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Opened 4 years ago
Last modified 4 years ago
#5525 closed defect
Morph problem — at Version 1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)Im trying to do a morph
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/figures.cxs
Log from Mon Oct 11 14:17:43 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> dep/closed_dimer-FINAL.ccp4
Opened closed_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
level 1.11, step 2, values float32
> volume #1 level 10.07
> volume #1 step 1
> set bgColor white
> lighting soft
> open
> C:/local_data/Cornell/research/fromme_lab/11_CryoEM/model_building/ScGea2/closed/dimer/closed_dimer-
> coot-1.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/11_CryoEM/model_building/ScGea2/closed/dimer/closed_dimer-
coot-1.pdb
---
warning | Ignored bad PDB record found on line 39765
END
Chain information for closed_dimer-coot-1.pdb #2
---
Chain | Description
A B | No description available
> hide #!1 models
> close session
[had to delete a substantial portion of the log to make it fit the ticket length; hopefully available in the diff. I can dredge it from my mail if necessary -- Eric]
> hide #59 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/1r8s.pdb C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
1r8s.pdb title:
ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the
catalytic glutamate to lysine [more info...]
Chain information for 1r8s.pdb #60
---
Chain | Description
A | adp-ribosylation factor 1
E | ARNO
Non-standard residues in 1r8s.pdb #60
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #61
---
Chain | Description
A B | No description available
> mmaker #60 to #61
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 closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#61)
with 1r8s.pdb, chain E (#60), sequence alignment score = 432.1
RMSD between 115 pruned atom pairs is 1.246 angstroms; (across all 185 pairs:
5.093)
> select #59/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> select #59
42850 atoms, 42862 bonds, 3148 residues, 1 model selected
> select #60/A
1471 atoms, 1345 bonds, 312 residues, 1 model selected
> select #60/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #61
39644 atoms, 39958 bonds, 2444 residues, 1 model selected
> ~select #61
Nothing selected
> select #60
1471 atoms, 1345 bonds, 312 residues, 1 model selected
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/arf1-closed.pdb models #60 relModel #61
> hide #61 models
> hide #60 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
arf1-morph.pdb
---
warning | Ignored bad PDB record found on line 41274
END
Chain information for closed-arf1-morph.pdb #62
---
Chain | Description
A B | No description available
C | No description available
> show #59 models
> morph #62,59 same true
Computed 21 frame morph #63
> coordset #63 1,21
> ~select #60
Nothing selected
> hide #63 models
> show #63 models
> hide #63 models
> show #62 models
> show #59 models
> hide #59 models
> hide #62 models
> show #62 models
> show #!56 models
> mmaker #62 to #56
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 complex-morph.pdb, chain A (#56) with closed-arf1-morph.pdb, chain
A (#62), sequence alignment score = 5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> morph #62,56 same true
Computed 21 frame morph #64
> coordset #64 1,21
> show #!56 models
> hide #!56,64 atoms
> hide #!56 models
> show #62 models
> hide #62#!64 cartoons
> show #62#!64 cartoons
> hide #62#!64 atoms
> hide #62 models
> hide #!64 models
> show #55 models
> show #50 models
> hide #50 models
> show #52 models
> hide #52 models
> select #55
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> ~select #55
Nothing selected
> show #!57 models
> hide #!57 models
> show #50 models
> hide #50 models
> show #39 models
> hide #55 models
> show #55 models
> coordset slider
Missing or invalid "structures" argument: empty atom specifier
> coordset slider#55
Missing or invalid "structures" argument: invalid structures specifier
> coordset slider #55
> hide #55 models
> hide #39 models
> show #!64 models
> coordset slider #64
> movie record
> movie record
Already recording a movie
> movie stop
> new
Unknown command: movie new
> movie reset
> start
Unknown command: movie start
> movie record
> movie stop
> movie encode
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> show #55 models
> show #50 models
> hide #50 models
> show #39 models
> hide #55 models
> show #55 models
> hide #55 models
> show #55 models
> hide #!64 models
> hide #39 models
> show #!64 models
> hide #55 models
> select #64
19783 atoms, 20100 bonds, 8 pseudobonds, 2466 residues, 2 models selected
> ~select #64
Nothing selected
> select #64 ::name="GDP"
Nothing selected
> show #!64 atoms
> hide #!64 atoms
> hide #!64 models
> show #62 models
> select #62 ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> move #62 ::name="GDP"
Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 28
atoms
> move x 5 #62 ::name="GDP"
Expected an integer >= 1 or a keyword
> move x 5 #62 ::name="GDP"
Expected an integer >= 1 or a keyword
> move x +5 #62 ::name="GDP"
Expected an integer >= 1 or a keyword
> move x 05 #62 ::name="GDP"
Expected an integer >= 1 or a keyword
> move x 0 5 #62 ::name="GDP"
Expected a keyword
> move x -2 10 #62 ::name="GDP"
Expected a keyword
> move x -2 10 #62
Expected a keyword
> move x -2 10 #62
Expected a keyword
> move x #62 ::name="GDP"
Expected a number or a keyword
> move x #62
Expected a number or a keyword
> move x #62
Expected a number or a keyword
> move y #64 ::name="GDP"
Expected a number or a keyword
> move y models #64 ::name="GDP"
> move y models #64 ::name="GDP"
> move y models #64 ::name="GDP"
> move y models #64 ::name="GDP"
> move y #64 ::name="GDP"
Expected a number or a keyword
> move y atoms #64 ::name="GDP"
> move y atoms #64::name="GDP"
> move y #64::name="GDP"
Expected a number or a keyword
> move y #64
Expected a number or a keyword
> move y 5 #64
Expected an integer >= 1 or a keyword
> move y 5 models #64
> move y atoms #64
> show #!64 models
> hide #!64 models
> move y atoms #62
> move y 10 atoms #62 ::name="GDP"
> move y -10 atoms #62 ::name="GDP"
> select #62/C:131
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show #!64 models
> hide #!64 models
> show #63 models
> hide #63 models
> show #63 models
> hide #63 models
> undo
> undo
> undo
> undo
> undo
> undo
> show #!64 models
> hide #!64 models
> hide #62 models
> show #!64 models
> show #63 models
> hide #63 models
> show #!58 models
> hide #!58 models
> show #55 models
> select #55/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> hide sel cartoons
> preset cartoons/nucleotides cylinders/stubs
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
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
> ui tool show "Show Sequence Viewer"
> sequence chain #64/C
Alignment identifier is 64/C
> color sel #788ae1ff
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #64/A
Alignment identifier is 64/A
> sequence chain #64/B
Alignment identifier is 64/B
> color sel #f8e266ff
> color sel #e7c3afff
> select clear
> select #64/A:756
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #aa0000ff
> color sel #8fc3faff
> select clear
> color sel #f8e266ff
> color sel #e7c3afff
> color sel #8fc3faff
> select clear
> coordset #64 1,21
> select #64 ::name="GDP"
Nothing selected
> hide #!64 models
> show #63 models
> show #!58 models
> hide #!58 models
> hide #63 models
> hide #55 models
> show #55 models
> show #39 models
> coordset #55 1,21
> wait
wait requires a frame count argument unless motion is in progress
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> show #55 models
> select #55/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!64 models
> show #39 models
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> show #39 models
> mmaker #39 to #64 bring #55
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 Morph - closed-arf1-morph.pdb, chain A (#64) with closed_dimer-
FINAL-coot-3_real_space_refined_206.pdb, chain A (#39), sequence alignment
score = 5834
RMSD between 753 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.351)
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> movie stop
> movie encode
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #!64 models
> show #54 models
> show #55 models
> hide #54 models
> show #39 models
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> movie stop
> movie encode
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #!64 models
> show #55 models
> show #39 models
> start
Unknown command: movie start
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> movie stop
> movie encode
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> movie encode
No frames have been recorded
> hide #!64 models
> show #39 models
> show #55 models
> start
Unknown command: movie start
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> show #60 models
> hide #60 models
> show #!31 models
> show #31.7 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
> Arf1-morph.pdb models #31 relModel #64
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
> Arf1-morph.pdb models #31 relModel #62
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
> Arf1-morph.pdb models #31 relModel #56
> show #!56 models
> hide #!56 models
> hide #!64 models
> show #!64 models
> hide #!64 models
> hide #!31 models
> hide #31.7 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex-morph_GTP-Arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
morph_GTP-Arf1-morph.pdb
---
warning | Ignored bad PDB record found on line 23604
END
Chain information for complex-morph_GTP-Arf1-morph.pdb #65
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex-morph_GTP-Arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
morph_GTP-Arf1-morph.pdb
---
warning | Ignored bad PDB record found on line 23604
END
Chain information for complex-morph_GTP-Arf1-morph.pdb #66
---
Chain | Description
A | No description available
B | No description available
C | No description available
> movie stop
> hide #66 models
> close #66
> show #61 models
> mmaker #65 to #61
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 closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#61)
with complex-morph_GTP-Arf1-morph.pdb, chain A (#65), sequence alignment score
= 5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> hide #61 models
> select #65
22979 atoms, 23333 bonds, 2670 residues, 1 model selected
> ~select #65
Nothing selected
> select #65
22979 atoms, 23333 bonds, 2670 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> cartoon style (sel & coil) xsection oval
> cartoon style sel xsection barbell modeHelix default
> cartoon style sel modeHelix tube sides 20
> select clear
> hide #65 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #65/A
Alignment identifier is 65/A
> sequence chain #65/B
Alignment identifier is 65/B
> sequence chain #65/C
Alignment identifier is 65/C
> select #65/C
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select clear
Drag select of 1 residues
> color sel #f8e266ff
> color sel #8fc3faff
> color sel #f8e266ff
Drag select of 7 residues
> color sel #e7c3afff
> color sel #788ae1ff
> color sel #e7c3afff
> color sel #8fc3faff
> select clear
> color sel #2e79abff
> color sel #8fc3faff
> color sel #788ae1ff
> select clear
> show #!56 models
> hide #!56 models
> show #!56 models
> morph #56,65 same true
Computed 21 frame morph #66
> coordset #66 1,21
> movie record
> movie encode C:\Users\Arnold/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> close #66
> show #!56 models
> show #65 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
morph.pdb
---
warning | Ignored bad PDB record found on line 19939
END
Chain information for complex-morph.pdb #66
---
Chain | Description
A B | No description available
C | No description available
> select #66/A
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!66 & sel)
> delete bonds (#!66 & sel)
> select #66/B
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!66 & sel)
> delete bonds (#!66 & sel)
> hide #!56 models
Drag select of 165 residues
> cartoon style sel modeHelix tube sides 20
> color sel #e7c3afff
> color sel #788ae1ff
> mmaker #66 to #65
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 complex-morph_GTP-Arf1-morph.pdb, chain A (#65) with complex-
morph.pdb, chain C (#66), sequence alignment score = 642.9
RMSD between 114 pruned atom pairs is 1.192 angstroms; (across all 165 pairs:
4.069)
> select clear
> show #31.7 models
> hide #!66 models
> hide #65 models
> show #65 models
> hide #65 models
> show #!66 models
> moprh #66 to #31.7
Unknown command: moprh #66 to #31.7
> morph #66 to #31.7
Expected a keyword
> morph #66 to #31.7 same true
Expected a keyword
> morph #66,31.7 same true
Require at least 2 structures for morph
> morph #66,31 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> morph #66,31 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> hide #31.7#!66 atoms
> morph #66,31 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2ksq.pdb
2ksq.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2ksq.pdb
---
Chain | Description
67.1/A | adp-ribosylation factor 1
67.2/A 67.3/A 67.4/A 67.5/A 67.6/A 67.7/A 67.8/A 67.9/A 67.10/A 67.11/A
67.12/A 67.13/A 67.14/A 67.15/A 67.16/A 67.17/A 67.18/A 67.19/A 67.20/A | adp-
ribosylation factor 1
> close #67.1-6
> close #67.8-20
> select #67.7 ::name="GDP"
Nothing selected
> select #67.7 ::name="GTP"
43 atoms, 45 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!31 models
> hide #31.7 models
> mmaker #67 to #66
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 complex-morph.pdb, chain C (#66) with 2ksq.pdb, chain A (#67.7),
sequence alignment score = 642.9
RMSD between 114 pruned atom pairs is 1.192 angstroms; (across all 165 pairs:
4.069)
> hide #67.7#!66 cartoons
> show #67.7#!66 cartoons
> hide #67.7#!66 atoms
> cartoon style #66-67 modeHelix tube sides 20
> morph #66,67
Computed 21 frame morph #68
> coordset #68 1,21
> hide #!68 models
> show #67.7 models
> show #!66 models
> hide #!66 models
> show #!66 models
> hide #!66 models
> morph #66,67 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> show #!68 models
> morph #66,67 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1660/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: OriginPC
Model: NEURON
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 17,093,591,040
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9600K CPU @ 3.70GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (1)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Comparison |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Morph problem |
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Reported by Arnold Muccini
May be easier to debug in daily build, where 'property' attribute errors give proper traceback.