Opened 22 months ago

Closed 22 months ago

#10445 closed defect (duplicate)

segger savePath arg allows folder

Reported by: disha-gajanan.hiregange@… 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 Eric Pettersen, 22 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → segger savePath arg allows folder

comment:2 by Eric Pettersen, 22 months ago

Resolution: → duplicate
Status: assigned → closed
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