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#5525 closed defect (fixed)
Morph problem
| 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 (5)
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 |
comment:2 by , 4 years ago
This ChimeraX error running the morph command with the "same true" option is because the two structures have no residues in common. Either the chain ids or residue numbers are different. Here is the documentation about the "same true" option which assumes the chain ids and residue numbers are identical in the two structures:
"The same option indicates that the input structures have the same sequences, atom names, residue numbering, and chain IDs, as is typically the case for members of an NMR ensemble (default false, atoms paired as described below). Setting this option to true may make the calculation slightly faster, but otherwise there is little harm in staying with the default if there is any doubt as to whether numbering/naming are the same."
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#same
I will fix ChimeraX so it gives a clear error message when this happens.
comment:3 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed in ChimeraX 1.3 and 1.4 daily build.
Morph code was checking for no atoms being paired but the check did not work because Structure.deleted returned false because the C++ layer deleted the structure since it had no atoms but the Python code is never told. Will make a separate ticket to address this underlying problem. As a quick fix I made the Structure.deleted method test if the C++ side was deleted.
follow-up: 4 comment:4 by , 4 years ago
Hi Tom! Thanks for the quick response. I didn't realize i was trying to morph two ortholongs! Thanks for the help! Arnold On Tue, Nov 2, 2021 at 4:05 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
follow-up: 5 comment:5 by , 4 years ago
If you leave out the "same true" morph option then it will do a sequence alignment to pair the residues. You only use the "same true" option if you want to avoid that sequence alignment step because you know the same residue numbering is used.
Note:
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for help on using tickets.
Reported by Arnold Muccini
May be easier to debug in daily build, where 'property' attribute errors give proper traceback.