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Opened 2 years ago
Closed 2 years ago
#9813 closed defect (duplicate)
Struct Measure: wrapped C/C++ object of type QLabel has been deleted
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
choose "Distances" from structure analysis
go to "centroids"
close the UI without doing anything
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\עופר\\\Dropbox\\\LAB_staff\\\HKR\\\alignment\\\MPAT-to-
> ESHL B\\\rank1\\\rank1.cxs"
Log from Tue Sep 19 18:43:44 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\\\Users\\\עופר\\\Dropbox\\\LAB_staff\\\HKR\\\alignment\\\MPAT-to-
> ESHL
> B\\\mpat2eshl_488ca_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
mpat2eshl_488ca_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1
---
Chain | Description
A | No description available
> open "C:/Users/עופר/Dropbox/LAB_staff/HKR/alignment/MPAT-to-ESHL
> B/mpat2eshl_488ca_scores_rank_001_alphafold2_ptm_model_3_seed_000.json"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 559, in dropEvent
_open_dropped_file(self.session, p)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1922, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
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 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, 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 193, 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 457, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mole\\__init__.py", line 27, in open
return mole.read_mole_json(session, data, file_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py",
line 40, in read_mole_json
models = channel_models(session, j['Channels'], transparency/100.0)
KeyError: 'Channels'
KeyError: 'Channels'
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py",
line 40, in read_mole_json
models = channel_models(session, j['Channels'], transparency/100.0)
See log for complete Python traceback.
> open "C:/Users/עופר/Dropbox/LAB_staff/HKR/alignment/MPAT-to-ESHL
> B/mpat2eshl_488ca_scores_rank_001_alphafold2_ptm_model_3_seed_000.json"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\graphics.py", line 51, in event
if self.handle_drag_and_drop(event):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\graphics.py", line 116, in handle_drag_and_drop
mw.dropEvent(event)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 559, in dropEvent
_open_dropped_file(self.session, p)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1922, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
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 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, 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 193, 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 457, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mole\\__init__.py", line 27, in open
return mole.read_mole_json(session, data, file_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py",
line 40, in read_mole_json
models = channel_models(session, j['Channels'], transparency/100.0)
KeyError: 'Channels'
KeyError: 'Channels'
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py",
line 40, in read_mole_json
models = channel_models(session, j['Channels'], transparency/100.0)
See log for complete Python traceback.
> color plddt
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> pallete
Unknown command: pallete
> palete
Unknown command: palete
> color bfactor palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> color bfactor palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> color bfactor
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> color bfactor palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> color bfactor
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> AlphaFold tool
Unknown command: AlphaFold tool
> AlphaFold
Unknown command: AlphaFold
> ui tool show AlphaFold
> alphafold pae #1 file
> "C:\\\\\\\Users\\\\\\\עופר\\\\\\\Dropbox\\\\\\\LAB_staff\\\\\\\HKR\\\\\\\alignment\\\\\\\MPAT-
> to-ESHL
> B\\\mpat2eshl_488ca_scores_rank_001_alphafold2_ptm_model_3_seed_000.json"
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> alphafold pae #1 file
> "C:\\\\\\\Users\\\\\\\עופר\\\\\\\Dropbox\\\\\\\LAB_staff\\\\\\\HKR\\\\\\\alignment\\\\\\\MPAT-
> to-ESHL
> B\\\mpat2eshl_488ca_scores_rank_001_alphafold2_ptm_model_3_seed_000.json"
> color #1:377-582 lime
> color #1:246-246 lime
> color #1:217-217 magenta
> color #1:42-234 lime
> color #1:32-273 lime
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> color #1:86-207 lime
> color #1:366-366 lime
> color #1:77-77 magenta
> color #1:634-634 lime
> color #1:166-166 magenta
> color #1:635-635 lime
> color #1:170-170 magenta
> color #1:626-626 lime
> color #1:161-161 magenta
> color #1:260-644 lime
> color #1:129-476 lime
> color #1:397-397 lime
> color #1:498-498 magenta
> color #1:338-338 lime
> color #1:355-355 magenta
> color #1:151-151 lime
> color #1:150-150 magenta
> color #1:192-192 lime
> color #1:256-256 magenta
> color #1:217-217 lime
> color #1:241-241 magenta
> color #1:324-324 lime
> color #1:308-308 magenta
> color #1:151-151 lime
> color #1:349-349 magenta
> color #1:186-190 lime
> color #1:390-390 magenta
> alphafold pae #1 colorDomains true
[Repeated 1 time(s)]
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> color #1:167-167 lime
> color #1:107-107 magenta
> color #1:141-141 lime
> color #1:105-105 magenta
> color #1:141-141 lime
> color #1:105-105 magenta
> color #1:141-141 lime
> color #1:105-105 magenta
> color #1:78-81 lime
> color #1:60-62 magenta
> color #1:8-15 lime
> color #1:27-30 magenta
> color #1:7-8 lime
> color #1:6-6 magenta
> color #1:2-248 lime
> color #1:229-229 lime
> color #1:554-554 magenta
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
Drag select of 878 residues
Drag select of 921 residues
> select add #1
14222 atoms, 14366 bonds, 921 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
14222 atoms, 14366 bonds, 921 residues, 1 model selected
> alphafold pae #1 file "C:/Users/עופר/Dropbox/LAB_staff/HKR/alignment/MPAT-
> to-ESHL
> B/mpat2eshl_488ca_scores_rank_001_alphafold2_ptm_model_3_seed_000.json"
> alphafold pae #1 colorDomains true
> select clear
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> legend
Unknown command: legend
> scalebar
> scalebar show
Expected a number or a keyword
> show scalebar
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui mousemode right "color key"
> key delete
> ui mousemode right translate
> ui mousemode right "color key"
> show scalebar
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> alphafold pae #1 file "C:/Users/עופר/Dropbox/LAB_staff/HKR/alignment/MPAT-
> to-ESHL
> B/mpat2eshl_488ca_scores_rank_001_alphafold2_ptm_model_3_seed_000.json"
> key pos 0.425802,0.590244 size 0.00671141,0.191463
> key pos 0.297539,0.221951 size 0.0171514,0.62561
> scalebar
> key pos 0.283371,0.857317 size 0,0.00121951
> key pos 0.281879,0.864634 size 0,0
> key pos 0.288591,0.407317 size 0.0231171,0.514634
> ui mousemode right "color key"
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x28ea76e7910, name="\\\\\\\\.\\\DISPLAY2") screenTo:
QScreen(0x28ea76e7910, name="\\\\\\\\.\\\DISPLAY2") wdgScreen:
QScreen(0x28ea76e7910, name="\\\\\\\\.\\\DISPLAY2") orgWdgScreen QScreen(0x0)
[Repeated 54 time(s)]
> key blue:min white: #d5e8f8:max
> key blue:min white: #cccccc:max
> key blue:min white: #f0f0f0:max
> key blue:min white: #ffaa00:max
> key blue:min white: #aaaaff:max
> key blue:min white: #00aa7f:max
> key blue:min white: #f0f0f0:max
> key blue:min white: #00aa00:max
> key blue:min white: #828790:max
> key blue:min white: #f0f0f0:max
> key blue:min white: #ffffdb:max
> key blue:min white: white:max
> key blue:min white: black:max
> key blue:min white: #192578:max
> key blue:min white: #1d2b8a:max
> key blue:min white: #2131e0:max
> key blue:min white: #243584:max
> key blue:min white: #2335f4:max
> key blue:min white: #263aff:max
> key blue:min white: #2c418a:max
> key blue:min white: #334c96:max
> key blue:min white: #537cf3:max
> key blue:min white: #5883ff:max
> key blue:min white: #2e4486:max
> key blue:min white: #36509d:max
> key blue:min white: #3854a5:max
> key blue:min white: #283b66:max
> key blue:min white: #73acff:max
> key blue:min white: #324a91:max
> key blue:min white: #334c95:max
> key blue:min white: #344d97:max
> key blue:min white: #273aec:max
> key blue:min white: #2639e7:max
> key blue:min white: #2638e4:max
> key blue:min white: #273bee:max
> key blue:min white: #293cf5:max
> key blue:min white: #2a3ffe:max
> key blue:min white: #2c41ff:max
> key blue:min white: #2b40ff:max
> key blue:min white: #2d42ff:max
> key blue:min white: #2e44ff:max
> key blue:min white: #3149ff:max
> key blue:min white: #3148ff:max
> key paired-3 :min : :max
> key #b2df8a:max #1f78b4: #a6cee3:min
> key paired-3 :min : :max
[Repeated 1 time(s)]
> key blue-white-red :min : :max
> key accent-3 :min : :max
> key bugn-3 :min : :max
> key ylgnbu-3 :min : :max
> key ticks true
> key ticks false
> key ticks true
> key bold true
> key bold false
> key italic true
> key italic false
> key labelSide left/top
> key labelSide right/bottom
> key border false
> key border true
> key border false
> key borderColor #bfbfbf
> key borderColor default
> key borderColor #bfbfbf
> key borderColor default
> key ylgnbu-3 :min : :max white:
> key #edf8b1:min #7fcdbb: #2c7fb8:max white: white:
> key alphafold :min : :max : :
> key ticks false
> key ticks true
> key labelColor #bfbfbf
> key labelColor default
> key alphafold :min : :max : :
> ui mousemode right "color key"
[Repeated 1 time(s)]
> key numericLabelSpacing equal
> key numericLabelSpacing proportional
> key tickLength 12.0
> key tickLength 14.0
> key tickLength 16.0
> key tickLength 18.0
> key tickLength 16.0
> key tickLength 14.0
> key tickLength 12.0
> key tickLength 10.0
> key alphafold :min : : : :
> key alphafold :min : : : :m
> key alphafold :min : : : :ma
> key alphafold :min : : : :max
> key alphafold :min : : : ":100\nto 90\n– high accuracy expected "
> key alphafold :min : : : ": high accuracy expected "
> key pos 0.140137,0.367073 size 0.019802,0.587805
> key pos 0.826352,0.419512 size 0.0228484,0.513415
> key pos 0.703732,0.426829 size 0.0243717,0.5
> key tickLength 12.0
> key tickLength 10.0
> key tickLength 8.0
> key tickLength 6.0
> key tickLength 4.0
> key tickLength 2.0
> key tickLength 4.0
> key tickLength 6.0
> key tickLength 8.0
> key tickThickness 5.0
> key tickThickness 6.0
> key tickThickness 7.0
> key tickThickness 8.0
> key tickThickness 9.0
> key tickThickness 10.0
> key tickThickness 11.0
> key tickThickness 10.0
> key tickThickness 9.0
> key tickThickness 8.0
> key tickThickness 7.0
> key tickThickness 6.0
> key tickThickness 5.0
> key tickThickness 4.0
> key tickLength 10.0
> key labelOffset 1.0
> key labelOffset 2.0
> key labelOffset 3.0
> key labelOffset 4.0
> key labelOffset 5.0
> key labelOffset 6.0
> key labelOffset 5.0
> key labelOffset 4.0
> key labelOffset 3.0
> key labelOffset 2.0
> key labelOffset 1.0
> key labelOffset 0.0
> key labelOffset -1.0
> key labelOffset -2.0
> key labelOffset -3.0
> key labelOffset -4.0
> key labelOffset -5.0
> key labelOffset -6.0
> key labelOffset -7.0
> key labelOffset -8.0
> key labelOffset -9.0
> key alphafold :min : : ":90\nto 70\n– backbone expected to be modeled well "
> ": high accuracy expected "
> key alphafold :min : : ":90-70\n– backbone expected to be modeled well " ":
> high accuracy expected "
> key alphafold :min : : ":90-70\n– backbone expected to be modeled well s" ":
> high accuracy expected "
> key alphafold :min : : ":90-70\n– backbone expected to be modeled well " ":
> high accuracy expected "
> key alphafold :min : : ":90-70\n– backbone expected to be modeled well" ":
> high accuracy expected "
> key alphafold :min : : ":90-70\n–backbone expected to be modeled well" ":
> high accuracy expected "
> key alphafold :min : : ":90-70\n–backbone expected to be modeled well"
> ":high accuracy expected "
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 19
> key fontSize 18
> key fontSize 17
> key fontSize 16
> key alphafold :min : : ":90-70\n–backbone modeled well" ":high accuracy
> expected "
> key alphafold :min : ":70\nto 50\n– low confidence, caution "
> ":90-70\n–backbone modeled well" ":high accuracy expected "
> key alphafold :min ":50\nto 0\n– should not be interpreted, may be
> disordered" ":70\nto 50\n– low confidence, caution " ":90-70\n–backbone
> modeled well" ":high accuracy expected "
> key alphafold :min ":50=0\n– should not be interpreted, may be disordered"
> ":70\nto 50\n– low confidence, caution " ":90-70\n–backbone modeled well"
> ":high accuracy expected "
> key alphafold :min ":50=0\n– should not be interpreted, may be disordered"
> ":70\nto 50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":high accuracy expected "
> key alphafold :min ":50=0\n– should not be interpreted, may be disordered"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":500\n– should not be interpreted, may be disordered"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":500\n– should not be interpreted, may be disordered-"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":500\n– should not be interpreted, may be disordered"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":50-0\n– should not be interpreted, may be disordered"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":50-0\n–should not be interpreted, may be disordered"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":50-0\n–should not be interpreted, disordered"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":50-0\n–should not be interpreted disordered"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":50-0\n–should not be interpreted disordered?"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":50-0\n–should not be interpreted disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold :min ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected "
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected "
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected 0"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected 00"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected 0"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected "
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected1"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected10"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected1"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy expected"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected0"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected00"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected0"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":1high
> accuracy expected"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":10high accuracy expected"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" :1
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" :10
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" :100
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" :100-
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" :100-9
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" :100-90
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 "
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 h"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 hi"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 hig"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high "
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high a"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high ac"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high acc"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high accu"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high accur"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high accura"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high accurac"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well"
> ":100-90 high accuracy"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":90-70\n–backbone modeled well" ":high
> accuracy"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)"
> ":70-50\n–low confidence, caution " ":backbone modeled well" ":high
> accuracy"
> key alphafold : ":50-0\n–should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key alphafold : ":should not be interpreted (disordered?)" ":low confidence,
> caution " ":backbone modeled well" ":high accuracy"
> key colorTreatment distinct
> key colorTreatment blended
> key alphafold :v ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key alphafold :ve ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key alphafold :ver ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key alphafold :very ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key alphafold ":very " ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key alphafold ":very b" ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key alphafold ":very ba" ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key alphafold ":very bad" ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> key justification left
> key labelOffset 0.0
> key pos 0.28789,0.362195 size 0.0137091,0.482927
> key pos 0.618431,0.567073 size 0.019802,0
> key pos 0.783701,0.281707 size 0.0159939,0.656098
> ui mousemode right translate
> ui mousemode right "color key"
> key pos 0.188119,0.228049 size 0.0213252,0.715854
> ui mousemode right translate
> ui mousemode right "color key"
> ui mousemode right translate
> ui mousemode right "color key"
> key pos 0.416603,0.312195 size 0.0159939,0.60122
> key pos 0.113481,0.330488 size 0.039604,0.623171
> key pos 0.364052,0.195122 size 0.0129474,0.742683
> key pos 0.179741,0.137805 size 0.0182788,0.845122
> ui mousemode right translate
> scalebar
> hide #4 models
> show #4 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> view #1
> zoom 1 #1
Expected an integer >= 1 or a keyword
> zoom 11 #1
Expected an integer >= 1 or a keyword
> zoom #1 11
Expected a number > 0 or a keyword
> view #1 clip false
> log metadata #1
The model has no metadata
> log chains #1
Chain information for
mpat2eshl_488ca_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1
---
Chain | Description
A | No description available
> ui mousemode right "color key"
> key pos 0.235339,0.0878049 size 0.0213252,0.87561
> key pos 0.116527,0.0317073 size 0.0144707,0.95122
> key pos 0.169078,0.97439 size 0.000761615,0.00121951
> key pos 0.172887,0.97561 size 0.000761615,0.00365854
> key pos 0.176695,0.0341463 size 0.0289414,0.952439
> key pos 0.239147,0.0109756 size 0.0190404,0.976829
> ui mousemode right translate
> ui mousemode right "color key"
> key pos 0.253618,0.221951 size 0.0274181,0.762195
> key pos 0.28789,0.0512195 size 0.0182788,0.919512
> key pos 0.155369,0.0597561 size 0.0327494,0.928049
> key pos 0.18888,0.054878 size 0.0228484,0.893902
> key alphafold ":very bad" ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy" white:
> key alphafold ":very bad" ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
> ui mousemode right translate
> save C:\Users\עופר\Desktop\image2.png supersample 3
> save C:\Users\עופר\Desktop\image3.png supersample 3
> view #1
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> alphafold pae #1 colorDomains true
> ui mousemode right "color key"
> key "red:very bad" "orange:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " "cornflowerblue:backbone modeled well"
> key "red:very bad" "orange:should not be interpreted (disordered?)"
> "yellow:low confidence, caution "
> key "red:very bad" "orange:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " white:
> key "red:very bad" "orange:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " white: white:
> key "red:very bad" "orange:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " white: white: white:
> key "red:very bad" "orange:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " white: white: white: white:
> key pae ":very bad" ":should not be interpreted (disordered?)" ":low
> confidence, caution " : : : :
> key paegreen ":very bad" ":should not be interpreted (disordered?)" ":low
> confidence, caution " : : : :
> key paired-7 ":very bad" ":should not be interpreted (disordered?)" ":low
> confidence, caution " : : : :
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #d7eaf8:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #f0f0f0:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #ff5500:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #f0f0f0:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2998af:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #278ca2:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2ea7c0:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #36c4e2:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #237d91:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #207586:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #35c1df:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2ea8c1:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #32b5d1:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #38cae9:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2a98af:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2fa9c3:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #32b6d2:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #34bdda:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #38cbea:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #26899e:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2a97ae:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2ea7c0:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #30afc9:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #31b3ce:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #33b7d3:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #34bad7:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #deedf9:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #cccccc:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #c881c1:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #6da5c8:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #8ec857:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #82b54f:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #f0f0f0:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #010101:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #1d6878:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #0e333b:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #1b6170:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #3fdcfe:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #ce5c00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #31b0cb:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2892a8:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #1c6675:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #39ceed:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #278ea4:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2da4bd:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #3ed9fa:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #86a3be:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #f0f0f0:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #62a4c8:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #c88952:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #f0f0f0:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #227c8f:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2ea5be:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: black:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #2ea5be:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #32b7d3:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #ac4d00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #b55100:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #ee6a00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #f56d00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #ff7500:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #ff7800:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #ff7a00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #e31a1c: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #dcecf9: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #cccccc: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #55ffff: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #6673c8: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #f0f0f0: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #ff7e00: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #164e5a: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: black: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #12424c: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #2890a6: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #2ca0b9: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: black: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #268ba0: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #2da1ba: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #32b6d2: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #33b7d3: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #fb9a99: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #daebf9: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #bfbfbf: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #c894a6: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #aec877: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: black: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #f727be: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #d10c9b: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: black: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #64064a: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #bc0b8b: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #cc0c97: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #d10c9b: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #d60c9e: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #d90da0: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #e214a9: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #33a02c: #e718ad: #35c0dd: #ff7b00:
> key pos 0.75019,0.173171 size 0.00456969,0.0695122
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #daebf9: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #cccccc: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #f0f0f0: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #7878c8: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #c8804f: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #648e13: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " black: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #6e9c15: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " black: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #679313: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #88c11a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #648e13: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #587d10: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " black: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #314509: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #80b618: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #99d91d: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " black: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #97d61c: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #90cd1b: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "#b2df8a:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#1f78b4:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#daebf9:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#cccccc:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#f0f0f0:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "black:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#6e7513:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "black:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#2f7e37:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#42b14d:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#45ba51:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#4dc659:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#53cd5f:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#4ec659:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#49c055:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#47bc52:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#45b951:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#a6cee3:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#d7eaf8:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ccccbe:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#f0f0f0:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "white:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "black:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#6d9a14:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "black:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#88c019:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "black:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ed4e99:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#e44b93:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#cf4486:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "black:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#bd3e7a:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#c74180:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#d04486:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#48182f:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "black:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#d6468a:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ea4c97:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ff57ac:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ff58ad:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#aa386e:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ff58ad:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ff5cb5:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#7f2952:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#7f2a52:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#d14487:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ff61bb:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "black:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#541b36:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#6b2345:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ff58ad:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ff58af:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#d34588:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#822a54:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#be3e7b:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ac386f:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#af3971:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "black:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ff66b9:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#cb4283:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ce4385:very bad" "#45b950:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key pos 0.104341,0.136585 size 0.0510282,0.75
> key "#ce4385:very bad" "#45b950:should not be interpreted (disordered?)"
> yellow: #89c21a: #e718ad: #35c0dd: #ff7b00:
> key "#ce4385:very bad" #45b950: yellow: #89c21a: #e718ad: #35c0dd: #ff7b00:
> key #ce4385: #45b950: yellow: #89c21a: #e718ad: #35c0dd: #ff7b00:
> key border true
> key border false
> key borderColor #bfbfbf
> key borderColor default
> key colorTreatment distinct
> view #1
> key delete
> ui mousemode right translate
> save C:\Users\עופר\Desktop\image4.png supersample 3
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> ui mousemode right "color key"
> key blue-white-red :min : :max white:
> key blue:min white: red:max white: white:
> key "#a6cee3:very bad" "#49c055:should not be interpreted (disordered?)"
> "yellow:low confidence, caution " #89c21a: #e718ad: #35c0dd: #ff7b00:
> key alphafold ":very bad" ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy" white:
> key alphafold ":very bad" ":should not be interpreted (disordered?)" ":low
> confidence, caution " ":backbone modeled well" ":high accuracy"
[Repeated 1 time(s)]
> key pos 0.194212,0.0365854 size 0.0266565,0.930488
> key justification left
> key pos 0.0685453,0.0439024 size 0.0236101,0.920732
> ui mousemode right translate
> save C:\Users\עופר\Desktop\image5.png supersample 3
> alphafold pae #1 colorDomains true
> hide #5 models
> save C:\Users\עופר\Desktop\image6.png supersample 3
> show #5 models
> color bfactor #1 palette alphafold
14222 atoms, 921 residues, atom bfactor range 20.4 to 96.3
> save C:\Users\עופר\Desktop\image7.png supersample 3
> ui mousemode right "color key"
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 19
> key fontSize 18
> key numericLabelSpacing equal
> key numericLabelSpacing proportional
> ui mousemode right translate
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> show #2.1 models
> hide #2.1 models
> save C:\Users\עופר\Desktop\image8.png supersample 3
> open "C:/Users/עופר/Dropbox/LAB_staff/HKR/alignment/MPAT-to-ESHL
> B/template/7jc3.pdb"
7jc3.pdb title:
Crystal structure of the transmembrane domain of salpingoeca rosetta rhodopsin
phosphodiesterase [more info...]
Chain information for 7jc3.pdb #6
---
Chain | Description | UniProt
A | phosphodiesterase | F2TZN0_SALR5
Non-standard residues in 7jc3.pdb #6
---
RET — retinal
> ui tool show Matchmaker
> matchmaker #1 to #6
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 7jc3.pdb, chain A (#6) with
mpat2eshl_488ca_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#1), sequence alignment score = 463
RMSD between 135 pruned atom pairs is 1.117 angstroms; (across all 254 pairs:
3.424)
> select #1:1-300
4879 atoms, 4945 bonds, 300 residues, 1 model selected
> select #1:1-290
4717 atoms, 4781 bonds, 290 residues, 1 model selected
> select #1:1-280
4536 atoms, 4600 bonds, 280 residues, 1 model selected
> select #1:1-270
4373 atoms, 4437 bonds, 270 residues, 1 model selected
> select #1:1-260
4186 atoms, 4250 bonds, 260 residues, 1 model selected
> transparency #1:1-260 60 cartoons
> select clear
> transparency #1:1-260 0 cartoons
> transparency :1-260 60 cartoons
> transparency :1-260,#6 60 cartoon
Missing or invalid "percent" argument: Expected a number
> transparency :1-260 #6 60 cartoons
> color :RET magenta
> color :RET #6:296 magenta
> color :RET #6:296 byhetero
> color #6 cartoon #d3d3d3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #6 #d3d3d3
> color :RET #6:296 byhetero
> color :RET #6:296 magenta
> color #6 #d3d3d3 cartoons
> color :RET #6:296 byhetero
> hide #6 atoms
> show :RET #6:296
> select clear
> show #6:296:<1 atoms
> select #6:296:<1
38 atoms, 36 bonds, 3 residues, 2 models selected
> color sel byhetero
> select clear
> save C:\Users\עופר\Desktop\image1.png supersample 3
> save C:\Users\עופר\Desktop\image2.png supersample 3
> save C:\Users\עופר\Desktop\image1.png supersample 3
> transparency #1:1-260 #6 90 cartoons
> transparency #1:1-260 #6 80 cartoons
QWindowsWindow::setGeometry: Unable to set geometry 431x318+735-724 (frame:
447x357+727-755) on QWidgetWindow/"QFileDialogWindow" on "\\\\.\DISPLAY2".
Resulting geometry: 431x342+735-724 (frame: 447x381+727-755) margins: 8, 31,
8, 8 minimum size: 363x318 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=379,
y=357)))
> save "C:/Users/עופר/Dropbox/LAB_staff/HKR/alignment/MPAT-to-ESHL
> B/rank1/rank1.cxs" includeMaps true
> select ::name="ASP"
608 atoms, 558 bonds, 54 residues, 2 models selected
> select up
8440 atoms, 8496 bonds, 626 residues, 2 models selected
> select down
608 atoms, 558 bonds, 54 residues, 2 models selected
> select down
608 atoms, 558 bonds, 54 residues, 2 models selected
> select clear
> select :AS*,GL*
3071 atoms, 2866 bonds, 281 residues, 2 models selected
> show sel cartoons
> show sel atoms
> color sel byhetero
> select clear
> hide cartoons
> size sel stickRadius 0.1
Changed 0 bond radii
> select :AS*,GL*
3071 atoms, 2866 bonds, 281 residues, 2 models selected
> size sel stickRadius 0.1
Changed 2866 bond radii
> select clear
> select down
Nothing selected
> hide sel
> select :AS*,GL*
3071 atoms, 2866 bonds, 281 residues, 2 models selected
> hide sel
> select up
14578 atoms, 14739 bonds, 1077 residues, 2 models selected
> select down
3071 atoms, 2866 bonds, 281 residues, 2 models selected
> select :RET:AS*,GL*<5
Expected an objects specifier or a keyword
> select :RET:<5&:AS*,GL*
64 atoms, 56 bonds, 8 residues, 2 models selected
> show sel
> hide #6 models
> show #6 models
> show cartoons
> hide cartoons
> select clear
> select :RET:<10&:AS*,GL*
182 atoms, 162 bonds, 21 residues, 2 models selected
> show sel
> hide sel
> select :RET:<8&:AS*,GL*
100 atoms, 88 bonds, 13 residues, 2 models selected
> show sel
> select up
1844 atoms, 1875 bonds, 192 residues, 2 models selected
> select down
100 atoms, 88 bonds, 13 residues, 2 models selected
> select :RET:<8&:AS*,GL*,his,lys,arg
210 atoms, 193 bonds, 20 residues, 2 models selected
> show sel
> select clear
> color sel byhetero
> select :RET:<8&:AS*,GL*,his,lys,arg
210 atoms, 193 bonds, 20 residues, 2 models selected
> color sel byhetero
> select clear
> select sel
Nothing selected
> select :RET:<8&:AS*,GL*,his,lys,arg
210 atoms, 193 bonds, 20 residues, 2 models selected
> select sel
104 atoms, 93 bonds, 13 residues, 1 model selected
> color sel&@C* gray
> select clear
> select :RET:<8&:AS*,GL*,his,lys,arg
210 atoms, 193 bonds, 20 residues, 2 models selected
> size sel stickRadius 0.1
Changed 193 bond radii
> select clear
> select :RET:<8&:AS*,GL*,his,lys,arg
210 atoms, 193 bonds, 20 residues, 2 models selected
> label
[Repeated 1 time(s)]
> ui mousemode right label
> label #1/A:143
> label #6/A:218
> label #6/A:194
> label #6/A:200
> label #1/A:150
> label #6/A:201
> label delete residues
[Repeated 1 time(s)]
> label #6/A:271
[Repeated 1 time(s)]
> label #6/A:201
> label #1/A:150
> label #6/A:218
> label #6/A:194
> label #1/A:143
> label delete residues
[Repeated 4 time(s)]
> select :RET:<8&:AS*,GL*,his,lys,arg
210 atoms, 193 bonds, 20 residues, 2 models selected
> label sel
> select clear
> select :RET:<8&:AS*,GL*,his,lys,arg
104 atoms, 93 bonds, 13 residues, 1 model selected
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> select clear
> color #6.1 #b69effff models
> color #6.1 #ac9dffff models
> color #6.1 black models
> color #6.1 #5f5f5fff models
> color #6.1 #4c4c4cff models
> color #6.1 #343434ff models
> color #6.1 #353535ff models
> color #6.1 #3a3a3aff models
> color #1.1 #5555ffff models
> color #1.1 #0055ffff models
> color #1.1 #55557fff models
> color #1.1 #5500ffff models
> set bgColor white
> set bgColor #ffffff00
> label delete residues
[Repeated 1 time(s)]
> select :RET:<8&:AS*,GL*,his,lys,arg
210 atoms, 193 bonds, 20 residues, 2 models selected
> label sel
> ui mousemode right translate
> select clear
> color #1.1 #5555ffff models
> color #1.1 #0055ffff models
> ui mousemode right "move label"
> color #6.1 #070707ff models
> color #6.1 black models
> color #6.1 #303030ff models
> color #6.1 #aaff00ff models
> color #6.1 black models
> color #6.1 #181818ff models
> color #6.1 #2b2b2bff models
> save C:\Users\עופר\Desktop\image1.png supersample 3
> select :RET:<8&:AS*,GL*,his,lys,arg
210 atoms, 193 bonds, 20 residues, 2 models selected
> hide sel
> select :RET:<8&:AS*,GLU,GLH,his,lys,arg
184 atoms, 170 bonds, 15 residues, 2 models selected
> show sel
> select clear
> select :asn
462 atoms, 426 bonds, 36 residues, 2 models selected
> hide :asn
> select clear
> select :RET:<8&:ASP,ASH,GLU,GLH,his,lys,arg
176 atoms, 163 bonds, 14 residues, 2 models selected
> show sel
> select clear
> save C:\Users\עופר\Desktop\image2.png supersample 3
> save C:\Users\עופר\Desktop\image3.png supersample 3
> select :RET:<8&:ASP,ASH,GLU,GLH,his,lys,arg
176 atoms, 163 bonds, 14 residues, 2 models selected
> info residues sel
residue id #1/A:110 name ARG index 109
residue id #1/A:143 name ASP index 142
residue id #1/A:222 name LYS index 221
residue id #1/A:239 name ASP index 238
residue id #1/A:243 name LYS index 242
residue id #6/A:130 name ASP index 98
residue id #6/A:161 name ARG index 129
residue id #6/A:164 name GLU index 132
residue id #6/A:194 name ASP index 162
residue id #6/A:271 name GLU index 239
residue id #6/A:274 name ARG index 242
residue id #6/A:275 name ARG index 243
residue id #6/A:292 name ASP index 260
residue id #6/A:296 name LYS index 264
> hide #5 models
> hide #2.1 models
> select clear
> set bgColor black
> set bgColor transparent
> set bgColor black
> color #6.1 #dededeff models
> color #6.1 #d8d8d8ff models
> hide #2.1 models
> save C:\Users\עופר\Desktop\image1.png supersample 3
> save C:\Users\עופר\Desktop\image2.png supersample 3
> show cartoons
> select clear
> save "C:/Users/עופר/Dropbox/LAB_staff/HKR/alignment/MPAT-to-ESHL
> B/rank1/rank1.cxs"
——— End of log from Tue Sep 19 18:43:44 2023 ———
opened ChimeraX session
> hide #!2 models
> show :RET:<8&~:RET
> hide :RET:<8&~:RET
> show :RET:<8&:his,lys,arg,ASP,ASH,GLU,GLH
> label delete :GLY
> show #1:271:<1
> show #1:271:<1 atoms
> hide #1:271:<1 atoms
> show #6:271:<1 atoms
> label #6:271:<1 residues
> color #1.1 #0167ffff models
> color #1.1 #033affff models
> color #1.1 #0346ffff models
> color #1.1 #0374ffff models
> color #1.1 #a7b3ffff models
> color #1.1 #8293ffff models
> color #1.1 #829fffff models
> color #1.1 #4f5bffff models
> color #1.1 #4f78ffff models
> color #1.1 #0a53ffff models
> color #1.1 #0f57ffff models
> color #1.1 #0f4fffff models
> color #1.1 #504fffff models
> color #1.1 #084fffff models
> color #1.1 #284fffff models
> color #1.1 #2828ffff models
> color #1.1 #2850ffff models
> color #1.1 #5050ffff models
> color #1.1 #0c1cffff models
> color #1.1 #0167ffff models
> size ~:RET stickRadius 0.1
Changed 16447 bond radii
> show #6:130,164,274,288:<1
> label #6:130,164,274,288:<1
> color #1.1 #0167ffff models
> select #6:130,164,274,288:<1
159 atoms, 152 bonds, 11 residues, 2 models selected
> select clear
> hide #1:234 atoms
> label delete #1:234
> select clear
> hide cartoons
> show cartoons
> transparency 90 cartoons
> ui mousemode right "move label"
> ui mousemode right translate
> hide cartoons
Drag select of 315 atoms, 302 bonds
> color sel byhetero
> show cartoons
> select clear
> hide sel@H* atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel&@H* atoms
> hide cartoons
Drag select of 315 atoms, 302 bonds
> select up
2491 atoms, 2522 bonds, 214 residues, 2 models selected
> select down
315 atoms, 302 bonds, 22 residues, 2 models selected
> select clear
Drag select of 315 atoms, 302 bonds
> hide sel@H* atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel&@H* atoms
> show cartoons
> select #1/A:84
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> color #6.1 gray models
> color #6.1 white models
> color #6.1 lightgray models
> select #1/A:220
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> label delete #1:220
> select clear
> ui mousemode right "move label"
> ui mousemode right translate
> ui tool show Distances
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\struct_measure\tool.py", line 626, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\struct_measure\tool.py", line 626, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 451.91
OpenGL renderer: GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: he_IL.cp65001
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: UX331UN
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 17,029,578,752
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: he-IL
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
argcomplete: 3.0.8
asttokens: 2.1.0
attrs: 23.1.0
Babel: 2.11.0
backcall: 0.2.0
basis-set-exchange: 0.9
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jsonschema: 4.17.3
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
pyrsistent: 0.19.3
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
regex: 2023.3.23
requests: 2.28.1
scipy: 1.9.0
Send2Trash: 1.8.0
SEQCROW: 1.8.1
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Struct Measure: wrapped C/C++ object of type QLabel has been deleted |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Ofer,
--Eric