group/disha/Downloads/ComplexModeler(2).cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom H is not in the residue template for MET /O:1
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for ComplexModeler(2).cif #3
---
Chain | Description
0 1 H L e f k l p | No description available
2 | No description available
4 | No description available
5 | No description available
6 | No description available
7 K V W | No description available
A | No description available
A | No description available
B | No description available
C | No description available
C | No description available
D | No description available
D | No description available
E | No description available
F | No description available
F N P | No description available
G | No description available
G | No description available
H | No description available
I | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
M Y | No description available
N | No description available
O | No description available
O T | No description available
P | No description available
Q | No description available
Q | No description available
R | No description available
R | No description available
S | 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
Z | No description available
a | No description available
a | No description available
b | No description available
b | No description available
c | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
g r t z | No description available
h | No description available
h | No description available
j | No description available
> hide #!2 models
> hide #!4 models
> close #1
> close #2
> close #4
> open
> /yonath_group/disha/Downloads/cryosparc_P10_J38_005_volume_map_sharp(3).mrc
Opened cryosparc_P10_J38_005_volume_map_sharp(3).mrc as #1, grid size
560,560,560, pixel 0.85, shown at level 0.171, step 4, values float32
> volume #1 step 1
> select /T/T
2156 atoms, 2177 bonds, 1 pseudobond, 131 residues, 2 models selected
> color (#!3 & sel) red
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms sel distance 5.1
> select ~sel
92490 atoms, 98870 bonds, 27 pseudobonds, 7464 residues, 4 models selected
> hide sel atoms
> volume sel style mesh
> surface zone #1 nearAtoms sel distance 3.53
> surface zone #1 nearAtoms sel distance 3.55
> surface zone #1 nearAtoms sel distance 2.89
> select ~sel
2156 atoms, 2177 bonds, 1 pseudobond, 131 residues, 2 models selected
> surface zone #1 nearAtoms sel distance 2.89
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> set bgColor white
> surface zone #1 nearAtoms sel distance 1
> surface zone #1 nearAtoms sel distance 1.5
No model chosen to save relative to
> save /yonath_group/disha/DBA/Leu2pro/40s_mutant/complexmodeler.pdb relModel
> #1
> select add #1
2156 atoms, 2177 bonds, 1 pseudobond, 131 residues, 4 models selected
> show sel atoms
> select add #3
94646 atoms, 101047 bonds, 28 pseudobonds, 7595 residues, 4 models selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> select clear
> open
> /yonath_group/disha/DBA/hES_D12/RPS19_4ug0_hek_real_space_refined_027-coot-8.cif
Summary of feedback from opening
/yonath_group/disha/DBA/hES_D12/RPS19_4ug0_hek_real_space_refined_027-coot-8.cif
---
warnings | Unknown polymer entity '1' near line 52
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for RPS19_4ug0_hek_real_space_refined_027-coot-8.cif #2
---
Chain | Description
ST | No description available
> ui tool show Matchmaker
> matchmaker #2 to #3
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 ComplexModeler(2).cif, chain G (#3) with
RPS19_4ug0_hek_real_space_refined_027-coot-8.cif, chain ST (#2), sequence
alignment score = 701.9
RMSD between 133 pruned atom pairs is 1.014 angstroms; (across all 141 pairs:
1.135)
> hide #!3 models
> select add #2
1094 atoms, 1113 bonds, 141 residues, 1 model selected
> surface zone #1 nearAtoms sel distance 1.5
> surface zone #1 nearAtoms sel distance 1.82
> show #!3 models
> save /yonath_group/disha/DBA/Leu2pro/40s_mutant/RPS19.pdb models #2 relModel
> #3
> open 7R4X
7r4x title:
Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map [more
info...]
Chain information for 7r4x #4
---
Chain | Description | UniProt
2 | 18S ribosomal RNA |
A | 40S ribosomal protein SA | RSSA_HUMAN 1-295
B | 40S ribosomal protein S3a | RS3A_HUMAN 1-264
C | 40S ribosomal protein S2 | RS2_HUMAN 1-293
D | 40S ribosomal protein S3 | RS3_HUMAN 1-243
E | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263
F | 40S ribosomal protein S5 | RS5_HUMAN 1-204
G | 40S ribosomal protein S6 | RS6_HUMAN 1-249
H | 40S ribosomal protein S7 | RS7_HUMAN 1-194
I | 40S ribosomal protein S8 | RS8_HUMAN 1-208
J | 40S ribosomal protein S9 | RS9_HUMAN 1-194
K | 40S ribosomal protein S10 | RS10_HUMAN 1-165
L | 40S ribosomal protein S11 | RS11_HUMAN 1-158
M | 40S ribosomal protein S12 | RS12_HUMAN 1-132
N | 40S ribosomal protein S13 | RS13_HUMAN 1-151
O | 40S ribosomal protein S14 | RS14_HUMAN 1-151
P | 40S ribosomal protein S15 | RS15_HUMAN 1-145
Q | 40S ribosomal protein S16 | RS16_HUMAN 1-146
R | 40S ribosomal protein S17 | RS17_HUMAN 1-135
S | 40S ribosomal protein S18 | RS18_HUMAN 1-152
T | 40S ribosomal protein S19 | RS19_HUMAN 1-145
U | 40S ribosomal protein S20 | RS20_HUMAN 1-119
V | 40S ribosomal protein S21 | RS21_HUMAN 1-83
W | 40S ribosomal protein S15a | RS15A_HUMAN 1-130
X | 40S ribosomal protein S23 | A0A4W2DI10_BOBOX 1-143
Y | 40S ribosomal protein S24 | RS24_HUMAN 1-133
Z | 40S ribosomal protein S25 | RS25_HUMAN 1-125
a | 40S ribosomal protein S26 | RS26_HUMAN 1-115
b | 40S ribosomal protein S27 | RS27_HUMAN 1-84
c | 40S ribosomal protein S28 | RS28_HUMAN 1-69
d | 40S ribosomal protein S29 | RS29_HUMAN 1-56
e | 40S ribosomal protein S30 | RS30_HUMAN 1-59
f | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156
g | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317
n | 60S ribosomal protein L41 | RL41_HUMAN 1-25
Non-standard residues in 7r4x #4
---
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
K — potassium ion
MG — magnesium ion
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #!4 to #3
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 ComplexModeler(2).cif, chain b (#3) with 7r4x, chain 2 (#4),
sequence alignment score = 5633.1
RMSD between 3 pruned atom pairs is 1.321 angstroms; (across all 1572 pairs:
81.916)
> select add #4
78858 atoms, 79390 bonds, 2388 pseudobonds, 10870 residues, 5 models selected
> show sel cartoons
> hide sel atoms
> color #4 #aa00ffff
> color #4 #00aaffff
> color #3 #ff5500ff
> ui tool show Matchmaker
> matchmaker #!4 to #3/G pairing bs
Specify a single 'to' chain only
> matchmaker #!4 to #3/G pairing bs
Specify a single 'to' chain only
> matchmaker #2/ST to #3/G pairing ss
Different number of reference/match chains (2 ref, 1 match)
> matchmaker #2/ST to #3/G pairing ss
Different number of reference/match chains (2 ref, 1 match)
> matchmaker #4/T to #2/ST pairing ss
Parameters
---
Chain pairing | ss
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 RPS19_4ug0_hek_real_space_refined_027-coot-8.cif, chain ST (#2)
with 7r4x, chain T (#4), sequence alignment score = 707.9
RMSD between 141 pruned atom pairs is 0.558 angstroms; (across all 141 pairs:
0.558)
> select subtract #2
77764 atoms, 78277 bonds, 2388 pseudobonds, 10729 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.4057,0.00049036,0.91401,-62.482,0.90301,0.15441,-0.4009,187.19,-0.14133,0.98801,0.062202,85.475
> view matrix models
> #4,0.42601,0.028151,0.90428,-70.427,0.73333,0.57463,-0.36337,124.96,-0.52985,0.81793,0.22415,166.54
> view matrix models
> #4,0.42095,0.10302,0.90121,-84.591,-0.078397,0.99394,-0.077007,141.37,-0.90369,-0.038237,0.42648,381.28
> view matrix models
> #4,0.83122,-0.23978,0.50158,-9.2103,0.098223,0.95135,0.29202,32.872,-0.5472,-0.19347,0.81434,255.28
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.83122,-0.23978,0.50158,-9.2646,0.098223,0.95135,0.29202,-21.252,-0.5472,-0.19347,0.81434,226.24
> surface zone #1 nearAtoms sel distance 1.82
[Repeated 1 time(s)]
> fitmap #4 inMap #1
Fit molecule 7r4x (#4) to map cryosparc_P10_J38_005_volume_map_sharp(3).mrc
(#1) using 77764 atoms
average map value = 0.1165, steps = 216
shifted from previous position = 21.7
rotated from previous position = 6.99 degrees
atoms outside contour = 57062, contour level = 0.17114
Position of 7r4x (#4) relative to
cryosparc_P10_J38_005_volume_map_sharp(3).mrc (#1) coordinates:
Matrix rotation and translation
0.81759725 -0.25174495 0.51784091 7.59082772
0.17152607 0.96501212 0.19831898 -33.31715110
-0.54964856 -0.07332183 0.83217208 194.36166118
Axis -0.23019739 0.90462583 0.35869384
Axis point 305.66024170 0.00000000 76.18983547
Rotation angle (degrees) 36.15822395
Shift along axis 37.82938701
> open
> /yonath_group/disha/Downloads/cryosparc_P9_J58_class_00_00300_volume.mrc
Opened cryosparc_P9_J58_class_00_00300_volume.mrc as #5, grid size
128,128,128, pixel 3.72, shown at level 0.939, step 1, values float32
> hide #2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> close session
> open
> /yonath_group/disha/Downloads/cryosparc_P10_J34_class_00_final_volume.mrc
Opened cryosparc_P10_J34_class_00_final_volume.mrc as #1, grid size 70,70,70,
pixel 6.8, shown at level 3.26, step 1, values float32
> volume #1 level 1.717
> ui tool show "Segment Map"
Segmenting cryosparc_P10_J34_class_00_final_volume.mrc, density threshold
1.717037
Showing 1 region surfaces
201 watershed regions, grouped to 1 regions
Showing cryosparc_P10_J34_class_00_final_volume.seg - 1 regions, 1 surfaces
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> close #2
Segmenting cryosparc_P10_J34_class_00_final_volume.mrc, density threshold
1.717037
Showing 1 region surfaces
201 watershed regions, grouped to 1 regions
Showing cryosparc_P10_J34_class_00_final_volume.seg - 1 regions, 1 surfaces
> close #2
> open /yonath_group/disha/Downloads/ComplexModeler(2).cif
Summary of feedback from opening
/yonath_group/disha/Downloads/ComplexModeler(2).cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom H is not in the residue template for MET /O:1
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for ComplexModeler(2).cif #2
---
Chain | Description
0 1 H L e f k l p | No description available
2 | No description available
4 | No description available
5 | No description available
6 | No description available
7 K V W | No description available
A | No description available
A | No description available
B | No description available
C | No description available
C | No description available
D | No description available
D | No description available
E | No description available
F | No description available
F N P | No description available
G | No description available
G | No description available
H | No description available
I | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
M Y | No description available
N | No description available
O | No description available
O T | No description available
P | No description available
Q | No description available
Q | No description available
R | No description available
R | No description available
S | 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
Z | No description available
a | No description available
a | No description available
b | No description available
b | No description available
c | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
g r t z | No description available
h | No description available
h | No description available
j | No description available
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule ComplexModeler(2).cif (#2) to map
cryosparc_P10_J34_class_00_final_volume.mrc (#1) using 94646 atoms
average map value = 2.217, steps = 100
shifted from previous position = 7.56
rotated from previous position = 30.3 degrees
atoms outside contour = 39266, contour level = 1.717
Position of ComplexModeler(2).cif (#2) relative to
cryosparc_P10_J34_class_00_final_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.99688774 -0.07513782 0.02385686 15.12072683
0.07701868 0.86368981 -0.49810445 127.48162334
0.01682155 0.49839164 0.86678879 -93.80447331
Axis 0.98851854 0.00697899 0.15093839
Axis point 0.00000000 239.59768359 190.34221796
Rotation angle (degrees) 30.26732135
Shift along axis 1.67811593
> transparency 50
> select add #2
94646 atoms, 101047 bonds, 28 pseudobonds, 7595 residues, 2 models selected
> view matrix models
> #2,0.99689,-0.075138,0.023857,-61.221,0.077019,0.86369,-0.4981,-35.136,0.016822,0.49839,0.86679,-71.556
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98923,-0.12615,-0.074299,-23.945,0.08507,0.90832,-0.40953,-68.69,0.11915,0.3988,0.90927,-80.434
> view matrix models
> #2,-0.11804,-0.99299,0.0054464,433.84,0.88884,-0.1081,-0.44528,5.6593,0.44275,-0.04772,0.89537,-41.282
> view matrix models
> #2,-0.12221,-0.99081,-0.057916,448.94,0.86227,-0.077096,-0.50054,16.914,0.49148,-0.11111,0.86377,-29.52
> view matrix models
> #2,-0.12143,-0.99138,-0.049243,446.89,0.8661,-0.081587,-0.49317,15.437,0.4849,-0.10253,0.86854,-31.228
> view matrix models
> #2,0.95694,-0.070738,-0.28152,17.714,-0.0026655,-0.97195,0.23516,273.13,-0.29026,-0.22428,-0.93029,597.14
> view matrix models
> #2,0.90624,-0.027946,-0.42185,51.362,0.0015069,-0.99759,0.069323,316.95,-0.42277,-0.063459,-0.90401,581.85
> view matrix models
> #2,0.84659,-0.039131,0.5308,-152.36,-0.3199,-0.83446,0.44871,263.6,0.42537,-0.54968,-0.71897,462.03
> view matrix models
> #2,0.9777,-0.030048,0.20782,-110.59,-0.072916,-0.97671,0.20181,298.49,0.19692,-0.21247,-0.95712,486.28
> view matrix models
> #2,0.78805,0.44284,-0.42763,-37.42,0.083198,-0.76489,-0.63877,403.48,-0.60996,0.46781,-0.63961,431.56
> view matrix models
> #2,0.97443,-0.033077,0.22225,-112.4,-0.082046,-0.97319,0.21489,296.72,0.20918,-0.22763,-0.95101,485.79
> view matrix models
> #2,0.95592,0.18442,-0.22849,-58.166,0.11418,-0.95038,-0.28939,361.77,-0.27052,0.25055,-0.92954,473.52
> view matrix models
> #2,0.83792,0.53141,-0.12442,-141.44,0.54239,-0.83617,0.081439,147.07,-0.060761,-0.13573,-0.98888,534.78
> view matrix models
> #2,0.77373,0.5897,-0.23149,-116.21,0.63084,-0.75071,0.19614,78.424,-0.05812,-0.2978,-0.95286,566.38
> view matrix models
> #2,0.76428,0.33055,0.55374,-230.89,-0.27422,-0.61058,0.74296,128.78,0.58368,-0.71968,-0.37601,388.11
> view matrix models
> #2,0.9126,0.25658,-0.31833,-45.282,0.28453,-0.95767,0.043794,246.58,-0.29362,-0.13054,-0.94697,578.32
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.9126,0.25658,-0.31833,63.149,0.28453,-0.95767,0.043794,376.41,-0.29362,-0.13054,-0.94697,554.28
> fitmap #2 inMap #1
Fit molecule ComplexModeler(2).cif (#2) to map
cryosparc_P10_J34_class_00_final_volume.mrc (#1) using 94646 atoms
average map value = 2.113, steps = 92
shifted from previous position = 14.6
rotated from previous position = 19.8 degrees
atoms outside contour = 41258, contour level = 1.717
Position of ComplexModeler(2).cif (#2) relative to
cryosparc_P10_J34_class_00_final_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.81765880 0.53891198 -0.20250424 -20.88565964
0.56384483 -0.82066489 0.09267234 277.32885084
-0.11624588 -0.18995533 -0.97488660 531.50009056
Axis -0.95305966 -0.29087514 0.08407701
Axis point 0.00000000 162.69159555 254.16526044
Rotation angle (degrees) 171.47309266
Shift along axis -16.07585225
Segmenting cryosparc_P10_J34_class_00_final_volume.mrc, density threshold
1.717037
Showing 1 region surfaces
201 watershed regions, grouped to 1 regions
Showing cryosparc_P10_J34_class_00_final_volume.seg - 1 regions, 1 surfaces
> hide #!2 models
Ungrouped to 4 regions
> close #3
Segmenting cryosparc_P10_J34_class_00_final_volume.mrc, density threshold
1.717037
Showing 1 region surfaces
201 watershed regions, grouped to 1 regions
Showing cryosparc_P10_J34_class_00_final_volume.seg - 1 regions, 1 surfaces
cryosparc_P10_J34_class_00_final_volume.seg has 1 regions
Ungrouped to 4 regions
> hide #3.3 models
> show #3.3 models
> hide #3.5 models
> show #3.5 models
Segmenting cryosparc_P10_J34_class_00_final_volume.mrc, density threshold
1.717037
Showing 1 region surfaces
201 watershed regions, grouped to 1 regions
Showing cryosparc_P10_J34_class_00_final_volume.seg - 1 regions, 1 surfaces
Ungrouped to 4 regions
> hide #3.5 models
> show #3.5 models
> hide #3.4 models
> show #3.4 models
> hide #3.3 models
> show #3.3 models
> hide #3.2 models
> show #3.2 models
> save /yonath_group/disha/DBA/Leu2pro/40s_mutant/segment_map/Segment1.mrc
> models #1
> save /yonath_group/disha/DBA/Leu2pro/40s_mutant/segment_map/Segment2.mrc
> models #1
> save /yonath_group/disha/DBA/Leu2pro/40s_mutant/segment_map/Segment3.mrc
> models #1
> save /yonath_group/disha/DBA/Leu2pro/40s_mutant/segment_map/Segment4.mrc
> models #1
> open /yonath_group/disha/DBA/Leu2pro/40s_mutant/segment_map/Segment4.mrc
> /yonath_group/disha/DBA/Leu2pro/40s_mutant/segment_map/Segment3.mrc
> /yonath_group/disha/DBA/Leu2pro/40s_mutant/segment_map/Segment2.mrc
> /yonath_group/disha/DBA/Leu2pro/40s_mutant/segment_map/Segment1.mrc
Opened Segment4.mrc as #4.1, grid size 70,70,70, pixel 6.8, shown at level
3.26, step 1, values float32
Opened Segment3.mrc as #4.2, grid size 70,70,70, pixel 6.8, shown at level
3.26, step 1, values float32
Opened Segment2.mrc as #4.3, grid size 70,70,70, pixel 6.8, shown at level
3.26, step 1, values float32
Opened Segment1.mrc as #4.4, grid size 70,70,70, pixel 6.8, shown at level
3.26, step 1, values float32
> hide #!3 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.4 models
> show #!4.4 models
> hide #!4.4 models
> show #!4.4 models
> hide #!4.4 models
> hide #!4.3 models
> hide #!4.2 models
> hide #!1 models
> volume #4.1 level 1.965
> close #4
> view matrix models
> #2,0.81766,0.53891,-0.2025,-21.11,0.56384,-0.82066,0.092672,274.85,-0.11625,-0.18996,-0.97489,529.25
> view
> hide #2.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> help help:user
> volume subtract #0 #3.2
volume subtract operation requires exactly two volumes
> volume subtract #0 #3.2
volume subtract operation requires exactly two volumes
> volume subtract #0 3.2
Expected a keyword
> segger exportmask
Missing or invalid "segmentation" argument: empty atom specifier
Must specify one segmentation, got 0
> segger exportmask #3 savePath /yonath_group/disha/DBA/Leu2pro/40s_mutant/
> format mrc
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/segger/segcmd.py", line 358, in export_mask
save_grid_data(g, save_path, session, format=format)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map_data/mrc/writemrc.py", line 61, in
write_mrc2000_grid_data
f = open(path, 'wb')
IsADirectoryError: [Errno 21] Is a directory:
'/yonath_group/disha/DBA/Leu2pro/40s_mutant/'
IsADirectoryError: [Errno 21] Is a directory:
'/yonath_group/disha/DBA/Leu2pro/40s_mutant/'
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map_data/mrc/writemrc.py", line 61, in
write_mrc2000_grid_data
f = open(path, 'wb')
See log for complete Python traceback.
> segger exportmask #3 savePath /yonath_group/disha/DBA/Leu2pro/40s_mutant
> format mrc
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/segger/segcmd.py", line 358, in export_mask
save_grid_data(g, save_path, session, format=format)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map_data/mrc/writemrc.py", line 61, in
write_mrc2000_grid_data
f = open(path, 'wb')
IsADirectoryError: [Errno 21] Is a directory:
'/yonath_group/disha/DBA/Leu2pro/40s_mutant'
IsADirectoryError: [Errno 21] Is a directory:
'/yonath_group/disha/DBA/Leu2pro/40s_mutant'
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map_data/mrc/writemrc.py", line 61, in
write_mrc2000_grid_data
f = open(path, 'wb')
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 418.113
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasma
XDG_SESSION_DESKTOP=plasma
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: CentOS Stream 8
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 15Gi 43Gi 235Mi 2.8Gi 45Gi
Swap: 31Gi 4.8Gi 26Gi
Graphics:
05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:12a0]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 22 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → segger savePath arg allows folder |
comment:2 by , 22 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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