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Opened 2 years ago
Closed 2 years ago
#10346 closed defect (duplicate)
Opening mmCIF file: MemoryError: not enough memory
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
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 "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J40_005_volume_map.mrc"
Opened cryosparc_P1_J40_005_volume_map.mrc as #1, grid size 360,360,360, pixel
0.84, shown at level 0.0318, step 2, values float32
> surface dust #1 size 8.4
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J39_005_volume_map.mrc"
Opened cryosparc_P1_J39_005_volume_map.mrc as #2, grid size 360,360,360, pixel
0.84, shown at level 0.0311, step 2, values float32
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J38_005_volume_map.mrc"
Opened cryosparc_P1_J38_005_volume_map.mrc as #3, grid size 360,360,360, pixel
0.84, shown at level 0.0325, step 2, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> close session
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 196/cryosparc_P22_J91_006_volume_map.mrc"
Opened cryosparc_P22_J91_006_volume_map.mrc as #1, grid size 320,320,320,
pixel 0.84, shown at level 0.057, step 2, values float32
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 196/cryosparc_P22_J92_005_volume_map.mrc"
Opened cryosparc_P22_J92_005_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.84, shown at level 0.0568, step 2, values float32
> hide #!1 models
> show #!1 models
> hide #!2 models
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 196/cryosparc_P22_J99_map_locres.mrc"
Opened cryosparc_P22_J99_map_locres.mrc as #3, grid size 320,320,320, pixel
0.84, shown at level 6.27, step 2, values float32
> hide #!1 models
> show #!2 models
> hide #!3 models
> ui tool show "Color Zone"
> ui tool show "Surface Color"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> color sample #2.1 map #3 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000
Map values for surface "surface": minimum 2.402, mean 3.482, maximum 42.14
> close session
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 196/cryosparc_P22_J104_005_volume_map.mrc"
Opened cryosparc_P22_J104_005_volume_map.mrc as #1, grid size 320,320,320,
pixel 0.84, shown at level 0.0585, step 2, values float32
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 196/cryosparc_P22_J105_005_volume_map.mrc"
Opened cryosparc_P22_J105_005_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.84, shown at level 0.0551, step 2, values float32
> ui tool show Log
> ui tool show "Model Panel"
> ui tool show Toolbar
> ui tool show "Model Panel"
> ui tool show "Command Line Interface"
> ui tool show "Model Panel"
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.26272,-0.95442,0.14167,206.69,-0.95893,-0.27454,-0.071263,307.1,0.10691,-0.11713,-0.98735,264.62
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map cryosparc_P22_J104_005_volume_map.mrc in map
cryosparc_P22_J105_005_volume_map.mrc using 40929 points
correlation = 0.8032, correlation about mean = 0.384, overlap = 440.3
steps = 252, shift = 8.95, angle = 12.7 degrees
Position of cryosparc_P22_J104_005_volume_map.mrc (#1) relative to
cryosparc_P22_J105_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.45130353 -0.88482438 0.11580560 179.25250085
-0.89224710 -0.44958340 0.04206977 310.35903921
0.01483992 -0.12231344 -0.99238057 285.46061381
Axis -0.85147501 0.52298378 -0.03844836
Axis point 0.00000000 218.33670692 129.84739805
Rotation angle (degrees) 174.46069926
Shift along axis -1.29177527
> hide #!1 models
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 196/cryosparc_P22_J106_004_volume_map.mrc"
Opened cryosparc_P22_J106_004_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.84, shown at level 0.0596, step 2, values float32
> hide #!3 models
> close #3
> show #!1 models
> hide #!1 models
> hide #!2 models
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J62_005_volume_map.mrc"
Opened cryosparc_P1_J62_005_volume_map.mrc as #3, grid size 360,360,360, pixel
0.84, shown at level 0.0322, step 2, values float32
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J62_005_volume_map_sharp.mrc"
Opened cryosparc_P1_J62_005_volume_map_sharp.mrc as #4, grid size 360,360,360,
pixel 0.84, shown at level 0.0504, step 2, values float32
> surface dust #3 size 8.4
> surface dust #4 size 8.4
> hide #!3 models
> hide #!4 models
> show #!3 models
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J63_map_sharp.mrc"
Opened cryosparc_P1_J63_map_sharp.mrc as #5, grid size 360,360,360, pixel
0.84, shown at level 0.000164, step 2, values float32
> surface dust #3 size 8.4
> surface dust #5 size 8.4
> hide #!3 models
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J64_map_sharp.mrc"
Opened cryosparc_P1_J64_map_sharp.mrc as #6, grid size 360,360,360, pixel
0.84, shown at level 0.00121, step 2, values float32
> surface dust #5 size 8.4
> surface dust #6 size 8.4
> hide #!5 models
> hide #!6 models
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J58_005_volume_map.mrc"
Opened cryosparc_P1_J58_005_volume_map.mrc as #7, grid size 360,360,360, pixel
0.84, shown at level 0.0311, step 2, values float32
> hide #!7 models
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J59_005_volume_map.mrc"
Opened cryosparc_P1_J59_005_volume_map.mrc as #8, grid size 360,360,360, pixel
0.84, shown at level 0.0326, step 2, values float32
> hide #!8 models
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 200/cryosparc_P1_J60_005_volume_map.mrc"
Opened cryosparc_P1_J60_005_volume_map.mrc as #9, grid size 360,360,360, pixel
0.84, shown at level 0.033, step 2, values float32
> open 27154 fromDatabase emdb
Summary of feedback from opening 27154 fetched from emdb
---
note | Fetching compressed map 27154 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-27154/map/emd_27154.map.gz
Opened emdb 27154 as #10, grid size 320,320,320, pixel 0.85, shown at level
2.33, step 2, values float32
> hide #!9 models
> surface dust #10 size 8.5
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 196/cryosparc_P22_J91_006_volume_map.mrc"
Opened cryosparc_P22_J91_006_volume_map.mrc as #11, grid size 320,320,320,
pixel 0.84, shown at level 0.057, step 2, values float32
> select add #11
4 models selected
> view matrix models
> #1,-0.2284,-0.93949,-0.25532,324.73,-0.6588,-0.043946,0.75103,129.87,-0.71681,0.33974,-0.6089,266.3,#11,0.69864,0.61542,0.3649,-95.673,-0.17146,0.63917,-0.74971,176.25,-0.69462,0.46121,0.55207,90.081
> transparency #11.1 50
> view matrix models
> #1,0.45596,0.8725,0.1756,-69.825,-0.87477,0.47569,-0.092127,199.36,-0.16391,-0.1116,0.98014,44.091,#11,-0.5459,-0.79171,-0.27421,352.02,-0.82636,0.56278,0.02026,167.04,0.13828,0.23766,-0.96146,220
> hide #!11 models
> lighting soft
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/C# 196/cryosparc_P22_J108_map.mrc"
Opened cryosparc_P22_J108_map.mrc as #12, grid size 320,320,320, pixel 0.84,
shown at level 0.057, step 2, values float32
> select subtract #11
2 models selected
> select add #12
4 models selected
> view matrix models
> #1,0.35032,0.93288,-0.08374,-31.612,-0.89478,0.3069,-0.3243,254.46,-0.27683,0.18854,0.94224,22.37,#12,0.95897,0.14503,-0.24361,17.177,-0.19716,0.9586,-0.20545,58.642,0.20373,0.24505,0.94786,-54.049
> ui tool show "Fit in Map"
> fitmap #11 inMap #12
Fit map cryosparc_P22_J91_006_volume_map.mrc in map cryosparc_P22_J108_map.mrc
using 40901 points
correlation = 0.6163, correlation about mean = 0.1382, overlap = 289.7
steps = 268, shift = 10.1, angle = 26.4 degrees
Position of cryosparc_P22_J91_006_volume_map.mrc (#11) relative to
cryosparc_P22_J108_map.mrc (#12) coordinates:
Matrix rotation and translation
-0.48384433 -0.87094715 -0.08570720 325.08709214
-0.87108462 0.48871280 -0.04869678 190.58454522
0.08429853 0.05109656 -0.99512959 250.08083631
Axis 0.50622826 -0.86239925 -0.00069737
Axis point 211.31708307 0.00000000 134.27427468
Rotation angle (degrees) 174.34342513
Shift along axis 0.03390699
> view matrix models
> #1,-0.055745,0.99725,-0.048845,8.5022,-0.87265,-0.072435,-0.48295,323.76,-0.48516,0.015702,0.87428,82.107,#12,0.83611,0.52765,-0.15003,-31.694,-0.5459,0.7734,-0.32224,145.66,-0.053995,0.35133,0.93469,-32.917
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.055745,0.99725,-0.048845,10.973,-0.87265,-0.072435,-0.48295,324.23,-0.48516,0.015702,0.87428,86.168,#12,0.83611,0.52765,-0.15003,-29.224,-0.5459,0.7734,-0.32224,146.13,-0.053995,0.35133,0.93469,-28.856
> fitmap #10 inMap #12
Fit map emdb 27154 in map cryosparc_P22_J108_map.mrc using 40937 points
correlation = 0.7934, correlation about mean = 0.663, overlap = 1.438e+04
steps = 312, shift = 6.98, angle = 14.2 degrees
Position of emdb 27154 (#10) relative to cryosparc_P22_J108_map.mrc (#12)
coordinates:
Matrix rotation and translation
0.91889112 -0.39439887 0.00941487 62.54787315
0.38506896 0.90183283 0.19600879 -70.20812229
-0.08579629 -0.17648537 0.98055694 31.95725946
Axis -0.42858274 0.10954764 0.89683675
Axis point 208.54473926 109.35918088 0.00000000
Rotation angle (degrees) 25.75762091
Shift along axis -5.83762826
> select clear
> select subtract #12
Nothing selected
> select add #12
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.83611,0.52765,-0.15003,-50.183,-0.5459,0.7734,-0.32224,200.27,-0.053995,0.35133,0.93469,-155.78
> select clear
> open 8D33 fromDatabase pdb
Summary of feedback from opening 8D33 fetched from pdb
---
note | Fetching compressed mmCIF 8d33 from
http://files.rcsb.org/download/8d33.cif
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
models, status = collated_open(session, database_name, ident,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data
return provider_open(self.session, [path], _return_status=True,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
> open "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/PolGamma/8d33.pdb"
8d33.pdb title:
Human mitochondrial DNA polymerase γ ternary complex with GC basepair [more
info...]
Chain information for 8d33.pdb #13
---
Chain | Description | UniProt
A | DNA polymerase subunit γ-1 | DPOG1_HUMAN 1-1239
B C | DNA polymerase subunit γ-2, mitochondrial | DPOG2_HUMAN 1-485
P | DNA (5'-
D(P*ap*ap*ap*ap*CP*GP*ap*CP*GP*GP*CP*CP*ap*GP*TP*GP*CP*CP*ap*TP*ap*C)
-3') |
T | DNA (25-mer) |
Non-standard residues in 8d33.pdb #13
---
CA — calcium ion
DCP — 2'-deoxycytidine-5'-triphosphate
> select add #13
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> select subtract #13
Nothing selected
> select add #10
2 models selected
> transparency #10.1 60
> fitmap #13 inMap #10
Fit molecule 8d33.pdb (#13) to map emdb 27154 (#10) using 15272 atoms
average map value = 6.052, steps = 140
shifted from previous position = 7.56
rotated from previous position = 14.2 degrees
atoms outside contour = 2956, contour level = 2.331
Position of 8d33.pdb (#13) relative to emdb 27154 (#10) coordinates:
Matrix rotation and translation
1.00000000 0.00008016 -0.00004019 -0.00018890
-0.00008016 0.99999999 0.00006525 -0.00065926
0.00004019 -0.00006525 1.00000000 0.00288120
Axis -0.58838773 -0.36237370 -0.72283136
Axis point -16.05731538 15.07237299 0.00000000
Rotation angle (degrees) 0.00635417
Shift along axis -0.00173258
> select add #12
4 models selected
> transparency #10.1#12.1 50
> transparency #10.1#12.1 60
> copy #13
Unknown command: copy #13
> construct #13
Unknown command: construct #13
> combine #13
> select add #14
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 7 models selected
> select subtract #12
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 5 models selected
> select subtract #10
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> view matrix models
> #14,0.98433,0.17265,-0.035848,-5.7545,-0.17625,0.96965,-0.16945,104.23,0.005504,0.17311,0.98489,-156.35
> view matrix models
> #14,0.98433,0.17265,-0.035848,-39.251,-0.17625,0.96965,-0.16945,106.01,0.005504,0.17311,0.98489,-151.54
> fitmap #14 inMap #12
Fit molecule copy of 8d33.pdb (#14) to map cryosparc_P22_J108_map.mrc (#12)
using 15272 atoms
average map value = 0.1238, steps = 84
shifted from previous position = 5.12
rotated from previous position = 0.354 degrees
atoms outside contour = 2962, contour level = 0.056973
Position of copy of 8d33.pdb (#14) relative to cryosparc_P22_J108_map.mrc
(#12) coordinates:
Matrix rotation and translation
0.92096202 -0.38955184 0.00884987 61.72844367
0.38068948 0.90438912 0.19275851 -69.47354846
-0.08309316 -0.17415422 0.98120632 31.17880154
Axis -0.42758315 0.10714616 0.89760367
Axis point 208.41137495 109.75165501 0.00000000
Rotation angle (degrees) 25.40755470
Shift along axis -5.85165981
> hide #!14 models
> hide #!13 models
> transparency #10.1#12.1 0
> volume #12 level 0.07615
> volume #12 step 1
> volume #12 step 2
> volume #12 step 1
> volume #12 step 2
> volume #12 step 4
> volume #12 step 1
> volume #12 level 0.09555
> volume #12 level 0.09001
> transparency #10.1#12.1 50
> lighting soft
> lighting full
> lighting soft
> lighting simple
> show #!14 models
> show #!13 models
> volume #10 level 1.374
> surface dust #10 size 8.5
> surface dust #12 size 8.4
> volume #10 level 1.948
> volume #12 level 0.06921
> hide #!10 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> show #!8 models
> volume #8 step 1
> volume #8 level 0.05348
> show #!10 models
> select add #8
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 5 models selected
> view matrix models
> #8,1,0,0,-14.01,0,1,0,13.292,0,0,1,108.91,#14,0.98336,0.17762,-0.038104,-53.917,-0.18155,0.96823,-0.17194,116.09,0.0063544,0.17599,0.98437,-45.472
> hide #!8 models
> hide #!10 models
> ui tool show AlphaFold
> show #!11 models
> transparency #11.1 0
> lighting soft
> show #!14 models
> hide #!14 models
> show #!12 models
> show #!13 models
> hide #!13 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!11 models
> show #!13 models
> show #!14 models
> hide #!13 models
> hide #!14 models
> select subtract #14
2 models selected
> transparency #12.1 0
> lighting full
> lighting soft
> volume #12 level 0.1205
> show #!14 models
> hide #!14 models
> show #!13 models
> show #!10 models
> hide #!13 models
> show #!14 models
> hide #!10 models
> select add #14
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 5 models selected
> view matrix models
> #8,1,0,0,-19.762,0,1,0,-30.117,0,0,1,-4.3092,#14,0.98336,0.17762,-0.038104,-59.669,-0.18155,0.96823,-0.17194,72.68,0.0063544,0.17599,0.98437,-158.69
> view matrix models
> #8,1,0,0,6.8808,0,1,0,-19.942,0,0,1,-10.998,#14,0.98336,0.17762,-0.038104,-33.026,-0.18155,0.96823,-0.17194,82.855,0.0063544,0.17599,0.98437,-165.38
> view matrix models
> #8,1,0,0,0.34683,0,1,0,-0.79417,0,0,1,-2.6543,#14,0.98336,0.17762,-0.038104,-39.56,-0.18155,0.96823,-0.17194,102,0.0063544,0.17599,0.98437,-157.04
> alphafold match
> MSRLLWRKVAGATVGPGPVPAPGRWVSSSVPASDPSDGQRRRQQQQQQQQQQQQQPQQPQVLSSEGGQLRHNPLDIQMLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAVPLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTRYGPEGEAVPVAIPEERALVFDVEVCLAEGTCPTLAVAISPSAWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTGASSPTQRDWQEQLVVGHNVSFDRAHIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKAKKVKKEPATASKLPIEGAGAPGDPMDQEDLGPCSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRLDDPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRRDNLAKLPTGTTLESAGVVCPYRAIESLYRKHCLEQGKQQLMPQEAGLAEEFLLTDNSAIWQTVEELDYLEVEAEAKMENLRAAVPGQPLALTARGGPKDTQPSYHHGNGPYNDVDIPGCWFFKLPHKDGNSCNVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWYRLSDEGEWLVRELNLPVDRTEGGWISLQDLRKVQRETARKSQWKKWEVVAERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELTKGSLEKRSQPGP
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold E5KNU5 from
https://alphafold.ebi.ac.uk/files/AF-E5KNU5-F1-model_v4.cif
Expected gap or linking atom in ASP /A:34 for SER /A:33
Expected gap or linking atom in ASP /A:34 for PRO /A:35
Expected gap or linking atom in ASP /A:37 for SER /A:36
Expected gap or linking atom in ASP /A:37 for GLY /A:38
Expected gap or linking atom in ASP /A:75 for LEU /A:74
Expected gap or linking atom in ASP /A:75 for ILE /A:76
Expected gap or linking atom in ASP /A:122 for PRO /A:121
Expected gap or linking atom in ASP /A:122 for VAL /A:123
Expected gap or linking atom in ASP /A:133 for GLY /A:132
Expected gap or linking atom in ASP /A:133 for ASN /A:134
Expected gap or linking atom in ASP /A:136 for LEU /A:135
Expected gap or linking atom in ASP /A:136 for GLN /A:137
Expected gap or linking atom in ASP /A:198 for PHE /A:197
Expected gap or linking atom in ASP /A:198 for VAL /A:199
Expected gap or linking atom in ASP /A:243 for ALA /A:242
Expected gap or linking atom in ASP /A:243 for LEU /A:244
Expected gap or linking atom in ASP /A:260 for ARG /A:259
Expected gap or linking atom in ASP /A:260 for TRP /A:261
Expected gap or linking atom in ASP /A:274 for PHE /A:273
Expected gap or linking atom in ASP /A:274 for ARG /A:275
Expected gap or linking atom in ASP /A:293 for LEU /A:292
Expected gap or linking atom in ASP /A:293 for THR /A:294
Expected gap or linking atom in ASP /A:346 for TRP /A:345
Expected gap or linking atom in ASP /A:346 for TRP /A:347
Expected gap or linking atom in ASP /A:349 for LEU /A:348
Expected gap or linking atom in ASP /A:349 for ILE /A:350
Expected gap or linking atom in ASP /A:384 for LYS /A:383
Expected gap or linking atom in ASP /A:384 for ILE /A:385
Expected gap or linking atom in ASP /A:391 for GLN /A:390
Expected gap or linking atom in ASP /A:391 for LEU /A:392
Expected gap or linking atom in ASP /A:399 for GLN /A:398
Expected gap or linking atom in ASP /A:399 for VAL /A:400
Expected gap or linking atom in ASP /A:465 for MET /A:464
Expected gap or linking atom in ASP /A:465 for LEU /A:466
Expected gap or linking atom in ASP /A:469 for ASN /A:468
Expected gap or linking atom in ASP /A:469 for ALA /A:470
Expected gap or linking atom in ASP /A:482 for GLU /A:481
Expected gap or linking atom in ASP /A:482 for PRO /A:483
Expected gap or linking atom in ASP /A:487 for TRP /A:486
Expected gap or linking atom in ASP /A:487 for LEU /A:488
Expected gap or linking atom in ASP /A:491 for TRP /A:490
Expected gap or linking atom in ASP /A:491 for LEU /A:492
Expected gap or linking atom in ASP /A:523 for GLY /A:522
Expected gap or linking atom in ASP /A:523 for PRO /A:524
Expected gap or linking atom in ASP /A:526 for MET /A:525
Expected gap or linking atom in ASP /A:526 for GLN /A:527
Expected gap or linking atom in ASP /A:529 for GLU /A:528
Expected gap or linking atom in ASP /A:529 for LEU /A:530
Expected gap or linking atom in ASP /A:542 for GLN /A:541
Expected gap or linking atom in ASP /A:542 for VAL /A:543
Expected gap or linking atom in ASP /A:581 for LEU /A:580
Expected gap or linking atoms for ASP /A:581 and ASP /A:582
Expected gap or linking atom in ASP /A:582 for PRO /A:583
Expected gap or linking atom in ASP /A:608 for TRP /A:607
Expected gap or linking atom in ASP /A:608 for GLY /A:609
Expected gap or linking atom in ASP /A:629 for ARG /A:628
Expected gap or linking atom in ASP /A:629 for ASN /A:630
Expected gap or linking atom in ASP /A:683 for THR /A:682
Expected gap or linking atom in ASP /A:683 for ASN /A:684
Expected gap or linking atom in ASP /A:695 for LEU /A:694
Expected gap or linking atom in ASP /A:695 for TYR /A:696
Expected gap or linking atom in ASP /A:727 for LYS /A:726
Expected gap or linking atom in ASP /A:727 for THR /A:728
Expected gap or linking atom in ASP /A:741 for ASN /A:740
Expected gap or linking atom in ASP /A:741 for VAL /A:742
Expected gap or linking atom in ASP /A:743 for VAL /A:742
Expected gap or linking atom in ASP /A:743 for ILE /A:744
Expected gap or linking atom in ASP /A:756 for LYS /A:755
Expected gap or linking atom in ASP /A:756 for GLY /A:757
Expected gap or linking atom in ASP /A:769 for LYS /A:768
Expected gap or linking atom in ASP /A:769 for PHE /A:770
Expected gap or linking atom in ASP /A:776 for GLU /A:775
Expected gap or linking atom in ASP /A:776 for GLY /A:777
Expected gap or linking atom in ASP /A:830 for PRO /A:829
Expected gap or linking atom in ASP /A:830 for TYR /A:831
Expected gap or linking atom in ASP /A:832 for TYR /A:831
Expected gap or linking atom in ASP /A:832 for GLU /A:833
Expected gap or linking atom in ASP /A:868 for PRO /A:867
Expected gap or linking atom in ASP /A:868 for ARG /A:869
Expected gap or linking atom in ASP /A:890 for ALA /A:889
Expected gap or linking atom in ASP /A:890 for VAL /A:891
Expected gap or linking atom in ASP /A:892 for VAL /A:891
Expected gap or linking atom in ASP /A:892 for SER /A:893
Expected gap or linking atom in ASP /A:904 for GLY /A:903
Expected gap or linking atom in ASP /A:904 for ALA /A:905
Expected gap or linking atom in ASP /A:930 for THR /A:929
Expected gap or linking atom in ASP /A:930 for LEU /A:931
Expected gap or linking atom in ASP /A:999 for SER /A:998
Expected gap or linking atom in ASP /A:999 for GLU /A:1000
Expected gap or linking atom in ASP /A:1013 for VAL /A:1012
Expected gap or linking atom in ASP /A:1013 for ARG /A:1014
Expected gap or linking atom in ASP /A:1024 for GLN /A:1023
Expected gap or linking atom in ASP /A:1024 for LEU /A:1025
Expected gap or linking atom in ASP /A:1068 for SER /A:1067
Expected gap or linking atom in ASP /A:1068 for ILE /A:1069
Expected gap or linking atom in ASP /A:1107 for VAL /A:1106
Expected gap or linking atom in ASP /A:1107 for TYR /A:1108
Expected gap or linking atom in ASP /A:1126 for ILE /A:1125
Expected gap or linking atom in ASP /A:1126 for GLY /A:1127
Expected gap or linking atom in ASP /A:1135 for HIS /A:1134
Expected gap or linking atom in ASP /A:1135 for GLU /A:1136
Expected gap or linking atom in ASP /A:1145 for GLU /A:1144
Expected gap or linking atom in ASP /A:1145 for ARG /A:1146
Expected gap or linking atom in ASP /A:1172 for ASN /A:1171
Expected gap or linking atom in ASP /A:1172 for LEU /A:1173
Expected gap or linking atom in ASP /A:1184 for VAL /A:1183
Expected gap or linking atom in ASP /A:1184 for ILE /A:1185
Expected gap or linking atom in ASP /A:1186 for ILE /A:1185
Expected gap or linking atom in ASP /A:1186 for ARG /A:1187
Expected gap or linking atom in ASP /A:1196 for MET /A:1195
Expected gap or linking atom in ASP /A:1196 for CYS /A:1197
Expected gap or linking atom in ASP /A:1219 for LEU /A:1218
Expected gap or linking atom in ASP /A:1219 for ILE /A:1220
1 AlphaFold model found using sequence similarity searches: E5KNU5 (1
sequences)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
E5KNU5_HUMAN | MSRLL...SQPGP | 100.0 | 100.0
Opened 1 AlphaFold model
> combine #13
> hide #!12 models
> hide #!14 models
> select subtract #14
2 models selected
> select add #15
9824 atoms, 10080 bonds, 1239 residues, 3 models selected
> select subtract #15
2 models selected
> select add #16
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 5 models selected
> select subtract #16
2 models selected
> select add #16
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 5 models selected
> select #16/T
494 atoms, 552 bonds, 24 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> select #16/P
451 atoms, 507 bonds, 22 residues, 1 model selected
> hide sel cartoons
> select #16/B
3307 atoms, 3386 bonds, 2 pseudobonds, 411 residues, 2 models selected
> hide sel cartoons
> select #16/C
3213 atoms, 3290 bonds, 2 pseudobonds, 399 residues, 2 models selected
> hide sel cartoons
> select add #16
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> view matrix models
> #16,0.98433,0.17265,-0.035848,-103.56,-0.17625,0.96965,-0.16945,-60.683,0.005504,0.17311,0.98489,-172.6
> select clear
> ui tool show "Fit in Map"
> select add #13
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> select subtract #13
Nothing selected
> select add #16
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> view matrix models
> #16,0.98433,0.17265,-0.035848,-86.159,-0.17625,0.96965,-0.16945,-43.476,0.005504,0.17311,0.98489,-172.68
> view matrix models
> #16,-0.77133,0.54417,-0.33005,136.56,-0.28673,0.16585,0.94355,-66.529,0.56819,0.82242,0.028104,-209.63
> view matrix models
> #16,-0.77133,0.54417,-0.33005,80.743,-0.28673,0.16585,0.94355,-113.75,0.56819,0.82242,0.028104,-186.05
> view matrix models
> #16,-0.77133,0.54417,-0.33005,68.373,-0.28673,0.16585,0.94355,-89.53,0.56819,0.82242,0.028104,-193.06
> ui tool show Matchmaker
> matchmaker #15 to #16
| 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 copy of 8d33.pdb, chain A (#16) with AlphaFold E5KNU5_HUMAN, chain
A (#15), sequence alignment score = 5920.9
RMSD between 655 pruned atom pairs is 0.842 angstroms; (across all 974 pairs:
6.019)
> select clear
> combine #15
> select add #17
9824 atoms, 10080 bonds, 1239 residues, 1 model selected
> view matrix models
> #17,0.93054,-0.36483,-0.031397,7.2495,0.35704,0.92302,-0.1434,77.259,0.081296,0.12223,0.98917,120.01
> select clear
[Repeated 1 time(s)]
> select add #17
9824 atoms, 10080 bonds, 1239 residues, 1 model selected
> view matrix models
> #17,0.93054,-0.36483,-0.031397,2.9799,0.35704,0.92302,-0.1434,128,0.081296,0.12223,0.98917,168.15
> select clear
> color #15 #ff557fff
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
> ui tool show "Blast Protein"
> ui tool show "Show Sequence Viewer"
> sequence chain #13/A #14/A #16/A
Alignment identifier is 1
> sequence chain #15/A #17/A
Alignment identifier is 2
> ui tool show "Show Sequence Viewer"
> sequence chain #17/A
Alignment identifier is 17/A
> sequence chain #13/A
Alignment identifier is 13/A
Drag select of 2213 residues, 6 pseudobonds
> ui tool show "Show Sequence Viewer"
Alignment identifier is 15/A
Alignment identifier is 16/A
> ui tool show "Modeller Comparative"
> modeller comparative 15/A:1 16/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> select clear
> ui tool show AlphaFold
> color #15 #fffcefff
> color #15 #fff9faff
> color #15 #a39fa0ff
> color #15 #aba7a8ff
> color #15 #bab6b6ff
> color #15 #cbc6c7ff
> hide #!16 models
> show #!16 models
> color #16 #ff007fff
Drag select of 2213 residues, 6 pseudobonds
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 45729 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> undo
> select clear
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain #16/A
Alignment identifier is 16/A
> sequence chain #15/A
Alignment identifier is 15/A
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
> ui tool show Matchmaker
> matchmaker #!16 to #15
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 AlphaFold E5KNU5_HUMAN, chain A (#15) with copy of 8d33.pdb, chain
A (#16), sequence alignment score = 5920.9
RMSD between 655 pruned atom pairs is 0.842 angstroms; (across all 974 pairs:
6.019)
> ui tool show "Show Sequence Viewer"
> ui tool show Matchmaker
> matchmaker #!16 to #15 showAlignment true
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 AlphaFold E5KNU5_HUMAN, chain A (#15) with copy of 8d33.pdb, chain
A (#16), sequence alignment score = 5920.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: AlphaFold E5KNU5_HUMAN #15/A,
copy of 8d33.pdb #16/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 655 pruned atom pairs is 0.842 angstroms; (across all 974 pairs:
6.019)
> select #15/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/A:1-44
330 atoms, 339 bonds, 44 residues, 1 model selected
> select #15/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #15/A:1-44
330 atoms, 339 bonds, 44 residues, 1 model selected
> select
> #15/A:70-74,76-88,90,95-96,98-100,102-103,106,114-115,117,119-162,164-179,183-217,219-232,234-248,262-316,345-365,367-371,375-457,594,620,736-737,751-752,762,764-766,784-785,789-790,792-922,948,950-952,989,992-993,1049-1133,1135-1234
> #16/A:70-74,76-88,90,95-96,98-100,102-103,106,114-115,117,119-162,164-179,183-217,219-232,234-248,262-316,345-365,367-371,375-457,594,620,736-737,751-752,762,764-766,784-785,789-790,792-922,948,950-952,989,992-993,1049-1133,1135-1234
10456 atoms, 10663 bonds, 1310 residues, 2 models selected
> select #15/A:68
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:1-68
523 atoms, 534 bonds, 68 residues, 1 model selected
> color sel red
> select clear
> color #16 blue
Drag select of 2213 residues, 6 pseudobonds
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 45729 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select #16/T
494 atoms, 552 bonds, 24 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #16/P
451 atoms, 507 bonds, 22 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #16/B
3307 atoms, 3386 bonds, 2 pseudobonds, 411 residues, 2 models selected
> delete atoms (#!16 & sel)
> delete bonds (#!16 & sel)
> select #16/C
3213 atoms, 3290 bonds, 2 pseudobonds, 399 residues, 2 models selected
> delete atoms (#!16 & sel)
> delete bonds (#!16 & sel)
> select #15/A:252
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #15/A:252-259
55 atoms, 55 bonds, 8 residues, 1 model selected
> color sel red
> select #15/A:317
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:317-341
196 atoms, 199 bonds, 25 residues, 1 model selected
> color sel red
> select #15/A:500-501
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #15/A:500-529
214 atoms, 217 bonds, 30 residues, 1 model selected
> color sel red
> select clear
> select #15/A:632
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #15/A:632-644
86 atoms, 86 bonds, 13 residues, 1 model selected
> color sel red
> select #15/A:664
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #15/A:664-700
297 atoms, 301 bonds, 37 residues, 1 model selected
> color sel red
> select #15/A:632
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #15/A:632-644
86 atoms, 86 bonds, 13 residues, 1 model selected
> color sel red
> ui tool show "Color Actions"
> select #15/A:701-702
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #15/A:701-729
208 atoms, 210 bonds, 29 residues, 1 model selected
> color sel red
> select clear
> select #15/A:998
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #15/A:998-1048
429 atoms, 437 bonds, 51 residues, 1 model selected
> color sel red
> select #15/A:1236-1237
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #15/A:1236-1239
28 atoms, 29 bonds, 4 residues, 1 model selected
> color sel red
> select #15/A:500
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #15/A:500-529
214 atoms, 217 bonds, 30 residues, 1 model selected
> select clear
> hide #!16 models
> show #!16 models
> hide #!16 models
> save "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/PolGamma/Alpha fold structure of PolG_A_in red missing fragments
> from pdb_8d33.bmp" width 1313 height 911 supersample 3
> save "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/PolGamma/Alpha fold structure of PolG_A.bmp" width 1313 height
> 911 supersample 3
> show #!16 models
> view orient
> hide #!16 models
> show #!16 models
> save "C:/Users/Ania/OneDrive - University of Gdansk/Ania/Cryo data
> processing/PolGamma/Alpha fold structure of PolG_A_in red missing fragments
> from pdb_8d33_blue.bmp" width 1313 height 911 supersample 3
> color #15::c_alpha_distance<3.0 lime
> show #15::c_alpha_distance<3.0 atoms,ribbons
[Repeated 1 time(s)]
> color #15::c_alpha_distance<3.0 lime
[Repeated 1 time(s)]
> show #15::c_alpha_distance<3.0 atoms,ribbons
> show #15::c_alpha_distance<2.0 atoms,ribbons
> alphafold match #16
Fetching compressed AlphaFold P54098 from
https://alphafold.ebi.ac.uk/files/AF-P54098-F1-model_v4.cif
Expected gap or linking atom in ASP /A:34 for SER /A:33
Expected gap or linking atom in ASP /A:34 for PRO /A:35
Expected gap or linking atom in ASP /A:37 for SER /A:36
Expected gap or linking atom in ASP /A:37 for GLY /A:38
Expected gap or linking atom in ASP /A:75 for LEU /A:74
Expected gap or linking atom in ASP /A:75 for ILE /A:76
Expected gap or linking atom in ASP /A:122 for PRO /A:121
Expected gap or linking atom in ASP /A:122 for VAL /A:123
Expected gap or linking atom in ASP /A:133 for GLY /A:132
Expected gap or linking atom in ASP /A:133 for ASN /A:134
Expected gap or linking atom in ASP /A:136 for LEU /A:135
Expected gap or linking atom in ASP /A:136 for GLN /A:137
Expected gap or linking atom in ASP /A:198 for PHE /A:197
Expected gap or linking atom in ASP /A:198 for VAL /A:199
Expected gap or linking atom in ASP /A:243 for ALA /A:242
Expected gap or linking atom in ASP /A:243 for LEU /A:244
Expected gap or linking atom in ASP /A:260 for ARG /A:259
Expected gap or linking atom in ASP /A:260 for TRP /A:261
Expected gap or linking atom in ASP /A:274 for PHE /A:273
Expected gap or linking atom in ASP /A:274 for ARG /A:275
Expected gap or linking atom in ASP /A:293 for LEU /A:292
Expected gap or linking atom in ASP /A:293 for THR /A:294
Expected gap or linking atom in ASP /A:346 for TRP /A:345
Expected gap or linking atom in ASP /A:346 for TRP /A:347
Expected gap or linking atom in ASP /A:349 for LEU /A:348
Expected gap or linking atom in ASP /A:349 for ILE /A:350
Expected gap or linking atom in ASP /A:384 for LYS /A:383
Expected gap or linking atom in ASP /A:384 for ILE /A:385
Expected gap or linking atom in ASP /A:391 for GLN /A:390
Expected gap or linking atom in ASP /A:391 for LEU /A:392
Expected gap or linking atom in ASP /A:399 for GLN /A:398
Expected gap or linking atom in ASP /A:399 for VAL /A:400
Expected gap or linking atom in ASP /A:465 for MET /A:464
Expected gap or linking atom in ASP /A:465 for LEU /A:466
Expected gap or linking atom in ASP /A:469 for ASN /A:468
Expected gap or linking atom in ASP /A:469 for ALA /A:470
Expected gap or linking atom in ASP /A:482 for GLU /A:481
Expected gap or linking atom in ASP /A:482 for PRO /A:483
Expected gap or linking atom in ASP /A:487 for TRP /A:486
Expected gap or linking atom in ASP /A:487 for LEU /A:488
Expected gap or linking atom in ASP /A:491 for TRP /A:490
Expected gap or linking atom in ASP /A:491 for LEU /A:492
Expected gap or linking atom in ASP /A:523 for GLY /A:522
Expected gap or linking atom in ASP /A:523 for PRO /A:524
Expected gap or linking atom in ASP /A:526 for MET /A:525
Expected gap or linking atom in ASP /A:526 for GLN /A:527
Expected gap or linking atom in ASP /A:529 for GLU /A:528
Expected gap or linking atom in ASP /A:529 for LEU /A:530
Expected gap or linking atom in ASP /A:542 for GLN /A:541
Expected gap or linking atom in ASP /A:542 for VAL /A:543
Expected gap or linking atom in ASP /A:581 for LEU /A:580
Expected gap or linking atoms for ASP /A:581 and ASP /A:582
Expected gap or linking atom in ASP /A:582 for PRO /A:583
Expected gap or linking atom in ASP /A:608 for TRP /A:607
Expected gap or linking atom in ASP /A:608 for GLY /A:609
Expected gap or linking atom in ASP /A:629 for ARG /A:628
Expected gap or linking atom in ASP /A:629 for ASN /A:630
Expected gap or linking atom in ASP /A:683 for THR /A:682
Expected gap or linking atom in ASP /A:683 for ASN /A:684
Expected gap or linking atom in ASP /A:695 for LEU /A:694
Expected gap or linking atom in ASP /A:695 for TYR /A:696
Expected gap or linking atom in ASP /A:727 for LYS /A:726
Expected gap or linking atom in ASP /A:727 for THR /A:728
Expected gap or linking atom in ASP /A:741 for ASN /A:740
Expected gap or linking atom in ASP /A:741 for VAL /A:742
Expected gap or linking atom in ASP /A:743 for VAL /A:742
Expected gap or linking atom in ASP /A:743 for ILE /A:744
Expected gap or linking atom in ASP /A:756 for LYS /A:755
Expected gap or linking atom in ASP /A:756 for GLY /A:757
Expected gap or linking atom in ASP /A:769 for LYS /A:768
Expected gap or linking atom in ASP /A:769 for PHE /A:770
Expected gap or linking atom in ASP /A:776 for GLU /A:775
Expected gap or linking atom in ASP /A:776 for GLY /A:777
Expected gap or linking atom in ASP /A:830 for PRO /A:829
Expected gap or linking atom in ASP /A:830 for TYR /A:831
Expected gap or linking atom in ASP /A:832 for TYR /A:831
Expected gap or linking atom in ASP /A:832 for GLU /A:833
Expected gap or linking atom in ASP /A:868 for PRO /A:867
Expected gap or linking atom in ASP /A:868 for ARG /A:869
Expected gap or linking atom in ASP /A:890 for ALA /A:889
Expected gap or linking atom in ASP /A:890 for VAL /A:891
Expected gap or linking atom in ASP /A:892 for VAL /A:891
Expected gap or linking atom in ASP /A:892 for SER /A:893
Expected gap or linking atom in ASP /A:904 for GLY /A:903
Expected gap or linking atom in ASP /A:904 for ALA /A:905
Expected gap or linking atom in ASP /A:930 for THR /A:929
Expected gap or linking atom in ASP /A:930 for LEU /A:931
Expected gap or linking atom in ASP /A:999 for SER /A:998
Expected gap or linking atom in ASP /A:999 for GLU /A:1000
Expected gap or linking atom in ASP /A:1013 for VAL /A:1012
Expected gap or linking atom in ASP /A:1013 for ARG /A:1014
Expected gap or linking atom in ASP /A:1024 for GLN /A:1023
Expected gap or linking atom in ASP /A:1024 for LEU /A:1025
Expected gap or linking atom in ASP /A:1068 for SER /A:1067
Expected gap or linking atom in ASP /A:1068 for ILE /A:1069
Expected gap or linking atom in ASP /A:1107 for VAL /A:1106
Expected gap or linking atom in ASP /A:1107 for TYR /A:1108
Expected gap or linking atom in ASP /A:1126 for ILE /A:1125
Expected gap or linking atom in ASP /A:1126 for GLY /A:1127
Expected gap or linking atom in ASP /A:1135 for HIS /A:1134
Expected gap or linking atom in ASP /A:1135 for GLU /A:1136
Expected gap or linking atom in ASP /A:1145 for GLU /A:1144
Expected gap or linking atom in ASP /A:1145 for ARG /A:1146
Expected gap or linking atom in ASP /A:1172 for ASN /A:1171
Expected gap or linking atom in ASP /A:1172 for LEU /A:1173
Expected gap or linking atom in ASP /A:1184 for VAL /A:1183
Expected gap or linking atom in ASP /A:1184 for ILE /A:1185
Expected gap or linking atom in ASP /A:1186 for ILE /A:1185
Expected gap or linking atom in ASP /A:1186 for ARG /A:1187
Expected gap or linking atom in ASP /A:1196 for MET /A:1195
Expected gap or linking atom in ASP /A:1196 for CYS /A:1197
Expected gap or linking atom in ASP /A:1219 for LEU /A:1218
Expected gap or linking atom in ASP /A:1219 for ILE /A:1220
1 AlphaFold model found using UniProt identifier: P54098 (chain A)
AlphaFold prediction matching copy of 8d33.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | P54098 | DPOG1_HUMAN | 7.57 | 1239 | 974 | 100
Associated AlphaFold DPOG1_HUMAN chain A (18.1) chain A to AlphaFold
E5KNU5_HUMAN, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: AlphaFold E5KNU5_HUMAN #15/A,
copy of 8d33.pdb #16/A, AlphaFold DPOG1_HUMAN chain A #18.1/A
Opened 1 AlphaFold model
> hide #!18 models
> show #!18 models
> hide #17 models
> hide #15 models
> hide #18.1 models
> show #18.1 models
> show #18.1::c_alpha_distance<2.0 atoms,ribbons
> hide #18.1::c_alpha_distance<2.0 atoms,ribbons
> color #18.1::c_alpha_distance<2.0 lime
> color #18.1::c_alpha_distance>=3.0 lime
> close #18
Chains used in RMSD evaluation for alignment 1: AlphaFold E5KNU5_HUMAN #15/A,
copy of 8d33.pdb #16/A
> show #15 models
> hide #!16 models
> show #!16 models
> color #15::c_alpha_distance>=3.0 lime
[Repeated 1 time(s)]
> color #15::c_alpha_distance>=2.0 lime
> color #16::c_alpha_distance>=2.0 lime
> undo
> color #15::c_alpha_distance>=3.0 lime
> color #15::missing_structure=true yellow
> color #15::missing_structure=true lime
[Repeated 3 time(s)]
> hide #15 models
> show #15 models
> color #15::c_alpha_distance>=3.0 lime
[Repeated 5 time(s)]
> alphafold match #15
Expected gap or linking atom in ASP /A:34 for SER /A:33
Expected gap or linking atom in ASP /A:34 for PRO /A:35
Expected gap or linking atom in ASP /A:37 for SER /A:36
Expected gap or linking atom in ASP /A:37 for GLY /A:38
Expected gap or linking atom in ASP /A:75 for LEU /A:74
Expected gap or linking atom in ASP /A:75 for ILE /A:76
Expected gap or linking atom in ASP /A:122 for PRO /A:121
Expected gap or linking atom in ASP /A:122 for VAL /A:123
Expected gap or linking atom in ASP /A:133 for GLY /A:132
Expected gap or linking atom in ASP /A:133 for ASN /A:134
Expected gap or linking atom in ASP /A:136 for LEU /A:135
Expected gap or linking atom in ASP /A:136 for GLN /A:137
Expected gap or linking atom in ASP /A:198 for PHE /A:197
Expected gap or linking atom in ASP /A:198 for VAL /A:199
Expected gap or linking atom in ASP /A:243 for ALA /A:242
Expected gap or linking atom in ASP /A:243 for LEU /A:244
Expected gap or linking atom in ASP /A:260 for ARG /A:259
Expected gap or linking atom in ASP /A:260 for TRP /A:261
Expected gap or linking atom in ASP /A:274 for PHE /A:273
Expected gap or linking atom in ASP /A:274 for ARG /A:275
Expected gap or linking atom in ASP /A:293 for LEU /A:292
Expected gap or linking atom in ASP /A:293 for THR /A:294
Expected gap or linking atom in ASP /A:346 for TRP /A:345
Expected gap or linking atom in ASP /A:346 for TRP /A:347
Expected gap or linking atom in ASP /A:349 for LEU /A:348
Expected gap or linking atom in ASP /A:349 for ILE /A:350
Expected gap or linking atom in ASP /A:384 for LYS /A:383
Expected gap or linking atom in ASP /A:384 for ILE /A:385
Expected gap or linking atom in ASP /A:391 for GLN /A:390
Expected gap or linking atom in ASP /A:391 for LEU /A:392
Expected gap or linking atom in ASP /A:399 for GLN /A:398
Expected gap or linking atom in ASP /A:399 for VAL /A:400
Expected gap or linking atom in ASP /A:465 for MET /A:464
Expected gap or linking atom in ASP /A:465 for LEU /A:466
Expected gap or linking atom in ASP /A:469 for ASN /A:468
Expected gap or linking atom in ASP /A:469 for ALA /A:470
Expected gap or linking atom in ASP /A:482 for GLU /A:481
Expected gap or linking atom in ASP /A:482 for PRO /A:483
Expected gap or linking atom in ASP /A:487 for TRP /A:486
Expected gap or linking atom in ASP /A:487 for LEU /A:488
Expected gap or linking atom in ASP /A:491 for TRP /A:490
Expected gap or linking atom in ASP /A:491 for LEU /A:492
Expected gap or linking atom in ASP /A:523 for GLY /A:522
Expected gap or linking atom in ASP /A:523 for PRO /A:524
Expected gap or linking atom in ASP /A:526 for MET /A:525
Expected gap or linking atom in ASP /A:526 for GLN /A:527
Expected gap or linking atom in ASP /A:529 for GLU /A:528
Expected gap or linking atom in ASP /A:529 for LEU /A:530
Expected gap or linking atom in ASP /A:542 for GLN /A:541
Expected gap or linking atom in ASP /A:542 for VAL /A:543
Expected gap or linking atom in ASP /A:581 for LEU /A:580
Expected gap or linking atoms for ASP /A:581 and ASP /A:582
Expected gap or linking atom in ASP /A:582 for PRO /A:583
Expected gap or linking atom in ASP /A:608 for TRP /A:607
Expected gap or linking atom in ASP /A:608 for GLY /A:609
Expected gap or linking atom in ASP /A:629 for ARG /A:628
Expected gap or linking atom in ASP /A:629 for ASN /A:630
Expected gap or linking atom in ASP /A:683 for THR /A:682
Expected gap or linking atom in ASP /A:683 for ASN /A:684
Expected gap or linking atom in ASP /A:695 for LEU /A:694
Expected gap or linking atom in ASP /A:695 for TYR /A:696
Expected gap or linking atom in ASP /A:727 for LYS /A:726
Expected gap or linking atom in ASP /A:727 for THR /A:728
Expected gap or linking atom in ASP /A:741 for ASN /A:740
Expected gap or linking atom in ASP /A:741 for VAL /A:742
Expected gap or linking atom in ASP /A:743 for VAL /A:742
Expected gap or linking atom in ASP /A:743 for ILE /A:744
Expected gap or linking atom in ASP /A:756 for LYS /A:755
Expected gap or linking atom in ASP /A:756 for GLY /A:757
Expected gap or linking atom in ASP /A:769 for LYS /A:768
Expected gap or linking atom in ASP /A:769 for PHE /A:770
Expected gap or linking atom in ASP /A:776 for GLU /A:775
Expected gap or linking atom in ASP /A:776 for GLY /A:777
Expected gap or linking atom in ASP /A:830 for PRO /A:829
Expected gap or linking atom in ASP /A:830 for TYR /A:831
Expected gap or linking atom in ASP /A:832 for TYR /A:831
Expected gap or linking atom in ASP /A:832 for GLU /A:833
Expected gap or linking atom in ASP /A:868 for PRO /A:867
Expected gap or linking atom in ASP /A:868 for ARG /A:869
Expected gap or linking atom in ASP /A:890 for ALA /A:889
Expected gap or linking atom in ASP /A:890 for VAL /A:891
Expected gap or linking atom in ASP /A:892 for VAL /A:891
Expected gap or linking atom in ASP /A:892 for SER /A:893
Expected gap or linking atom in ASP /A:904 for GLY /A:903
Expected gap or linking atom in ASP /A:904 for ALA /A:905
Expected gap or linking atom in ASP /A:930 for THR /A:929
Expected gap or linking atom in ASP /A:930 for LEU /A:931
Expected gap or linking atom in ASP /A:999 for SER /A:998
Expected gap or linking atom in ASP /A:999 for GLU /A:1000
Expected gap or linking atom in ASP /A:1013 for VAL /A:1012
Expected gap or linking atom in ASP /A:1013 for ARG /A:1014
Expected gap or linking atom in ASP /A:1024 for GLN /A:1023
Expected gap or linking atom in ASP /A:1024 for LEU /A:1025
Expected gap or linking atom in ASP /A:1068 for SER /A:1067
Expected gap or linking atom in ASP /A:1068 for ILE /A:1069
Expected gap or linking atom in ASP /A:1107 for VAL /A:1106
Expected gap or linking atom in ASP /A:1107 for TYR /A:1108
Expected gap or linking atom in ASP /A:1126 for ILE /A:1125
Expected gap or linking atom in ASP /A:1126 for GLY /A:1127
Expected gap or linking atom in ASP /A:1135 for HIS /A:1134
Expected gap or linking atom in ASP /A:1135 for GLU /A:1136
Expected gap or linking atom in ASP /A:1145 for GLU /A:1144
Expected gap or linking atom in ASP /A:1145 for ARG /A:1146
Expected gap or linking atom in ASP /A:1172 for ASN /A:1171
Expected gap or linking atom in ASP /A:1172 for LEU /A:1173
Expected gap or linking atom in ASP /A:1184 for VAL /A:1183
Expected gap or linking atom in ASP /A:1184 for ILE /A:1185
Expected gap or linking atom in ASP /A:1186 for ILE /A:1185
Expected gap or linking atom in ASP /A:1186 for ARG /A:1187
Expected gap or linking atom in ASP /A:1196 for MET /A:1195
Expected gap or linking atom in ASP /A:1196 for CYS /A:1197
Expected gap or linking atom in ASP /A:1219 for LEU /A:1218
Expected gap or linking atom in ASP /A:1219 for ILE /A:1220
1 AlphaFold model found using UniProt identifier: E5KNU5 (chain A)
AlphaFold prediction matching AlphaFold E5KNU5_HUMAN
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | E5KNU5 | E5KNU5_HUMAN | 0.00 | 1239 | 1239 | 100
Associated AlphaFold E5KNU5_HUMAN chain A (18.1) chain A to AlphaFold
E5KNU5_HUMAN, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: AlphaFold E5KNU5_HUMAN #15/A,
copy of 8d33.pdb #16/A, AlphaFold E5KNU5_HUMAN chain A #18.1/A
Opened 1 AlphaFold model
> hide #15 models
> color #15::c_alpha_distance>=3.0 lime
> color #18.1::c_alpha_distance>=3.0 lime
[Repeated 1 time(s)]
> hide #!16 models
> show #!16 models
> show #18.1::c_alpha_distance>=3.0 atoms,ribbons
> color #18.1::c_alpha_distance>=3.0 lime
[Repeated 1 time(s)]
> ui tool show "Command Line Interface"
> show #15 models
> hide #!18 models
> show #!18 models
> hide #18.1 models
> show #18.1 models
> close #18
Chains used in RMSD evaluation for alignment 1: AlphaFold E5KNU5_HUMAN #15/A,
copy of 8d33.pdb #16/A
> color #15::c_alpha_distance>=3.0 magenta
> color #15::c_alpha_distance>=5.0 magenta
[Repeated 1 time(s)]
> color #15::c_alpha_distance>=2.0 magenta
[Repeated 1 time(s)]
> color #16::c_alpha_distance>=2.0 magenta
> color #16::c_alpha_distance>=3.0 magenta
[Repeated 1 time(s)]
> color #16::c_alpha_distance>=5.0 yellow
> undo
[Repeated 3 time(s)]
> color #16::c_alpha_distance>=3.0 lime
> undo
> hide #!16 models
> hide #15 models
> show #15 models
> select #15::c_alpha_distance>=3.0
Nothing selected
> show #15::c_alpha_distance>=3.0 atoms,ribbons
> show #17 models
> show #17::c_alpha_distance>=3.0 atoms,ribbons
> color #17::c_alpha_distance>=3.0 lime
> show #15::c_alpha_distance>=3.0 atoms,ribbons
> select #15::c_alpha_distance>=3.0
Nothing selected
> show #!16 models
> hide #!16 models
> hide #17 models
> show #!12 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!12 models
> select add #15
9824 atoms, 10080 bonds, 1239 residues, 1 model selected
> view matrix models
> #15,0.93054,-0.36483,-0.031397,-12.809,0.35704,0.92302,-0.1434,172.62,0.081296,0.12223,0.98917,-20.902
> view matrix models
> #15,0.93054,-0.36483,-0.031397,-14.194,0.35704,0.92302,-0.1434,201.77,0.081296,0.12223,0.98917,-76.379
> ui tool show Matchmaker
> matchmaker #15 to #14 showAlignment true
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 copy of 8d33.pdb, chain A (#14) with AlphaFold E5KNU5_HUMAN, chain
A (#15), sequence alignment score = 5920.9
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: copy of 8d33.pdb #14/A,
AlphaFold E5KNU5_HUMAN #15/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 655 pruned atom pairs is 0.842 angstroms; (across all 974 pairs:
6.019)
> show #!12 models
> select clear
> volume #12 level 0.0803
> hide #!14 models
> transparency #12.1 50
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #15 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> open 27155 from embd
No such database 'embd'
> open 27155 fromDatabase emdb
Summary of feedback from opening 27155 fetched from emdb
---
note | Fetching compressed map 27155 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-27155/map/emd_27155.map.gz
Opened emdb 27155 as #18, grid size 320,320,320, pixel 0.85, shown at level
2.28, step 2, values float32
> close #1-9
> surface dust #12 size 8.4
> surface dust #18 size 8.5
> select add #18
2 models selected
> view matrix models #18,1,0,0,11.577,0,1,0,-4.5443,0,0,1,-9.4709
> view matrix models
> #18,-0.38759,0.92142,0.027633,68.775,0.74716,0.29645,0.59487,-87.52,0.53993,0.25121,-0.80335,121.67
> hide #!18 models
> volume #12 step 2
> volume #12 step 1
> volume #12 level 0.04842
> volume gaussian #12 sDev 2
Opened cryosparc_P22_J108_map.mrc gaussian as #1, grid size 320,320,320, pixel
0.84, shown at step 1, values float32
> volume #1 level 0.06148
> ui tool show "Fit in Map"
> fitmap #14 inMap #1
Fit molecule copy of 8d33.pdb (#14) to map cryosparc_P22_J108_map.mrc gaussian
(#1) using 15272 atoms
average map value = 0.07739, steps = 72
shifted from previous position = 2.74
rotated from previous position = 0.202 degrees
atoms outside contour = 4555, contour level = 0.061477
Position of copy of 8d33.pdb (#14) relative to cryosparc_P22_J108_map.mrc
gaussian (#1) coordinates:
Matrix rotation and translation
0.92103258 -0.38942555 0.00683556 61.84981821
0.38068138 0.90378483 0.19558799 -69.81264559
-0.08234484 -0.17754074 0.98066234 31.50702957
Axis -0.43368218 0.10365310 0.89508424
Axis point 209.54691730 109.80769424 0.00000000
Rotation angle (degrees) 25.47941839
Shift along axis -5.85801510
> volume #1 level 0.08287
> transparency #1.1 50
> volume #1 level 0.07311
> volume #1 level 0.08925
> volume #1 level 0.07311
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right "contour level"
> volume #1 level 0.05265
> volume #1 level 0.07802
> volume #1 level 0.03922
> ui mousemode right zone
> ui tool show "Side View"
> ui mousemode right "clip rotate"
> undo
> hide #!18 models
> ui mousemode right "clip rotate"
> undo clip
Expected fewer arguments
> undo clipping
Expected fewer arguments
> ui mousemode right clip
> ui mousemode right "rotate selected models"
> volume #1 level 0.04785
> volume #1 level 0.07562
> ui mousemode right clip
> hide #!18 models
> show #!1 models
> hide #!1 models
> show #!12 models
> volume #12 level 0.08308
> fitmap #18 inMap #12
Fit map emdb 27155 in map cryosparc_P22_J108_map.mrc using 40897 points
correlation = 0.4329, correlation about mean = 0.2712, overlap = 3503
steps = 864, shift = 104, angle = 7.69 degrees
Position of emdb 27155 (#18) relative to cryosparc_P22_J108_map.mrc (#12)
coordinates:
Matrix rotation and translation
-0.79660504 0.51542983 -0.31583619 220.05358921
0.51699673 0.85166588 0.08590465 -66.44322980
0.31326473 -0.09485420 -0.94491687 256.67114705
Axis -0.27615471 -0.96111022 0.00239384
Axis point 97.10390740 0.00000000 147.60605564
Rotation angle (degrees) 160.89634111
Shift along axis 3.70486125
> select clear
> select add #12
3 models selected
> select subtract #12
Nothing selected
> select add #18
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.44026,0.89457,-0.076979,62.001,0.73377,0.40788,0.54335,-53.269,0.51746,0.18273,-0.83597,33.072
> view matrix models
> #18,-0.66849,0.74362,0.012464,104.01,0.38475,0.33143,0.86146,-36.029,0.63647,0.58068,-0.50766,-86.002
> view matrix models
> #18,-0.82767,0.4663,-0.31229,210.68,0.51612,0.85098,-0.097231,-0.65141,0.22042,-0.24166,-0.945,151.41
> view matrix models
> #18,-0.82767,0.4663,-0.31229,206.05,0.51612,0.85098,-0.097231,1.857,0.22042,-0.24166,-0.945,144.65
> fitmap #18 inMap #12
Fit map emdb 27155 in map cryosparc_P22_J108_map.mrc using 40897 points
correlation = 0.7859, correlation about mean = 0.6983, overlap = 1.212e+04
steps = 664, shift = 11.4, angle = 31.5 degrees
Position of emdb 27155 (#18) relative to cryosparc_P22_J108_map.mrc (#12)
coordinates:
Matrix rotation and translation
-0.98285240 -0.18409232 0.01054395 292.68774437
-0.18405963 0.97602251 -0.11619861 40.78881732
0.01110014 -0.11614680 -0.99317003 283.43451505
Axis 0.09259549 -0.99398755 0.05843651
Axis point 148.22379338 0.00000000 142.93681996
Rotation angle (degrees) 179.98396987
Shift along axis 3.12091307
> select clear
> select add #18
2 models selected
> view matrix models
> #18,-0.92056,0.3785,0.096511,168.92,0.39061,0.89278,0.22442,-38.938,-0.0012217,0.24429,-0.9697,239.65
> open "C:/Users/Ania/OneDrive - University of
> Gdansk/Ania/CEM_images_data_processing/C#68/cryosparc_P7_J100_003_volume_map_sharp.mrc"
Opened cryosparc_P7_J100_003_volume_map_sharp.mrc as #2, grid size
420,420,420, pixel 0.86, shown at level 0.0385, step 2, values float32
> hide #!18 models
> hide #!12 models
> hide #!2 models
> show #!2 models
> surface dust #2 size 8.6
> volume #2 level 0.07052
> hide #!14 models
> lighting soft
> volume #2 level 0.06137
> volume #2 step 1
> volume #2 level 0.08252
> open //153.19.18.125/MRSlab/Ania/c#68/J38_map.mrc
Opened J38_map.mrc as #3, grid size 500,500,500, pixel 0.86, shown at level
0.0325, step 2, values float32
> surface dust #2 size 8.6
> surface dust #3 size 8.6
> close #1
> select add #3
5 models selected
> view matrix models
> #18,-0.63165,0.34995,0.69177,109.46,-0.775,-0.30761,-0.55204,381.28,0.019609,-0.88482,0.46551,389.84,#3,0.78069,0.22094,-0.58455,126.28,0.54373,-0.70124,0.46112,151.62,-0.30803,-0.67783,-0.66758,575.47
> view matrix models
> #18,-0.63165,0.34995,0.69177,106.73,-0.775,-0.30761,-0.55204,296.07,0.019609,-0.88482,0.46551,307.21,#3,0.78069,0.22094,-0.58455,123.55,0.54373,-0.70124,0.46112,66.412,-0.30803,-0.67783,-0.66758,492.84
> view matrix models
> #18,-0.057614,-0.9981,-0.021949,443.11,0.99025,-0.054342,-0.12823,129.77,0.1268,-0.029123,0.9915,67.732,#3,-0.32686,-0.91852,-0.22247,515.87,-0.94453,0.30951,0.10986,275.04,-0.032055,0.24604,-0.96873,314.89
> select add #2
8 models selected
> select subtract #3
5 models selected
> view matrix models
> #18,0.097259,0.98161,0.16426,-102.6,-0.89698,0.014943,0.44181,197.9,0.43123,-0.19031,0.88194,97.55,#2,-0.98895,0.021905,0.14661,322.84,0.027068,-0.94571,0.32388,286.69,0.14574,0.32427,0.93467,-72.418
> view matrix models
> #18,-0.45004,0.81425,0.36668,-38.898,-0.8712,-0.49052,0.019991,376.58,0.19614,-0.31046,0.93013,141.99,#2,-0.79482,-0.53693,0.28279,363.82,0.53935,-0.83862,-0.076358,251.59,0.27815,0.09183,0.95614,-57.938
> view matrix models
> #18,-0.45004,0.81425,0.36668,-41.191,-0.8712,-0.49052,0.019991,343.37,0.19614,-0.31046,0.93013,105.45,#2,-0.79482,-0.53693,0.28279,361.52,0.53935,-0.83862,-0.076358,218.38,0.27815,0.09183,0.95614,-94.476
> fitmap #2 inMap #3
Fit map cryosparc_P7_J100_003_volume_map_sharp.mrc in map J38_map.mrc using
249249 points
correlation = 0.6355, correlation about mean = 0.1849, overlap = 2377
steps = 204, shift = 19.3, angle = 9.57 degrees
Position of cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) relative to
J38_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.40390322 0.91473874 0.01073392 124.72718660
0.91422695 0.40403754 -0.03070377 -8.11101118
-0.03242284 -0.00258811 -0.99947087 410.83745025
Axis 0.54583142 0.83783611 -0.00993571
Axis point 68.16781913 -0.00000000 204.65193693
Rotation angle (degrees) 178.52419008
Shift along axis 57.20235577
> view matrix models
> #18,0.029639,0.94271,0.33231,-102.12,-0.99762,0.0072169,0.068506,213.58,0.062183,-0.33355,0.94068,118.96,#2,-0.92601,-0.22896,0.30013,341.46,0.20061,-0.97198,-0.12253,322.78,0.31977,-0.05325,0.946,-72.577
> volume #3 level 0.04577
> volume #3 level 0.04958
> fitmap #2 inMap #3
Fit map cryosparc_P7_J100_003_volume_map_sharp.mrc in map J38_map.mrc using
249249 points
correlation = 0.6438, correlation about mean = 0.1679, overlap = 2415
steps = 92, shift = 4.43, angle = 3.12 degrees
Position of cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) relative to
J38_map.mrc (#3) coordinates:
Matrix rotation and translation
0.11895607 0.99284773 0.01013987 15.64442337
0.99236236 -0.11854963 -0.03410133 68.64474237
-0.03265535 0.01411899 -0.99936692 407.93945123
Axis 0.74790608 0.66376187 -0.00752820
Axis point 0.00000000 22.97883030 204.40063137
Rotation angle (degrees) 178.15264274
Shift along axis 54.19327307
Correlation = 0.6699, Correlation about mean = 0.1763, Overlap = 2395
> fitmap #2 inMap #3
Fit map cryosparc_P7_J100_003_volume_map_sharp.mrc in map J38_map.mrc using
249249 points
correlation = 0.6438, correlation about mean = 0.1679, overlap = 2415
steps = 44, shift = 0.014, angle = 0.0321 degrees
Position of cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) relative to
J38_map.mrc (#3) coordinates:
Matrix rotation and translation
0.11947260 0.99278510 0.01019967 15.54165090
0.99229404 -0.11906104 -0.03430703 68.79160058
-0.03284513 0.01421982 -0.99935927 407.94400337
Axis 0.74807782 0.66356783 -0.00756994
Axis point 0.00000000 23.07542956 204.40664062
Rotation angle (degrees) 178.14132180
Shift along axis 54.18614476
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #2 level 0.06666
> show #!12 models
> construct #12
Unknown command: construct #12
> combine #12
No structures specified
> hide #!12 models
> show #!11 models
> select add #11
3 models selected
> view matrix models
> #11,-0.61086,-0.77678,0.15317,268.32,-0.75695,0.6297,0.17466,110.65,-0.23212,-0.0092475,-0.97264,251.64
> view matrix models
> #11,-0.61086,-0.77678,0.15317,251.84,-0.75695,0.6297,0.17466,101.21,-0.23212,-0.0092475,-0.97264,222.47
> view matrix models
> #11,-0.80022,0.58824,-0.1167,125.43,0.58788,0.8079,0.041202,-82.981,0.11852,-0.035634,-0.99231,182.43
> volume #11 level 0.06081
> view matrix models
> #11,-0.79553,0.58922,-0.14122,128.06,0.5912,0.80589,0.0321,-81.885,0.13272,-0.057951,-0.98946,183.24
> view matrix models
> #11,-0.7122,0.55732,-0.42682,160.88,0.63984,0.76549,-0.068103,-68.899,0.28877,-0.3216,-0.90177,186.96
> view matrix models
> #11,-0.70614,0.53113,-0.46826,169.42,0.54986,0.82799,0.10996,-90.221,0.44611,-0.17983,-0.87672,143.06
> view matrix models
> #11,-0.089907,0.84264,-0.53093,53.387,0.99211,0.028985,-0.122,-6.1633,-0.087413,-0.5377,-0.83859,257.95
> view matrix models
> #11,-0.089907,0.84264,-0.53093,133.13,0.99211,0.028985,-0.122,12.315,-0.087413,-0.5377,-0.83859,385.22
> view matrix models
> #11,-0.089907,0.84264,-0.53093,153.53,0.99211,0.028985,-0.122,32.964,-0.087413,-0.5377,-0.83859,374.78
> fitmap #11 inMap #2
Fit map cryosparc_P22_J91_006_volume_map.mrc in map
cryosparc_P7_J100_003_volume_map_sharp.mrc using 38224 points
correlation = 0.4491, correlation about mean = 0.1037, overlap = 251.1
steps = 264, shift = 17.9, angle = 24.2 degrees
Position of cryosparc_P22_J91_006_volume_map.mrc (#11) relative to
cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.18976303 -0.97879184 0.07717848 278.01871811
-0.97762961 -0.19562982 -0.07726135 345.29839719
0.09072118 -0.06079062 -0.99401920 340.43229215
Axis 0.77127834 -0.63416697 0.05442411
Axis point 0.00000000 285.77101045 161.63295230
Rotation angle (degrees) 179.38820983
Shift along axis 13.98070245
> hide #!11 models
> show #!11 models
> hide #!11 models
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J108_map.mrc"
Opened cryosparc_P22_J108_map.mrc as #1, grid size 320,320,320, pixel 0.84,
shown at level 0.057, step 2, values float32
> close #1
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J108_map.mrc"
Opened cryosparc_P22_J108_map.mrc as #1, grid size 320,320,320, pixel 0.84,
shown at level 0.057, step 2, values float32
> color #1 #23e574ff models
> volume #1 step 1
> volume #1 level 0.06226
> select add #1
4 models selected
> view matrix models
> #11,0.057168,0.95066,-0.30493,81.73,0.97562,0.011627,0.21916,8.0243,0.21189,-0.31003,-0.92682,311.09,#1,1,0,0,-22.801,0,1,0,8.7908,0,0,1,-1.4243
> view matrix models
> #11,0.092663,0.66397,0.742,-97.005,0.97793,0.079451,-0.19322,80.634,-0.18725,0.74353,-0.64196,207.09,#1,0.41025,0.26074,-0.87391,133.42,0.19036,0.91267,0.36166,-51.59,0.89189,-0.31473,0.32479,12.12
> view matrix models
> #11,-0.011557,-0.96131,-0.27522,244.7,-0.88859,-0.11634,0.44369,160.37,-0.45855,0.24968,-0.85287,315.91,#1,-0.83062,-0.082769,0.55066,159.37,-0.2967,-0.77104,-0.56344,366.88,0.47122,-0.63138,0.61589,73.692
> view matrix models
> #11,-0.46245,-0.75042,-0.47225,308.97,-0.87251,0.47987,0.091878,175.36,0.15767,0.45453,-0.87666,242.18,#1,-0.59582,-0.5634,0.57235,191.95,0.3783,-0.82553,-0.4188,266.06,0.70844,-0.033015,0.705,-52.224
> view matrix models
> #11,-0.50521,-0.82784,-0.24382,276.23,-0.85463,0.51918,0.0080908,186.23,0.11989,0.21247,-0.96979,284.15,#1,-0.74152,-0.55595,0.37558,235.94,0.44223,-0.82598,-0.34954,248.6,0.50455,-0.093099,0.85835,-36.911
> view matrix models
> #11,-0.50521,-0.82784,-0.24382,353.11,-0.85463,0.51918,0.0080908,155.29,0.11989,0.21247,-0.96979,321.34,#1,-0.74152,-0.55595,0.37558,312.82,0.44223,-0.82598,-0.34954,217.67,0.50455,-0.093099,0.85835,0.27874
> ui tool show "Volume Viewer"
> ui tool show "Model Panel"
> ui tool show "Side View"
> view matrix models
> #11,-0.50521,-0.82784,-0.24382,373.03,-0.85463,0.51918,0.0080908,195.64,0.11989,0.21247,-0.96979,325.5,#1,-0.74152,-0.55595,0.37558,332.74,0.44223,-0.82598,-0.34954,258.01,0.50455,-0.093099,0.85835,4.4461
> fitmap #1 inMap #2
Fit map cryosparc_P22_J108_map.mrc in map
cryosparc_P7_J100_003_volume_map_sharp.mrc using 297538 points
correlation = 0.7487, correlation about mean = 0.431, overlap = 4291
steps = 268, shift = 9.24, angle = 30.4 degrees
Position of cryosparc_P22_J108_map.mrc (#1) relative to
cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97356246 -0.14746213 -0.17444528 93.72145620
0.13523419 0.98757182 -0.08008534 35.58986774
0.18408681 0.05437709 0.98140474 46.63980635
Axis 0.28250491 -0.75327418 0.59394358
Axis point -113.52192237 0.00000000 510.13562037
Rotation angle (degrees) 13.76749366
Shift along axis 27.36925673
> volume #2 level 0.06162
> select clear
> hide #!1 models
> show #!18 models
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!14 models
> select add #14
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> view matrix models
> #14,0.9833,0.17791,-0.038214,-1.8103,-0.18184,0.96879,-0.16847,119.89,0.0070472,0.17261,0.98497,-8.8541
> view matrix models
> #14,0.9833,0.17791,-0.038214,26.287,-0.18184,0.96879,-0.16847,75.659,0.0070472,0.17261,0.98497,-29.403
> view matrix models
> #14,-0.91084,0.15924,0.3808,223.14,-0.32914,-0.83692,-0.43731,392.01,0.24906,-0.52365,0.81471,62.017
> view matrix models
> #14,-0.91084,0.15924,0.3808,245.98,-0.32914,-0.83692,-0.43731,382.48,0.24906,-0.52365,0.81471,99.694
> fitmap #14 inMap #2
Fit molecule copy of 8d33.pdb (#14) to map
cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) using 15272 atoms
average map value = 0.1266, steps = 112
shifted from previous position = 3.84
rotated from previous position = 9.86 degrees
atoms outside contour = 4874, contour level = 0.061617
Position of copy of 8d33.pdb (#14) relative to
cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.84121312 -0.50447350 -0.19459450 164.02097935
0.53062424 0.83938234 0.11779327 -28.56776125
0.10391560 -0.20234579 0.97378528 86.95946488
Axis -0.28486084 -0.26561532 0.92103355
Axis point 126.68300811 308.38599188 0.00000000
Rotation angle (degrees) 34.18880908
Shift along axis 40.95746520
> transparency #2.1 50
> volume #2 color #a1fffc80
> volume #2 color #a5ff8a80
> volume #2 color #ffa58e80
> volume #2 color #f1b7ff80
> color zone #2 near sel & #14 distance 5.16
> select clear
> hide #!14 models
> volume #2 level 0.0969
> show #!14 models
> volume #2 level 0.06666
> volume #2 level 0.0843
> show #17 models
> hide #17 models
> show #17 models
> ui tool show Matchmaker
> matchmaker #!14 to #17
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 copy of AlphaFold E5KNU5_HUMAN, chain A (#17) with copy of
8d33.pdb, chain A (#14), sequence alignment score = 5920.9
RMSD between 655 pruned atom pairs is 0.842 angstroms; (across all 974 pairs:
6.019)
> select add #17
9824 atoms, 10080 bonds, 1239 residues, 1 model selected
> view matrix models
> #17,0.93054,-0.36483,-0.031397,98.074,0.35704,0.92302,-0.1434,113.7,0.081296,0.12223,0.98917,79.318
> undo
[Repeated 3 time(s)]
> select add #14
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> view matrix models
> #14,-0.77133,0.54417,-0.33005,252.75,-0.28673,0.16585,0.94355,-16.372,0.56819,0.82242,0.028104,-19.448
> view matrix models
> #14,-0.97724,0.15672,0.14294,257.03,-0.17529,-0.97614,-0.12815,281.01,0.11945,-0.15029,0.9814,40.961
> view matrix models
> #14,-0.97724,0.15672,0.14294,296.87,-0.17529,-0.97614,-0.12815,295.33,0.11945,-0.15029,0.9814,53.579
> view matrix models
> #14,-0.97724,0.15672,0.14294,319.09,-0.17529,-0.97614,-0.12815,315.3,0.11945,-0.15029,0.9814,43.802
> view matrix models
> #14,-0.97724,0.15672,0.14294,300.62,-0.17529,-0.97614,-0.12815,320.26,0.11945,-0.15029,0.9814,44.289
> fitmap #14 inMap #2
Fit molecule copy of 8d33.pdb (#14) to map
cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) using 15272 atoms
average map value = 0.1266, steps = 236
shifted from previous position = 20.4
rotated from previous position = 20.4 degrees
atoms outside contour = 6308, contour level = 0.084297
Position of copy of 8d33.pdb (#14) relative to
cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.84128136 -0.50450104 -0.19422775 163.97061720
0.53057033 0.83942352 0.11774260 -28.55952801
0.10363808 -0.20210612 0.97386462 86.94830515
Axis -0.28467290 -0.26510761 0.92123791
Axis point 126.65199993 308.30125578 0.00000000
Rotation angle (degrees) 34.17918426
Shift along axis 40.99343230
> select clear
> ui tool show Matchmaker
> matchmaker #17 to #14
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 copy of 8d33.pdb, chain A (#14) with copy of AlphaFold
E5KNU5_HUMAN, chain A (#17), sequence alignment score = 5920.9
RMSD between 655 pruned atom pairs is 0.842 angstroms; (across all 974 pairs:
6.019)
> hide #!2 models
> color #17::c_alpha_distance>=3.0 lime
> color #14 white
> show #!2 models
> hide #!2 models
> show #!2 models
> transparency #2.1 0
> transparency #2.1 50
> transparency #2.1 0
> hide #!2 models
> hide #!14 models
> show #!14 models
> color #17::c_alpha_distance>=3.0 cyan
> show #17::c_alpha_distance>=3.0 atoms,ribbons
> color #14::c_alpha_distance>=3.0 lime
[Repeated 1 time(s)]
> hide #17 models
> show #17 models
> hide #17 models
> show #!2 models
> transparency #2.1 50
> volume #2 level 0.07674
> color zone #2 near #14 distance 5.16
> select #14/T
494 atoms, 552 bonds, 24 residues, 1 model selected
> color sel magenta
> volume #2 color #ffff0080
> volume #2 color #ffff7f80
> volume #2 color #ffffff80
> select #14/P
451 atoms, 507 bonds, 22 residues, 1 model selected
> color sel blue
> color zone #2 near sel & #14 distance 5.16
> hide #!2 models
> show #!2 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!16 models
> hide #!16 models
> show #!13 models
> hide #!13 models
> show #!14 models
> color zone #2 near sel & #14 distance 5.16
> select clear
> color zone #2 near #14 distance 5.16
> transparency #2.1 0
> transparency #2.1 50
> hide #!14 models
> show #17 models
> hide #17 models
> show #15 models
> hide #15 models
> show #17 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide #!2 models
> hide #17 models
> show #!16 models
> hide #!16 models
> show #!16 models
> transparency #1.1 50
> hide #!16 models
> show #!14 models
> show #17 models
> hide #17 models
> color zone #1 near #14 distance 5.04
> show #17 models
> hide #17 models
> show #!16 models
> hide #!16 models
> show #15 models
> hide #15 models
> hide #!14 models
> show #!14 models
> ui tool show Matchmaker
> show #15 models
> matchmaker #15 to #14
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 copy of 8d33.pdb, chain A (#14) with AlphaFold E5KNU5_HUMAN, chain
A (#15), sequence alignment score = 5920.9
RMSD between 655 pruned atom pairs is 0.842 angstroms; (across all 974 pairs:
6.019)
> hide #!14 models
> show #!14 models
> hide #!14 models
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 257/cryosparc_P21_J20_class_00_final_volume.mrc"
Opened cryosparc_P21_J20_class_00_final_volume.mrc as #4, grid size
128,128,128, pixel 2.85, shown at level 0.119, step 1, values float32
> surface dust #1 size 8.4
> surface dust #4 size 28.5
> hide #!1 models
> hide #15 models
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 257/cryosparc_P21_J22_002_volume_map.mrc"
Opened cryosparc_P21_J22_002_volume_map.mrc as #5, grid size 500,500,500,
pixel 0.73, shown at level 0.0141, step 2, values float32
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 257/cryosparc_P21_J25_003_volume_map.mrc"
Opened cryosparc_P21_J25_003_volume_map.mrc as #6, grid size 500,500,500,
pixel 0.73, shown at level 0.00992, step 2, values float32
> hide #!5 models
> hide #!4 models
> volume #6 level 0.02329
> show #!5 models
> close #5
> show #!4 models
> hide #!4 models
> show #!4 models
> close #4
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> transparency #2.1#6.1 0
> select add #6
2 models selected
> view matrix models #6,1,0,0,15.199,0,1,0,-26.817,0,0,1,-15.091
> view matrix models
> #6,0.73198,0.64225,0.22742,-99.969,-0.4318,0.69549,-0.57432,210.83,-0.52703,0.32219,0.78641,55.713
> view matrix models
> #6,-0.33642,0.8983,0.28264,33.305,-0.92228,-0.25364,-0.29164,430.97,-0.19029,-0.35879,0.91382,103.16
> view matrix models
> #6,-0.33642,0.8983,0.28264,36.446,-0.92228,-0.25364,-0.29164,428.77,-0.19029,-0.35879,0.91382,92.25
> fitmap #6 inMap #2
Fit map cryosparc_P21_J25_003_volume_map.mrc in map
cryosparc_P7_J100_003_volume_map_sharp.mrc using 84300 points
correlation = 0.5459, correlation about mean = 0.1887, overlap = 232.6
steps = 448, shift = 15.7, angle = 43.3 degrees
Position of cryosparc_P21_J25_003_volume_map.mrc (#6) relative to
cryosparc_P7_J100_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.59095906 -0.78468253 -0.18719170 470.41875801
0.80651578 -0.57967610 -0.11622364 150.84667709
-0.01731189 -0.21965648 0.97542368 52.33562298
Axis -0.06450119 -0.10593783 0.99227858
Axis point 198.61286353 197.27160998 0.00000000
Rotation angle (degrees) 126.69861296
Shift along axis 5.60857659
> transparency sel 50
> close #6
> hide #!2 models
> show #!3 models
> show #!12 models
> hide #!12 models
> show #!1 models
> hide #!3 models
> show #!3 models
> fitmap #3 inMap #1
Fit map J38_map.mrc in map cryosparc_P22_J108_map.mrc using 65694 points
correlation = 0.5932, correlation about mean = 0.2725, overlap = 306
steps = 300, shift = 0.941, angle = 13.2 degrees
Position of J38_map.mrc (#3) relative to cryosparc_P22_J108_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.23890076 0.97053686 -0.03137765 -126.49566840
0.96716006 -0.23493374 0.09699250 -41.02078675
0.08676314 -0.05351882 -0.99479035 320.72265727
Axis -0.78649564 -0.61734371 -0.01764546
Axis point 0.00000000 38.97598022 160.78842714
Rotation angle (degrees) 174.50926555
Shift along axis 119.15291692
> hide #!1 models
> show #!11 models
> select add #1
2 models selected
> view matrix models
> #1,-0.90165,-0.062889,0.42786,239.77,0.030107,-0.9961,-0.082965,321.87,0.43141,-0.061924,0.90003,56.742
> select subtract #1
Nothing selected
> select add #3
3 models selected
> view matrix models
> #3,-0.23911,-0.88321,-0.40344,495.08,-0.96339,0.26768,-0.015026,331.86,0.12126,0.38508,-0.91488,294.23
> view matrix models
> #3,-0.23911,-0.88321,-0.40344,507.21,-0.96339,0.26768,-0.015026,306.19,0.12126,0.38508,-0.91488,298.17
> view matrix models
> #3,-0.80438,-0.5834,0.11234,461.24,0.39221,-0.66347,-0.63717,326.52,0.44626,-0.46846,0.76249,35.974
> view matrix models
> #3,0.057233,0.92293,-0.38068,75.614,0.94686,0.070707,0.31378,-147.6,0.31652,-0.37841,-0.86984,397.97
> view matrix models
> #3,0.057233,0.92293,-0.38068,43.493,0.94686,0.070707,0.31378,-164.76,0.31652,-0.37841,-0.86984,412.96
> view matrix models
> #3,0.057233,0.92293,-0.38068,25.031,0.94686,0.070707,0.31378,-124.14,0.31652,-0.37841,-0.86984,403.59
> fitmap #3 inMap #11
Fit map J38_map.mrc in map cryosparc_P22_J91_006_volume_map.mrc using 65694
points
correlation = 0.8216, correlation about mean = 0.6531, overlap = 527.5
steps = 460, shift = 17.3, angle = 24.1 degrees
Position of J38_map.mrc (#3) relative to cryosparc_P22_J91_006_volume_map.mrc
(#11) coordinates:
Matrix rotation and translation
-0.95167353 -0.25890283 -0.16518701 426.31634735
0.26145908 -0.96519286 0.00646228 289.13613284
-0.16111041 -0.03703969 0.98624104 -14.57617053
Axis -0.08330630 -0.00780669 0.99649341
Axis point 193.30230800 172.63878194 0.00000000
Rotation angle (degrees) 164.86486418
Shift along axis -52.29709049
> select clear
> transparency #3.1#11.1 50
> transparency #3.1#11.1 0
> hide #!11 models
> show #!11 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!11 models
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J135_003_volume_map.mrc"
Opened cryosparc_P22_J135_003_volume_map.mrc as #4, grid size 320,320,320,
pixel 0.84, shown at level 0.0282, step 2, values float32
> volume #4 step 1
> close #4
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J136_002_volume_map.mrc"
Opened cryosparc_P22_J136_002_volume_map.mrc as #4, grid size 320,320,320,
pixel 0.84, shown at level 0.136, step 2, values float32
> close #4
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J137_003_volume_map.mrc"
Opened cryosparc_P22_J137_003_volume_map.mrc as #4, grid size 320,320,320,
pixel 0.84, shown at level 0.0285, step 2, values float32
> close #4
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J138_006_volume_map.mrc"
Opened cryosparc_P22_J138_006_volume_map.mrc as #4, grid size 320,320,320,
pixel 0.84, shown at level 0.0496, step 2, values float32
> volume #4 step 1
> volume #4 level 0.05901
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J138_006_volume_map_sharp.mrc"
Opened cryosparc_P22_J138_006_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.84, shown at level 0.0699, step 2, values float32
> surface dust #4 size 8.4
> surface dust #5 size 8.4
> volume #5 step 1
> volume #5 level 0.07564
> color #5 #50eeffff models
> color #5 #ff6fffff models
> hide #!5 models
> show #!4 models
> hide #!4 models
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J139_003_volume_map.mrc"
Opened cryosparc_P22_J139_003_volume_map.mrc as #6, grid size 320,320,320,
pixel 0.84, shown at level 0.0278, step 2, values float32
> close #6
> show #!5 models
> volume #5 step 2
> volume #5 step 4
> volume #5 step 1
> open "//153.19.18.125/MRSlab/Ania/CEM_images_data_processing/C#
> 196/cryosparc_P22_J140_map_locres.mrc"
Opened cryosparc_P22_J140_map_locres.mrc as #6, grid size 320,320,320, pixel
0.84, shown at level 6.14, step 2, values float32
> ui tool show "Surface Color"
> color sample #5.1 map #6 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 0, mean 3.379, maximum 40.73
> hide #!6 models
> key red-white-blue :0.0 :20.4 :40.7 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> color sample #5.1 map #6 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000
Map values for surface "surface": minimum 0, mean 3.379, maximum 40.73
> key rainbow :2 :4 :6 :8 :10 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> volume #!5 style surface
> lighting soft
> lighting full
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> hide #!5 models
> show #!4 models
> color sample #4.1 map #6 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000
Map values for surface "surface": minimum 2.349, mean 3.102, maximum 40.71
> hide #7 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> show #!5 models
> color single #4.1
> color single #5.1
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> select add #14
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> view matrix models
> #14,-0.88335,0.24196,0.40144,198.08,-0.36932,-0.88667,-0.27824,395.62,0.28863,-0.39404,0.8726,118.64
> fitmap #14 inMap #1
Fit molecule copy of 8d33.pdb (#14) to map cryosparc_P22_J108_map.mrc (#1)
using 15272 atoms
average map value = 0.1238, steps = 64
shifted from previous position = 2.82
rotated from previous position = 1.63 degrees
atoms outside contour = 3365, contour level = 0.062258
Position of copy of 8d33.pdb (#14) relative to cryosparc_P22_J108_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.92101308 -0.38942096 0.00928239 61.65929527
0.38049379 0.90449189 0.19266266 -69.46015197
-0.08342273 -0.17391291 0.98122113 31.18236009
Axis -0.42736717 0.10807901 0.89759469
Axis point 208.40236400 109.62410371 0.00000000
Rotation angle (degrees) 25.39628890
Shift along axis -5.86922189
> volume #!1 style mesh
[Repeated 1 time(s)]
> transparency #1.1 0
> volume #!1 style surface
> transparency #1.1 50
> select #14/A
7807 atoms, 8017 bonds, 14 pseudobonds, 976 residues, 3 models selected
> hide (#!14 & sel) target a
> select #14/A
7807 atoms, 8017 bonds, 14 pseudobonds, 976 residues, 3 models selected
> hide (#!14 & sel) target a
> cartoon hide (#!14 & sel)
> select #14/B
3307 atoms, 3386 bonds, 2 pseudobonds, 411 residues, 2 models selected
> cartoon hide (#!14 & sel)
> select #14/C
3213 atoms, 3290 bonds, 2 pseudobonds, 399 residues, 2 models selected
> cartoon hide (#!14 & sel)
> lighting soft
> lighting flat
> lighting full
> lighting soft
> transparency #1.1 0
> hide #!1 models
> show #!1 models
> hide #!1 models
> molmap #14 3
Opened copy of 8d33.pdb map 3 as #8, grid size 115,132,159, pixel 1, shown at
level 0.111, step 1, values float32
> undo
> hide #!8 models
> show #!8 models
> undo
> close #8
> hide #!14 models
> show #!14 models
> hide #!1 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> select #14/B
3307 atoms, 3386 bonds, 2 pseudobonds, 411 residues, 2 models selected
> select #14/A
7807 atoms, 8017 bonds, 14 pseudobonds, 976 residues, 3 models selected
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> select #14/B
3307 atoms, 3386 bonds, 2 pseudobonds, 411 residues, 2 models selected
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show "Command Line Interface"
> molmap #14 3
Opened copy of 8d33.pdb map 3 as #8, grid size 62,85,84, pixel 1, shown at
level 0.131, step 1, values float32
> color zone #8 near #14 distance 6
> hide #!14 models
> hide #!8 models
> show #!8 models
> show #!1 models
> vop subtract #1 #8 minrms True
Opened volume difference as #9, grid size 320,320,320, pixel 0.84, shown at
step 1, values float32
Minimum RMS scale factor for "copy of 8d33.pdb map 3 #8" above level 0.13108
is 0.16013
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!1 models
> hide #!1 models
> show #!8 models
> close #9
> show #!1 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select add #5
3 models selected
> view matrix models #5,1,0,0,3.9606,0,1,0,-0.79701,0,0,1,5.2733
> view matrix models
> #5,0.14612,-0.98927,0.0015414,252.29,-0.9368,-0.13787,0.32156,234.97,-0.3179,-0.048432,-0.94689,321.07
> view matrix models
> #5,0.14612,-0.98927,0.0015414,271.68,-0.9368,-0.13787,0.32156,250.12,-0.3179,-0.048432,-0.94689,402.95
> view matrix models
> #5,0.14612,-0.98927,0.0015414,237.24,-0.9368,-0.13787,0.32156,192.92,-0.3179,-0.048432,-0.94689,433.54
> hide #!5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!1 models
> show #!14 models
> hide #!1 models
> show #!13 models
> hide #!13 models
> hide #!14 models
> hide #!8 models
> show #!8 models
> show #!14 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> molmap #14 5
Opened copy of 8d33.pdb map 5 as #8, grid size 44,58,58, pixel 1.67, shown at
level 0.0861, step 1, values float32
> select subtract #5
Nothing selected
> hide #!14 models
> show #!14 models
> hide #!8 models
> show #!8 models
> color zone #8 near #14 distance 10
> show #!1 models
> vop subtract #1 #8 minrms True
Opened volume difference as #9, grid size 320,320,320, pixel 0.84, shown at
step 1, values float32
Minimum RMS scale factor for "copy of 8d33.pdb map 5 #8" above level 0.08611
is 0.2508
> hide #!14 models
> show #!1 models
> vop subtract #1 #9 minrms True
Opened volume difference as #19, grid size 320,320,320, pixel 0.84, shown at
step 1, values float32
Minimum RMS scale factor for "volume difference #9" above level 0.062258 is
1.0115
> hide #!19 models
> show #!19 models
> hide #!19 target m
> close #19
> show #!8 models
> close #8
> show #!9 models
> close #9
> show #!1 models
> volume gaussian #1 sDev 2
Opened cryosparc_P22_J108_map.mrc gaussian as #8, grid size 320,320,320, pixel
0.84, shown at step 1, values float32
> volume #8 step 2
> volume #8 level 0.03963
> show #!1 models
> hide #!8 models
> show #!13 models
> select add #13
15272 atoms, 15752 bonds, 18 pseudobonds, 1832 residues, 3 models selected
> view matrix models
> #13,0.98433,0.17265,-0.035848,3.4321,-0.17625,0.96965,-0.16945,64.098,0.005504,0.17311,0.98489,75.568
> view matrix models
> #13,-0.59048,0.27963,0.75706,92.497,-0.36467,-0.92928,0.058809,321.28,0.71996,-0.24135,0.6507,78.824
> view matrix models
> #13,-0.60844,0.12287,0.78403,113.49,-0.34923,-0.92859,-0.12549,345.37,0.71263,-0.35016,0.6079,101.47
> view matrix models
> #13,-0.60844,0.12287,0.78403,129.34,-0.34923,-0.92859,-0.12549,365.65,0.71263,-0.35016,0.6079,92.88
> view matrix models
> #13,-0.66186,0.17773,0.72825,136.6,-0.4017,-0.90432,-0.14438,371.9,0.63291,-0.3881,0.66993,100.16
> transparency #1.1 50
> fitmap #13 inMap #1
Fit molecule 8d33.pdb (#13) to map cryosparc_P22_J108_map.mrc (#1) using 15272
atoms
average map value = 0.1238, steps = 216
shifted from previous position = 11.4
rotated from previous position = 23.6 degrees
atoms outside contour = 3361, contour level = 0.062258
Position of 8d33.pdb (#13) relative to cryosparc_P22_J108_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.92101073 -0.38942881 0.00918575 61.66961781
0.38051707 0.90447899 0.19267727 -69.45971564
-0.08334242 -0.17396247 0.98121918 31.18043267
Axis -0.42742391 0.10786816 0.89759304
Axis point 208.40372994 109.65150082 0.00000000
Rotation angle (degrees) 25.39743900
Shift along axis -5.86422118
> hide #!1 models
> select #13/T
494 atoms, 552 bonds, 24 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #14/P
451 atoms, 507 bonds, 22 residues, 1 model selected
> delete atoms #13
> delete bonds #13
> undo
> show #!1 models
> show #!14 models
> hide #!14 models
> show #!8 models
> hide #!8 models
> show #!16 models
> hide #!16 models
> show #!14 models
> hide #!14 models
> open 8d33
Summary of feedback from opening 8d33 fetched from pdb
---
warnings | Expected gap or linking atom in ASP /A:75 for LEU /A:74
Expected gap or linking atom in ASP /A:75 for ILE /A:76
Expected gap or linking atom in ASP /A:122 for PRO /A:121
Expected gap or linking atom in ASP /A:122 for VAL /A:123
Expected gap or linking atom in ASP /A:133 for GLY /A:132
153 messages similar to the above omitted
notes | Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
Fetching CCD DCP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/DCP/DCP.cif
8d33 title:
Human mitochondrial DNA polymerase γ ternary complex with GC basepair [more
info...]
Chain information for 8d33 #9
---
Chain | Description | UniProt
A | DNA polymerase subunit gamma-1 | DPOG1_HUMAN 1-1239
B C | DNA polymerase subunit gamma-2, mitochondrial | DPOG2_HUMAN 1-485
P | DNA
(5'-D(P*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*TP*AP*C)-3')
|
T | DNA (25-MER) |
Non-standard residues in 8d33 #9
---
CA — calcium ion
DCP — 2'-deoxycytidine-5'-triphosphate
Associated 8d33 chain A to copy of 8d33.pdb, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 8d33 #9/A, AlphaFold
E5KNU5_HUMAN #15/A, copy of 8d33.pdb #16/A
> select add #9
15272 atoms, 15752 bonds, 74 pseudobonds, 1832 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> view matrix models #9,1,0,0,-14.254,0,1,0,19.13,0,0,1,93.19
> view matrix models
> #9,-0.97124,-0.21352,0.10539,265.48,0.17319,-0.93721,-0.30273,316.17,0.16341,-0.27577,0.94723,118.26
> view matrix models
> #9,-0.76572,0.61274,0.19551,106.89,-0.64172,-0.70745,-0.29615,391.59,-0.043146,-0.35224,0.93492,158.63
> view matrix models
> #9,-0.76572,0.61274,0.19551,154.66,-0.64172,-0.70745,-0.29615,402.99,-0.043146,-0.35224,0.93492,146.72
> fitmap #9 inMap #1
Fit molecule 8d33 (#9) to map cryosparc_P22_J108_map.mrc (#1) using 15272
atoms
average map value = 0.1238, steps = 220
shifted from previous position = 8.56
rotated from previous position = 27.7 degrees
atoms outside contour = 3364, contour level = 0.062258
Position of 8d33 (#9) relative to cryosparc_P22_J108_map.mrc (#1) coordinates:
Matrix rotation and translation
0.92100761 -0.38943541 0.00921573 61.66526371
0.38051843 0.90447862 0.19267617 -69.45862516
-0.08337038 -0.17394944 0.98121904 31.18281623
Axis -0.42740377 0.10793477 0.89759462
Axis point 208.39637711 109.63944731 0.00000000
Rotation angle (degrees) 25.39767413
Shift along axis -5.86343850
> color zone #1 near sel & #9 distance 5.04
> hide #!1 models
> select subtract #9
Nothing selected
> select #9/T
494 atoms, 552 bonds, 24 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/P
451 atoms, 507 bonds, 22 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> molmap #9 6
Opened 8d33 map 6 as #13, grid size 67,69,89, pixel 2, shown at level 0.0938,
step 1, values float32
> hide #!13 models
> show #!13 models
> color zone #13 near #9 distance 12
> hide #!13 models
> hide #!9 models
> show #!13 models
> show #!1 models
> fitmap #13 inMap #1
Fit map 8d33 map 6 in map cryosparc_P22_J108_map.mrc using 35736 points
correlation = 0.8168, correlation about mean = 0.5567, overlap = 1021
steps = 40, shift = 0.0765, angle = 0.109 degrees
Position of 8d33 map 6 (#13) relative to cryosparc_P22_J108_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.92045279 -0.39076910 0.00812826 62.00346592
0.38206729 0.90395121 0.19208530 -69.52835127
-0.08240858 -0.17369989 0.98134449 31.00391984
Axis -0.42542602 0.10529877 0.89884641
Axis point 208.01935057 109.97617344 0.00000000
Rotation angle (degrees) 25.46150715
Shift along axis -5.83137562
> vop subtract #1 #13 minrms True
Opened volume difference as #19, grid size 320,320,320, pixel 0.84, shown at
step 1, values float32
Minimum RMS scale factor for "8d33 map 6 #13" above level 0.093752 is 0.24944
> close #19
> show #!1 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!13 models
> vop subtract #8 #13 minrms True
Opened volume difference as #19, grid size 320,320,320, pixel 0.84, shown at
step 1, values float32
Minimum RMS scale factor for "8d33 map 6 #13" above level 0.093752 is 0.20898
> close #19
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!9 models
> molmap #9 8
Opened 8d33 map 8 as #13, grid size 55,56,71, pixel 2.67, shown at level
0.083, step 1, values float32
> hide #!13 models
> show #!13 models
> hide #!9 models
> show #!1 models
> hide #!1 models
> show #!8 models
> fitmap #13 inMap #8
Fit map 8d33 map 8 in map cryosparc_P22_J108_map.mrc gaussian using 17223
points
correlation = 0.9455, correlation about mean = 0.6444, overlap = 337.9
steps = 48, shift = 0.265, angle = 0.124 degrees
Position of 8d33 map 8 (#13) relative to cryosparc_P22_J108_map.mrc gaussian
(#8) coordinates:
Matrix rotation and translation
0.92090027 -0.38973201 0.00718008 61.76563862
0.38111146 0.90409216 0.19331677 -69.66599759
-0.08183322 -0.17528904 0.98111004 31.14021876
Axis -0.42907773 0.10361646 0.89730481
Axis point 208.84078302 109.73424914 0.00000000
Rotation angle (degrees) 25.43790834
Shift along axis -5.77853557
> vop subtract #8 #13 minrms True
Opened volume difference as #19, grid size 320,320,320, pixel 0.84, shown at
step 1, values float32
Minimum RMS scale factor for "8d33 map 8 #13" above level 0.083027 is 0.2339
> show #!1 models
> hide #!1 models
> surface dust #19 size 8.4
> show #!1 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!1 models
> show #!14 models
> transparency #19.1 50
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!9 models
> hide #!9 models
> hide #!14 models
> hide #!19 models
> show #!1 models
> show #!13 models
> vop subtract #1 #13 minrms True
Opened volume difference as #20, grid size 320,320,320, pixel 0.84, shown at
step 1, values float32
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1335, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run
f(s)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 885, in subtract_maps
run(session, 'vop subtract #%s #%s minrms True' % (map1.id_string,
map2.id_string))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 513, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2918, in run
result = ci.function(session, *args, optional=optional,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 3457, in __call__
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 912, in volume_subtract
sv = combine_op(volumes, 'subtract', on_grid, bounding_grid, subregion, step,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 388, in combine_op
cv = [combine_operation(volumes, operation, subregion, step,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 388, in <listcomp>
cv = [combine_operation(volumes, operation, subregion, step,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 447, in combine_operation
rv.combine_interpolated_values(v, op, subregion = subregion, step = step,
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1498, in combine_interpolated_values
scale = -minimum_rms_scale(values, m, level)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 2560, in minimum_rms_scale
vc = v.copy()
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 125. MiB for an
array with shape (320, 320, 320) and data type float32
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 125. MiB for an
array with shape (320, 320, 320) and data type float32
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 2560, in minimum_rms_scale
vc = v.copy()
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.8280
OpenGL renderer: Intel(R) HD Graphics 630
OpenGL vendor: Intel
Python: 3.9.11
Locale: pl_PL.cp1250
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B250M-DS3H
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,472,567,808
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7500 CPU @ 3.40GHz
OSLanguage: pl-PL
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-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
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
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
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
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
pywin32: 305
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
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArrayMemoryError in vop subtract |
comment:2 by , 2 years ago
| Cc: | added |
|---|---|
| Resolution: | → duplicate |
| Status: | assigned → closed |
| Summary: | ArrayMemoryError in vop subtract → Opening mmCIF file: MemoryError: not enough memory |
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After failing to open PDB 8d33 also failed making map copy. Had 1.5 Gbytes of maps open (12 maps, 320 x 320 x 320 float) on machine with 8 GB memory. Looks like the out-of-memory was most likely the Windows mmCIF memory leak.