![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8350 closed defect (duplicate)
MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | 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-glibc2.14
ChimeraX Version: 1.2 (2021-04-27 05:33:30 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2 (2021-04-27)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /yonath_group/disha/Giardia_DH_AR_AB/Chimera/chimeraX_poster.cxs
Opened new_shiny_postprocess_resampled_for_LSU.mrc as #2, grid size
320,320,320, pixel 0.85, shown at level 0.03, step 1, values float32
Log from Sun Jan 31 17:28:48 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/yonath_group/disha/Giardia_DH_AR_AB/model/last one/50S_GL-
> coot_18_1_21.pdb"
Chain information for 50S_GL-coot_18_1_21.pdb #1
---
Chain | Description
1 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | 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
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 1331, resource id:
29877240, major code: 40 (TranslateCoords), minor code: 0
> open /yonath_group/disha/Giardia_DH_AR_AB/Refmac/refmac-multisharp-
> new_shiny_postpro_resampled_for_SSU.log
Unrecognized file suffix '.log'
QXcbConnection: XCB error: 3 (BadWindow), sequence: 2071, resource id:
29878477, major code: 40 (TranslateCoords), minor code: 0
> open
> /yonath_group/disha/Giardia_DH_AR_AB/Refmac/new_shiny_postprocess_resampled_for_LSU.mrc
Opened new_shiny_postprocess_resampled_for_LSU.mrc, grid size 320,320,320,
pixel 0.85, shown at level 0.0397, step 2, values float32
> volume hide
> volume show
> volume style mesh
> volume #2 level 0.005
> volume #2 step 1
> set bgColor white
> style stick
Changed 103204 atom styles
> select /l:26@CD2
1 atom, 1 residue, 1 model selected
Drag select of 7 atoms, 4 bonds, 2 new_shiny_postprocess_resampled_for_LSU.mrc
Drag select of 4 atoms, 2 bonds, 2 new_shiny_postprocess_resampled_for_LSU.mrc
Drag select of 3 atoms, 3 bonds, 2 new_shiny_postprocess_resampled_for_LSU.mrc
Drag select of 8 atoms, 9 bonds, 2 new_shiny_postprocess_resampled_for_LSU.mrc
Drag select of 5 atoms, 3 bonds, 2 new_shiny_postprocess_resampled_for_LSU.mrc
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /1
Alignment identifier is 1/1
> volume #2 level 0.05
Drag select of 3 atoms, 2 bonds, 2 new_shiny_postprocess_resampled_for_LSU.mrc
Drag select of 1 bonds, 2 new_shiny_postprocess_resampled_for_LSU.mrc
> select clear
> select #1
103204 atoms, 110766 bonds, 112 pseudobonds, 8439 residues, 2 models selected
> hide #!2 models
Drag select of 1 bonds
Drag select of 18 atoms, 23 bonds
Drag select of 15 atoms, 14 bonds
Drag select of 34 atoms, 37 bonds
Drag select of 13 atoms, 12 bonds
Drag select of 57 atoms, 60 bonds
Drag select of 1 bonds
Drag select of 13 atoms, 17 bonds
Drag select of 8 atoms, 4 bonds
> view sel
> show #!2 models
> view sel
> hide #!2 models
> view sel
> view sel
> ui tool show "Side View"
> select #1/1
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> color sel pink
> select clear
> show #!2 models
> hide #!2 models
> select #1/1
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> color sel darkred pink
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel orchid
> select clear
> select sequence CUCCCAGGA
190 atoms, 211 bonds, 9 residues, 1 model selected
> view sel
> show #!2 models
> select clear
> volume #2 style surface
> volume #2 style mesh
> volume #2 style surface style image
Repeated keyword argument "style"
> volume #2 maximumIntensityProjection true
> volume #2 region 0,0,159,319,319,159 step 1 maximumIntensityProjection false
> showOutlineBox true
> volume #2 region 0,0,0,319,319,319 step 1
> volume #2 region 0,0,0,319,319,319 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 159,159,159 imageMode orthoplanes
> volume #2 imageMode "box faces"
> volume #2 colorMode auto8 imageMode "tilted slab" tiltedSlabAxis
> -0.9007,-0.4229,0.09955 tiltedSlabOffset -193.2 tiltedSlabSpacing 0.85
> tiltedSlabPlaneCount 64
> volume #2 style mesh
> toolshed show
> volume #2 level 0.03
> volume #2 change image level -0.002702,0 level 0.03974,0.8 level 0.1846,1
> volume #2 level 0.035
> volume #2 level 0.04
> surfaceSmoothing true
Unknown command: surfaceSmoothing true
> volume #2 surfaceSmoothing true
> volume #2 surfaceSmoothing false
> volume #2 surfaceSmoothing true
> lighting full
> lighting simple
> volume #2 subdivideSurface true
> volume #2 level 0.03
> volume #2 tiltedSlabAxis -0.2782,-0.9504,-0.1393 tiltedSlabOffset -212.4
> volume #2 tiltedSlabAxis 0.3672,-0.08083,-0.9266 tiltedSlabOffset -113.6
> select #1/1/679-681
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> select #1/1/679
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> select #1/1/679
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> select #1/1/679
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> select #1/1/679
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> select #1/1/679
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> select #1/1/679
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> select #1/
Expected an objects specifier or a keyword
> select #1
103204 atoms, 110766 bonds, 112 pseudobonds, 8439 residues, 2 models selected
> select #1/1
51649 atoms, 57715 bonds, 84 pseudobonds, 2406 residues, 2 models selected
> select clear
Drag select of 1 bonds, 2 new_shiny_postprocess_resampled_for_LSU.mrc
> select clear
> hide #!2 models
Drag select of 1 bonds
Drag select of 41 atoms, 45 bonds
> show #!2 models
> view sel
> view sel
> volume #2 tiltedSlabAxis 0.7803,0.3108,-0.5428 tiltedSlabOffset 47.88
> volume #2 tiltedSlabAxis -0.4157,-0.4195,-0.807 tiltedSlabOffset -237.3
> volume #2 tiltedSlabAxis -0.2385,0.8797,-0.4114 tiltedSlabOffset 31.47
> volume #2 tiltedSlabAxis -0.1696,0.9363,-0.3075 tiltedSlabOffset 64.31
> volume #2 tiltedSlabAxis 0.3538,-0.9353,-0.003705 tiltedSlabOffset -134.9
> volume #2 tiltedSlabAxis -0.9822,-0.1816,-0.04814 tiltedSlabOffset -196.7
> volume #2 tiltedSlabAxis 0.2411,-0.9442,0.2246 tiltedSlabOffset -90.27
> volume #2 tiltedSlabAxis -0.1595,0.7458,0.6468 tiltedSlabOffset 139.3
> volume #2 tiltedSlabAxis -0.7145,0.6942,0.08703 tiltedSlabOffset -19.74
> select clear
> save /yonath_group/andre/Desktop/image1.png supersample 3
> save /yonath_group/disha/Giardia_DH_AR_AB/Chimera/chimeraX_poster.cxs
——— End of log from Sun Jan 31 17:28:48 2021 ———
opened ChimeraX session
> close session
> open
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/50S_delta266_lefamulin_new-
> coot-0.pdb format pdb
Chain information for 50S_delta266_lefamulin_new-coot-0.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | 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
h | No description available
> open
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/iverted_FR_50S.mrc
Opened iverted_FR_50S.mrc as #2, grid size 440,440,440, pixel 0.85, shown at
level 0.0168, step 2, values float32
> volume all step 1
> ui tool show "Map Coordinates"
> ui tool show "Hide Dust"
> surface dust #2 size 5.1
> select #1
76356 atoms, 81945 bonds, 86 pseudobonds, 6402 residues, 2 models selected
> select #2
2 models selected
> select #1
76356 atoms, 81945 bonds, 86 pseudobonds, 6402 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> hide sel atoms
> select ::name="62B"
35 atoms, 38 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> style sel ball
Changed 35 atom styles
> ui tool show "Surface Zone"
> surface zone #2 nearAtoms sel distance 5.1
> ui tool show "Side View"
> surface zone #2 nearAtoms sel distance 2.46
> surface zone #2 nearAtoms sel distance 1.82
> volume style mesh
> surface zone #2 nearAtoms sel distance 2.66
> surface dust #2 size 6.91
> surface dust #2 size 6.91
> surface zone #2 nearAtoms sel distance 2.66
> surface zone #2 nearAtoms sel distance 1.73
> select clear
Drag select of 35 atoms, 69 residues, 2 pseudobonds, 38 bonds, 2
iverted_FR_50S.mrc
> show sel atoms
> style sel stick
Changed 1463 atom styles
> undo
> undo
> select clear
> lighting simple
> lighting shadows true
> lighting shadows false
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> cartoon style nucleic xsection round width 1.6 thickness 0.7
> cartoon style nucleic xsection round width 0.5 thickness 0.7
> cartoon style nucleic xsection round width1.0 thickness 0.7
Expected a keyword
> cartoon style nucleic xsection round width 1.0 thickness 0.7
> volume style mesh
> volume style mesh
> volume style mesh subdivideSurface true
No atoms selected for zoning
> select ::name="62B"
35 atoms, 38 bonds, 1 residue, 1 model selected
> surface zone #2 nearAtoms sel distance 1.79
> select clear
> select ::name="62B"
35 atoms, 38 bonds, 1 residue, 1 model selected
> color sel forest green
> vop gaussian #2 sdev 2.55
Opened iverted_FR_50S.mrc gaussian as #3, grid size 440,440,440, pixel 0.85,
shown at step 1, values float32
> undo
> undo
> fitmap #1 inMap #3
Fit molecule 50S_delta266_lefamulin_new-coot-0.pdb (#1) to map
iverted_FR_50S.mrc gaussian (#3) using 76356 atoms
average map value = 0.008017, steps = 40
shifted from previous position = 0.0286
rotated from previous position = 0.0399 degrees
atoms outside contour = 40745, contour level = 0.0082166
Position of 50S_delta266_lefamulin_new-coot-0.pdb (#1) relative to
iverted_FR_50S.mrc gaussian (#3) coordinates:
Matrix rotation and translation
0.99999976 0.00055249 0.00041489 -0.15909787
-0.00055253 0.99999984 0.00008884 0.06790366
-0.00041485 -0.00008907 0.99999991 0.07301631
Axis -0.12769542 0.59553595 -0.79311463
Axis point 119.74851866 287.35858119 0.00000000
Rotation angle (degrees) 0.03991414
Shift along axis 0.00284484
> show #!2 models
> hide #!3 models
No atoms selected for zoning
> select ::name="62B"
35 atoms, 38 bonds, 1 residue, 1 model selected
> surface zone #2 nearAtoms sel distance 2.2
> surface zone #2 nearAtoms sel distance 1.85
> color sel forest green
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select ::name="62B"
35 atoms, 38 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 35 atom styles
> color sel bynucleotide
> color sel byhetero
> select clear
> select ::name="62B"
35 atoms, 38 bonds, 1 residue, 1 model selected
> select ~sel
76321 atoms, 81907 bonds, 86 pseudobonds, 6401 residues, 6 models selected
> hide sel cartoons
> select clear
> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/lefa_map.jpg
> width 1339 height 813 supersample 3
> undo
> undo
> show sel cartoons
> select ::name="62B"
35 atoms, 38 bonds, 1 residue, 1 model selected
> surface sel
> hide #!2 models
> color (#!1 & sel) forest green
> select /A:2901@C22
1 atom, 1 residue, 1 model selected
> select #1
76356 atoms, 81945 bonds, 86 pseudobonds, 6402 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select #1
76356 atoms, 81945 bonds, 86 pseudobonds, 6402 residues, 2 models selected
> color (#!1 & sel) dark gray
> select ::name="62B"
35 atoms, 38 bonds, 1 residue, 1 model selected
> color (#!1 & sel) forest green
> select clear
> select clear
> select clear
> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/lefa_50s.jpg
> width 1339 height 813 supersample 3
> select clear
> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/lefa.cxs
> close session
> open
> /yonath_group/disha/Downloads/cryosparc_P8_J44_class_00_final_volume.mrc
Opened cryosparc_P8_J44_class_00_final_volume.mrc as #1, grid size 64,64,64,
pixel 2.12, shown at level 0.525, step 1, values float32
> volume #1 level 0.2166
> volume #1 level 0.593
> volume #1 level 0.4071
> close session
> open
> /yonath_group/disha/Downloads/cryosparc_P8_J47_class_00_final_volume.mrc
Opened cryosparc_P8_J47_class_00_final_volume.mrc as #1, grid size 64,64,64,
pixel 2.12, shown at level 0.576, step 1, values float32
> volume #1 level 1.128
> volume #1 level 0.3307
> volume #1 level 0.2756
> volume #1 level 0.3006
> close session
> open
> /archive/processing/disha/protoribosome/relion/InitialModel/job049/run_it300_class001.mrc
Opened run_it300_class001.mrc as #1, grid size 240,240,240, pixel 0.85, shown
at level 0.00181, step 1, values float32
> volume #1 level 0.001468
> volume #1 level -0.0004489
> volume #1 level 0.004175
> close session
> open
> /yonath_group/disha/Downloads/cryosparc_P8_J44_class_00_final_volume.mrc
> format mrc
Opened cryosparc_P8_J44_class_00_final_volume.mrc as #1, grid size 64,64,64,
pixel 2.12, shown at level 0.525, step 1, values float32
> close session
> open
> /archive/processing/disha/protoribosome/relion/InitialModel/job046/run_it300_class001.mrc
Opened run_it300_class001.mrc as #1, grid size 160,160,160, pixel 0.85, shown
at level 0.00816, step 1, values float32
> volume #1 level 0.004643
> volume #1 level 0.002191
> open
> /archive/processing/disha/protoribosome/relion/maps/cryosparc_P8_J33_006_volume_map.mrc
MRC file is truncated. Failed reading 1 values, type int32
> close session
> open INKW
'INKW' has no suffix
> open 1NKW
Summary of feedback from opening 1NKW fetched from pdb
---
note | Fetching compressed mmCIF 1nkw from
http://files.rcsb.org/download/1nkw.cif
1nkw title:
Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans
[more info...]
Chain information for 1nkw #1
---
Chain | Description
0 | 23S ribosomal RNA
1 | 50S ribosomal protein L33
2 | 50S ribosomal protein L34
3 | 50S ribosomal protein L35
4 | 50S ribosomal protein L36
9 | 5S ribosomal RNA
A | 50S ribosomal protein L2
B | 50S ribosomal protein L3
C | 50S ribosomal protein L4
D | 50S ribosomal protein L5
E | 50S ribosomal protein L6
F | 50S ribosomal protein L9
G | 50S ribosomal protein L11
H | 50S ribosomal protein L13
I | 50S ribosomal protein L14
J | 50S ribosomal protein L15
K | 50S ribosomal protein L16
L | 50S ribosomal protein L17
M | 50S ribosomal protein L18
N | 50S ribosomal protein L19
O | 50S ribosomal protein L20
P | 50S ribosomal protein L21
Q | 50S ribosomal protein L22
R | 50S ribosomal protein L23
S | 50S ribosomal protein L24
T | general stress protein CTC
U | 50S ribosomal protein L27
W | 50S ribosomal protein L29
X | 50S ribosomal protein L30
Y | 50S ribosomal protein L31
Z | 50S ribosomal protein L32
> sequence chain #1/Q
Alignment identifier is 1/Q
> select ~sel
65300 atoms, 69283 bonds, 5900 pseudobonds, 6306 residues, 3 models selected
> hide sel atoms
> sequence chain #1/Q
Destroying pre-existing alignment with identifier 1/Q
Alignment identifier is 1/Q
> show sel cartoons
> sequence chain #1/Q
Destroying pre-existing alignment with identifier 1/Q
Alignment identifier is 1/Q
> select clear
> sequence chain #1/Q
Destroying pre-existing alignment with identifier 1/Q
Alignment identifier is 1/Q
> sequence chain #1/Q
Destroying pre-existing alignment with identifier 1/Q
Alignment identifier is 1/Q
> select /Q
130 atoms, 129 pseudobonds, 130 residues, 2 models selected
> select ~sel
65170 atoms, 69283 bonds, 5771 pseudobonds, 6176 residues, 3 models selected
> hide sel cartoons
> select clear
> hide #1.1 models
> hide #1.2 models
> sequence chain #1/H
Alignment identifier is 1/H
> select /H
143 atoms, 142 pseudobonds, 143 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select /C
197 atoms, 196 pseudobonds, 197 residues, 2 models selected
> show sel cartoons
> select clear
> select /Q
130 atoms, 129 pseudobonds, 130 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> select /C
197 atoms, 196 pseudobonds, 197 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> select clear
> graphics silhouettes true
> select clear
> lighting shadows false
> open
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/50S_new_map_combined_WITH_MOD_09_02.pdb
Summary of feedback from opening
/yonath_group/disha/Gingivalis/Models_and_maps/delta266/50S_new_map_combined_WITH_MOD_09_02.pdb
---
warnings | Start residue of secondary structure not found: HELIX 17 17 PRO V
13 MET V 22 1 10
Start residue of secondary structure not found: HELIX 18 18 VAL V 28 PHE V 37
1 10
Start residue of secondary structure not found: HELIX 19 19 GLU V 41 LYS V 60
5 20
Start residue of secondary structure not found: SHEET 1 M 3 PHE V 3 LEU V 6 0
Start residue of secondary structure not found: SHEET 2 M 3 ASN V 102 TYR V
107 -1 N ILE V 106 O ALA V 4
3 messages similar to the above omitted
Chain information for 50S_new_map_combined_WITH_MOD_09_02.pdb #2
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | 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
h | No description available
> ui tool show Matchmaker
> matchmaker #!2 to #1
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 1nkw, chain A (#1) with 50S_new_map_combined_WITH_MOD_09_02.pdb,
chain D (#2), sequence alignment score = 660.1
RMSD between 101 pruned atom pairs is 1.185 angstroms; (across all 268 pairs:
5.792)
> select #2/F
1636 atoms, 1659 bonds, 209 residues, 1 model selected
> hide #!1 models
> select ~sel
139327 atoms, 148861 bonds, 5986 pseudobonds, 12419 residues, 5 models
selected
> hide sel & #!2 atoms
> show sel & #!2 cartoons
> show sel & #!2 cartoons
> hide sel & #!2 cartoons
> select #2/F
1636 atoms, 1659 bonds, 209 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #2/V
1021 atoms, 1034 bonds, 127 residues, 1 model selected
> show sel cartoons
> select clear
> show #!1 models
> open
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/Final_files_Giardia/MODEL/LSU_real_space_refined-a40_real_space_refined.pdb
Chain information for LSU_real_space_refined-a40_real_space_refined.pdb #3
---
Chain | Description
1 | No description available
3 | No description available
4 | 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
I | No description available
J | 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
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
w | No description available
> hide #!3 models
> select #2
75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 2 models selected
> show sel surfaces
> transparency (#!2 & sel) 80
> ui tool show "Side View"
> select #2/A:482@O2'
1 atom, 1 residue, 1 model selected
> ui tool show Matchmaker
> matchmaker #2/V to #1/Q 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 1nkw, chain Q (#1) with 50S_new_map_combined_WITH_MOD_09_02.pdb,
chain V (#2), sequence alignment score = 6.2
RMSD between 93 pruned atom pairs is 1.123 angstroms; (across all 112 pairs:
3.626)
> select #2
75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 58 models selected
> color (#!2 & sel) light gray
> color (#!2 & sel) dim gray
> transparency (#!2 & sel) 90
> select #2/A:1683@C5'
1 atom, 1 residue, 1 model selected
> select #2/A:2443@O5'
1 atom, 1 residue, 1 model selected
> select clear
> open 6hma
Summary of feedback from opening 6hma fetched from pdb
---
note | Fetching compressed mmCIF 6hma from
http://files.rcsb.org/download/6hma.cif
6hma title:
Improved model derived from cryo-EM map of Staphylococcus aureus large
ribosomal subunit [more info...]
Chain information for 6hma #4
---
Chain | Description
1 | 50S ribosomal protein L33
2 | 50S ribosomal protein L34
3 | 50S ribosomal protein L35
4 | 50S ribosomal protein L36
A | 23S ribosomal RNA
B | 5S ribosomal RNA
C | 50S ribosomal protein L2
D | 50S ribosomal protein L3
E | 50S ribosomal protein L4
F | 50S ribosomal protein L5
G | 50S ribosomal protein L6
H | 50S ribosomal protein L13
I | 50S ribosomal protein L14
J | 50S ribosomal protein L15
K | 50S ribosomal protein L16
L | 50S ribosomal protein L17
M | 50S ribosomal protein L18
N | 50S ribosomal protein L19
O | 50S ribosomal protein L20
P | 50S ribosomal protein L21
Q | 50S ribosomal protein L22
R | 50S ribosomal protein L23
S | 50S ribosomal protein L24
T | 50S ribosomal protein L25
U | 50S ribosomal protein L27
V | 50S ribosomal protein L28
W | 50S ribosomal protein L29
X | 50S ribosomal protein L30
Z | 50S ribosomal protein L32
Non-standard residues in 6hma #4
---
MG — magnesium ion
> ui tool show Matchmaker
> matchmaker #!4 to #1
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 1nkw, chain A (#1) with 6hma, chain C (#4), sequence alignment
score = 745.8
RMSD between 111 pruned atom pairs is 1.258 angstroms; (across all 269 pairs:
6.003)
> hide #!1 models
> hide #!2 models
> select #4/Q
854 atoms, 862 bonds, 112 residues, 1 model selected
> select ~sel
331263 atoms, 355865 bonds, 9147 pseudobonds, 27513 residues, 67 models
selected
> hide sel & #!4 atoms
> select #4/Q
854 atoms, 862 bonds, 112 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #4/E
1572 atoms, 1595 bonds, 206 residues, 1 model selected
> show sel cartoons
> color sel forest green
> select #4
86401 atoms, 94020 bonds, 3066 pseudobonds, 6225 residues, 4 models selected
> color (#!4 & sel) forest green
> select #2
75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 58 models selected
> show #!2 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #4/Q to #3/V 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 LSU_real_space_refined-a40_real_space_refined.pdb, chain V (#3)
with 6hma, chain Q (#4), sequence alignment score = 11.7
RMSD between 6 pruned atom pairs is 1.357 angstroms; (across all 42 pairs:
15.685)
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
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
Manufacturer: ASUS
Model: System Product Name
OS: CentOS Stream 8
Architecture: 64bit ELF
Virutal 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 24Gi 17Gi 1.1Gi 20Gi 36Gi
Swap: 31Gi 1.4Gi 30Gi
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
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.3
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Hi Disha,
--Eric