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)
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/moprh.cxs
Log from Fri Nov 5 12:06:34 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-
> 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 #1
---
Chain | Description
A B | No description available
C | No description available
> set bgColor white
> lighting soft
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/compled-FIXED-coot-0.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/compled-
FIXED-coot-0.pdb
---
warning | Ignored bad PDB record found on line 21237
END
Chain information for compled-FIXED-coot-0.pdb #2
---
Chain | Description
A C | No description available
B | No description available
D | No description available
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed-arf1-morph.pdb, chain A (#1) with compled-FIXED-coot-0.pdb,
chain A (#2), sequence alignment score = 5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> select #2/D
1311 atoms, 1334 bonds, 2 pseudobonds, 164 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> morph #1,2 same true
Computed 21 frame morph #3
> coordset #3 1,21
> close #3
> show #!2 models
> show #1 models
> select #1/C#2/C
10772 atoms, 10794 bonds, 22 pseudobonds, 1471 residues, 3 models selected
> select clear
> close #2
> 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 19926
END
Chain information for complex-morph.pdb #2
---
Chain | Description
A B | No description available
C | No description available
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed-arf1-morph.pdb, chain A (#1) with complex-morph.pdb, chain A
(#2), sequence alignment score = 5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> morph #1,2 same true
Computed 21 frame morph #3
> coordset #3 1,21
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/1r8s.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 #4
---
Chain | Description
A | adp-ribosylation factor 1
E | ARNO
Non-standard residues in 1r8s.pdb #4
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
> mmaker #4 to #3/C
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 C (#3) with 1r8s.pdb, chain A
(#4), sequence alignment score = 831.5
RMSD between 160 pruned atom pairs is 0.001 angstroms; (across all 160 pairs:
0.001)
> select #4/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #4#!3 atoms
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/1r8s.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 #5
---
Chain | Description
A | adp-ribosylation factor 1
E | ARNO
Non-standard residues in 1r8s.pdb #5
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
> mmaker #5 to #4
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 1r8s.pdb, chain A (#4) with 1r8s.pdb, chain A (#5), sequence
alignment score = 846.2
RMSD between 160 pruned atom pairs is 0.000 angstroms; (across all 160 pairs:
0.000)
> hide #4-5#!3 atoms
> select #5
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> ui mousemode right "translate selected models"
> morph #4,5 same true
Computed 21 frame morph #6
> coordset #6 1,21
> close #6
> morph #5,4 same true
Computed 21 frame morph #6
> coordset #6 1,21
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/1r8s.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 #7
---
Chain | Description
A | adp-ribosylation factor 1
E | ARNO
Non-standard residues in 1r8s.pdb #7
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
> mmaker #7 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 Morph - 1r8s.pdb, chain A (#6) with 1r8s.pdb, chain A (#7),
sequence alignment score = 846.2
RMSD between 160 pruned atom pairs is 0.000 angstroms; (across all 160 pairs:
0.000)
> hide #!3 models
> hide #6 models
> ~select #5
Nothing selected
> hide #7 atoms
> select #7/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #7 atoms
> hide #7 atoms
> show #7 ::name="GDP"
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> delete atoms sel
> delete bonds sel
> delete atoms sel
> delete bonds sel
> show #!3 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/1r8s.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 #8
---
Chain | Description
A | adp-ribosylation factor 1
E | ARNO
Non-standard residues in 1r8s.pdb #8
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
> mmaker #8 to #7
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> mmaker #8 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 Morph - 1r8s.pdb, chain A (#6) with 1r8s.pdb, chain A (#8),
sequence alignment score = 846.2
RMSD between 160 pruned atom pairs is 0.000 angstroms; (across all 160 pairs:
0.000)
> select #8
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> morph #7,8 same true
Computed 21 frame morph #9
> coordset #9 1,21
> hide #!3 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 19926
END
Chain information for complex-morph.pdb #10
---
Chain | Description
A B | No description available
C | No description available
> mmaker #10 to #2
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 (#2) with complex-morph.pdb, chain A
(#10), sequence alignment score = 5965.7
RMSD between 1159 pruned atom pairs is 0.000 angstroms; (across all 1159
pairs: 0.000)
> select #10/A
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> select #10/C
1320 atoms, 1344 bonds, 165 residues, 1 model selected
> select #10/B
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2KSQ-7.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/2KSQ-7.pdb
---
warnings | Ignored bad PDB record found on line 3843
END
Cannot find LINK/SSBOND atom SG in residue MTN /A:182
Cannot find LINK/SSBOND atom SG in residue MTN /A:183
Cannot find LINK/SSBOND atom SG in residue MTN /A:184
Cannot find LINK/SSBOND atom SG in residue MTN /A:185
Cannot find LINK/SSBOND atom SG in residue MTN /A:186
2KSQ-7.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2KSQ-7.pdb #11
---
Chain | Description
A | adp-ribosylation factor 1
Non-standard residues in 2KSQ-7.pdb #11
---
GTP — guanosine-5'-triphosphate
MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]
methanesulfonothioate (MTSL)
MYR — myristic acid
> mmaker #11 to #10
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 (#10) with 2KSQ-7.pdb, chain A (#11),
sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> hide #9,11#!10 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #10/C
Alignment identifier is 10/C
> sequence chain #11/A
Alignment identifier is 11/A
> delete atoms sel
> delete bonds sel
> morph #10,11 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 #10,11
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 111, in interpolate
results = segment.segmentHingeExact(sm, m, cf, mhs, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\segment.py", line 109, in segmentHingeExact
% (s0.name, cid0, len(r0list), s1.name, cid1, len(r1list)))
chimerax.morph.segment.AtomPairingError: Morph - complex-morph.pdb chain C
(165) and 2KSQ-7.pdb chain A (172) have different number of residues
During handling of the above exception, another exception occurred:
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 114, in interpolate
results = segment.segmentHingeApproximate(sm, m, cf, mhs, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\segment.py", line 158, in segmentHingeApproximate
m1map = dict((s.chain.chain_id, s) for s in m1seqs)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\segment.py", line 158, in <genexpr>
m1map = dict((s.chain.chain_id, s) for s in m1seqs)
AttributeError: 'NoneType' object has no attribute 'chain_id'
AttributeError: 'NoneType' object has no attribute 'chain_id'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\segment.py", line 158, in
m1map = dict((s.chain.chain_id, s) for s in m1seqs)
See log for complete Python traceback.
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
> Arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
Arf1-morph.pdb
---
warnings | Ignored bad PDB record found on line 3130
END
Start residue of secondary structure not found: HELIX 1 1 GLY A 2 ASN A 11 1
10
Start residue of secondary structure not found: HELIX 2 2 LEU A 12 GLY A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 GLY A 29 GLY A 40 1
12
Start residue of secondary structure not found: HELIX 4 4 GLN A 71 SER A 76 1
6
Start residue of secondary structure not found: HELIX 5 5 LEU A 77 TYR A 81 1
5
11 messages similar to the above omitted
Cannot find LINK/SSBOND residue MYR (1 )
Cannot find LINK/SSBOND residue CYS (55 )
Cannot find LINK/SSBOND residue CYS (59 )
Cannot find LINK/SSBOND residue CYS (83 )
Cannot find LINK/SSBOND residue CYS (117 )
1 messages similar to the above omitted
GTP-Arf1-morph.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for GTP-Arf1-morph.pdb #12
---
Chain | Description
D | No description available
> mmaker #12 to #11
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 2KSQ-7.pdb, chain A (#11) with GTP-Arf1-morph.pdb, chain D (#12),
sequence alignment score = 877.5
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> ui tool show "Show Sequence Viewer"
> sequence chain #12/D
Alignment identifier is 12/D
No statusbar messages will be shown due to inadequate OpenGL
> close #11
> delete atoms sel
> delete bonds sel
> morph #10,12 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 #10,12
Computed 21 frame morph #11
> coordset #11 1,21
> show #!3 models
> hide #!3 models
> show #!10 models
> hide #9 models
> hide #!11 models
> hide #!10 models
> show #!2 models
> show #12 models
> hide #12 models
> show #!11 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2KSQ-7.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/2KSQ-7.pdb
---
warnings | Ignored bad PDB record found on line 3843
END
Cannot find LINK/SSBOND atom SG in residue MTN /A:182
Cannot find LINK/SSBOND atom SG in residue MTN /A:183
Cannot find LINK/SSBOND atom SG in residue MTN /A:184
Cannot find LINK/SSBOND atom SG in residue MTN /A:185
Cannot find LINK/SSBOND atom SG in residue MTN /A:186
2KSQ-7.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2KSQ-7.pdb #13
---
Chain | Description
A | adp-ribosylation factor 1
Non-standard residues in 2KSQ-7.pdb #13
---
GTP — guanosine-5'-triphosphate
MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]
methanesulfonothioate (MTSL)
MYR — myristic acid
> mmaker #13 to #12
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 GTP-Arf1-morph.pdb, chain D (#12) with 2KSQ-7.pdb, chain A (#13),
sequence alignment score = 880.5
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> hide #!11 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #13/A
Alignment identifier is 13/A
> delete atoms sel
> delete bonds sel
> delete atoms sel
> delete bonds sel
Drag select of 39 atoms, 38 bonds
> delete atoms sel
> delete bonds sel
Drag select of 36 atoms, 36 bonds
> delete atoms sel
> delete bonds sel
> show #12 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2KSQ-7.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/2KSQ-7.pdb
---
warnings | Ignored bad PDB record found on line 3843
END
Cannot find LINK/SSBOND atom SG in residue MTN /A:182
Cannot find LINK/SSBOND atom SG in residue MTN /A:183
Cannot find LINK/SSBOND atom SG in residue MTN /A:184
Cannot find LINK/SSBOND atom SG in residue MTN /A:185
Cannot find LINK/SSBOND atom SG in residue MTN /A:186
2KSQ-7.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2KSQ-7.pdb #14
---
Chain | Description
A | adp-ribosylation factor 1
Non-standard residues in 2KSQ-7.pdb #14
---
GTP — guanosine-5'-triphosphate
MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]
methanesulfonothioate (MTSL)
MYR — myristic acid
> mmaker #14 to #13
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 2KSQ-7.pdb, chain A (#13) with 2KSQ-7.pdb, chain A (#14), sequence
alignment score = 0
Fewer than 3 residues aligned; cannot match 2KSQ-7.pdb, chain A with
2KSQ-7.pdb, chain A
> mmaker #14 to #12
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 GTP-Arf1-morph.pdb, chain D (#12) with 2KSQ-7.pdb, chain A (#14),
sequence alignment score = 880.5
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> hide #!13 models
> hide #12 models
> select #14
3045 atoms, 3079 bonds, 187 residues, 1 model selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> hide #14 models
> show #!13 models
> morph #13,14 same true
Computed 21 frame morph #15
> coordset #15 1,21
> hide #!15 models
> ~select #14
Nothing selected
> show #12 models
> morph #12,14 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 #12,13 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 #12,13
Computed 21 frame morph #16
> coordset #16 1,21
> show #12 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
> Arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
Arf1-morph.pdb
---
warnings | Ignored bad PDB record found on line 3130
END
Start residue of secondary structure not found: HELIX 1 1 GLY A 2 ASN A 11 1
10
Start residue of secondary structure not found: HELIX 2 2 LEU A 12 GLY A 14 1
3
Start residue of secondary structure not found: HELIX 3 3 GLY A 29 GLY A 40 1
12
Start residue of secondary structure not found: HELIX 4 4 GLN A 71 SER A 76 1
6
Start residue of secondary structure not found: HELIX 5 5 LEU A 77 TYR A 81 1
5
11 messages similar to the above omitted
Cannot find LINK/SSBOND residue MYR (1 )
Cannot find LINK/SSBOND residue CYS (55 )
Cannot find LINK/SSBOND residue CYS (59 )
Cannot find LINK/SSBOND residue CYS (83 )
Cannot find LINK/SSBOND residue CYS (117 )
1 messages similar to the above omitted
GTP-Arf1-morph.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for GTP-Arf1-morph.pdb #17
---
Chain | Description
D | No description available
> mmaker #17 to #12
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 GTP-Arf1-morph.pdb, chain D (#12) with GTP-Arf1-morph.pdb, chain D
(#17), sequence alignment score = 905
RMSD between 165 pruned atom pairs is 0.000 angstroms; (across all 165 pairs:
0.000)
> select #17
2829 atoms, 2856 bonds, 180 residues, 1 model selected
> morph #12,17
Computed 21 frame morph #18
> coordset #18 1,21
> preset cartoons/nucleotides licorice/ovals
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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
No statusbar messages will be shown due to inadequate OpenGL
No statusbar messages will be shown due to inadequate OpenGL
> show #!2 models
> 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 #1/A #1/B #3/A #3/B
Alignment identifier is 1
> show #!3 models
> hide #!2 models
> select #1
41115 atoms, 41303 bonds, 2756 residues, 1 model selected
> ~select #1
Nothing selected
> color (#!3 & sel) #d6e7f4ff
> color (#!3 & sel) #ccccccff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #9ac2f5ff
> color (#!3 & sel) #fdfcf2ff
> color (#!3 & sel) #f4e379ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #310064ff
> color (#!3 & sel) #ccccccff
> color (#!3 & sel) #9ac2f5ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #fdfdffff
> color (#!3 & sel) #f2e5dfff
> color (#!3 & sel) #f0e6e0ff
> color (#!3 & sel) #f0e3dcff
> color (#!3 & sel) #e1c4b2ff
> color (#!3 & sel) #310000ff
> color (#!3 & sel) #b1ccccff
> color (#!3 & sel) #ccccccff
> color (#!3 & sel) #9ec2e5ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #9ac2f5ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #f0f0f0ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #f0f0f0ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #310000ff
> color (#!3 & sel) #f0f0f0ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #9ac2f5ff
> select clear
> select #1/C#2/C#3/C#10/C#11/C
6659 atoms, 6625 bonds, 967 residues, 5 models selected
> select clear
> undo
> undo
> undo
> undo
> color (#!3 & sel) #6f7dd5ff
> color (#!3 & sel) #9ac2f5ff
> select clear
> color (#!3 & sel) #e1c4b2ff
> color (#!3 & sel) #f4e379ff
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> select clear
> lighting soft
> select ::name="GDP"
196 atoms, 210 bonds, 7 residues, 7 models selected
> show ::name="GDP"
> show #1 models
> color (#1 & sel) #ff007fff
> color (#1 & sel) #ff00ffff
> color sel & #1 byhetero
> select clear
> hide #1 models
> show #4 models
> hide #4 models
> show #6 models
> coordset slider #6
> show #9 models
> coordset slider #9
> show #!11 models
> coordset slider #11
> show #!15 models
> coordset #15 #16
> coordset slider #15 #16
> hide #18 models
> show #18 models
> coordset slider #18
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> color (#!15 & sel) #55aa00ff
> color sel & #!15 byhetero
> hide #18 models
> hide #16 models
> hide #!15 models
> ~select #15
86 atoms, 90 bonds, 2 residues, 2 models selected
> select #14
3045 atoms, 3079 bonds, 187 residues, 1 model selected
> ~select #14
Nothing selected
> hide #!11 models
> show #!10 models
> hide #9 models
> hide #!10 models
> hide #6 models
> hide #!3 models
> show #!3 models
> coordset slider #3
> hide #3/C models
> show #3
> show #3 models
> hide #!3 atoms
> select #3/C
1228 atoms, 1248 bonds, 160 residues, 1 model selected
> hide sel cartoons
> show #6 models
> select #6 ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> color sel #ff00ffff
> color sel byhetero
> coordset #6 1,21
> select clear
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9
> coordset #9 1,21
> show #9 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9 ::name="GDP"
> coordset #9 1,21
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9 ::name="GDP"
> coordset #9 1,21
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9 ::name="GDP"
> coordset #9 1,21
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9 ::name="GDP"
> coordset #9 1,21
> show #6 ::name="GDP"
> coordset #6 1,21
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9 ::name="GDP"
> show #55 ::name="GDP"
> coordset #55 1,21
No structures specified
> show #6 ::name="GDP"
> coordset #6 1,21
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9 ::name="GDP"
> show #9 ::name="GDP"
> show #9
> show #9 models
> hide #9 models
> show #9 models
> hide #9
> show #9 ::name="GDP"
> hide #6 models
> show #6 models
> hide #9 models
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9 ::name="GDP"
> coordset #9 1,21
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #9 ::name="GDP"
> coordset #9 1,21
> hide #!3 models
> hide #6 models
> show #9 models
> show #9
Drag select of 71 atoms, 7 bonds
> delete atoms sel
> delete bonds sel
Drag select of 115 atoms, 30 bonds
> select clear
Drag select of 115 atoms, 30 bonds
> select #9/A:401@PB
1 atom, 1 residue, 1 model selected
Drag select of 115 atoms, 30 bonds
> select #9/A:401@PB
1 atom, 1 residue, 1 model selected
Drag select of 115 atoms, 30 bonds
Drag select of 50 atoms
> delete atoms sel
> delete bonds sel
Drag select of 14 atoms
> delete atoms sel
> delete bonds sel
Drag select of 15 atoms
> delete atoms sel
> delete bonds sel
Drag select of 1 atoms
> select clear
Drag select of 1 atoms
Drag select of 1 atoms
Drag select of 1 atoms
Drag select of 1 atoms
Drag select of 1 atoms
Drag select of 1 atoms
> delete atoms sel
> delete bonds sel
Drag select of 2 atoms
> delete atoms sel
> delete bonds sel
> hide #9 models
> show #6 models
> show #!3 models
> show #6 ::name="GDP"
> coordset #6 1,21
> show #6 ::name="GDP"
> coordset #6 1,21
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #6 ::name="GDP"
> coordset #6 1,21
> hide #6 ::name="GDP"
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9
> coordset 1,21
Missing or invalid "structures" argument: invalid structures specifier
> show #9 models
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset 1,21
Missing or invalid "structures" argument: invalid structures specifier
> hide #9 models
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> wait 21
> hide #6
> show #3/C cartoons
> coordset #3 1,21
> hide #!3 models
> show #!3 models
> hide #6 models
> show #6 models
> hide #3/C models
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> wait 21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/C
1228 atoms, 1248 bonds, 160 residues, 1 model selected
> hide sel cartoons
> show #6 models
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> wait 21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> select clear
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> wait 21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #!11 models
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> wait 21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> coordset #11 1,21
> hide #9 models
> hide #!11 models
> show #6 models
> show #!15 models
> hide #!15 models
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> wait 21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> show #18 models
> hide #18 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> wait 21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11
> show #18
> coordset #18 1,21
> hide #!15 models
> hide #!11 models
> hide #9 models
> show #6 models
> movie record
Already recording a movie
> movie stop
> movie reset
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> wait 21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11
> show #18
> coordset #18 1,21
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> show #6 models
> hide #!15 models
> hide #!11 models
> hide #9 models
> show #18 models
> hide #6,18#!3 atoms
> coordset #18 1,21
> hide #18 models
> show #18 models
> coordset slider #18
> hide #18 models
> show #17 models
> close #18
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2KSQ-7.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/2KSQ-7.pdb
---
warnings | Ignored bad PDB record found on line 3843
END
Cannot find LINK/SSBOND atom SG in residue MTN /A:182
Cannot find LINK/SSBOND atom SG in residue MTN /A:183
Cannot find LINK/SSBOND atom SG in residue MTN /A:184
Cannot find LINK/SSBOND atom SG in residue MTN /A:185
Cannot find LINK/SSBOND atom SG in residue MTN /A:186
2KSQ-7.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2KSQ-7.pdb #18
---
Chain | Description
A | adp-ribosylation factor 1
Non-standard residues in 2KSQ-7.pdb #18
---
GTP — guanosine-5'-triphosphate
MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]
methanesulfonothioate (MTSL)
MYR — myristic acid
> show #!11 models
> hide #!11 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> hide #6,17-18#!3 cartoons
> show #6,17-18#!3 cartoons
> hide #6,17-18#!3 atoms
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> 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
> morph #18,17
Computed 21 frame morph #19
> coordset #19 1,21
> coordset slider #19
> select #19 ::name="GTP"
Nothing selected
> hide #* target a
> show #3,6,19 target ab
> hide #6,19#!3 atoms
> select #19 ::name="GTP"
Nothing selected
> select #19 ::name="GTP"
Nothing selected
> select #18 ::name="GTP"
43 atoms, 45 bonds, 1 residue, 1 model selected
> hide #19 models
> show #18 models
> hide #6 models
> hide #!3 models
> morph #18,17 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.
> view orient
> show #19 models
> hide #19 models
> show #!3 models
> show #18 ::name="GTP"
> color sel #55aa00ff
> color sel #55aa7fff
> show #!15 models
> color sel #55aa00ff
> color sel byhetero
> select clear
> move x 10 #18
Expected an integer >= 1 or a keyword
> move x 10 10 #18
Expected a keyword
> move 10 #18
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> move x 10 #18 models
Expected an integer >= 1 or a keyword
> move x 10 10 #18
Expected a keyword
> move x 10 10 #18 models
Expected a keyword
> move x 10 25 models #18
> hide #18 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #18 models
> move x -10 25 models #18
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> hide #18 models
> select #3/C
1228 atoms, 1248 bonds, 160 residues, 1 model selected
> hide sel cartoons
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11
> show #18
> move x -10 25 models #18
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> select #3
19726 atoms, 20040 bonds, 8 pseudobonds, 2466 residues, 2 models selected
> ~select #3
Nothing selected
> select #3/C
1228 atoms, 1248 bonds, 160 residues, 1 model selected
> select #3/C
1228 atoms, 1248 bonds, 160 residues, 1 model selected
> select #3
19726 atoms, 20040 bonds, 8 pseudobonds, 2466 residues, 2 models selected
> ~select #3
Nothing selected
> hide #9 models
> show #9 models
> hide #9 models
> hide #!15 models
> show #!15 models
> hide #!11 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11
> show #18
> move x -10 25 models #18
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #9 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11
> show #18
> move x -10 25 models #18
> movie stop
> show #9 ::name="GDP"
> hide #9 models
> show #9 models
> hide #9 models
> show #15 models
> show #15 ::name="GTP"
> coordset slider #15
> hide #!11 models
> show #6 models
> show #3 ::name="GDP"
> show #6 ::name="GDP"
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11
> show #18
> move x -10 25 models #18
> show #6 models
> hide #!3 models
> show #!3 models
> hide #!11 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11
> show #18
> move x -10 25 models #18
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #9 models
> hide #!15 models
> show #!15 models
> hide #!11 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11
> show #18
> move x 10 25 models #18
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #!11 models
> hide #9 models
> show #6 models
> show #18 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> hide #6,18#!3,15 atoms
> hide #18 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11 models
> show #18
> show #18 ::name="GTP"
> move x 10 25 models #18
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #!15 models
> show #!15 models
> show #15 ::name="GTP"
> hide #9 models
> show #6 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11 models
> show #18 cartoons
> show #18 ::name="GTP"
> move x 10 25 models #18
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> hide #!15 models
> show #!15 models
> show #17 models
> hide #9 models
> hide #17 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11 models
> show #18 cartoons
> show #18 ::name="GTP"
> move x 10 25 models #18
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> show #18 models
> hide #9,18#!3,15 atoms
> move x 10 #18 models
Expected an integer >= 1 or a keyword
> move x 10 25 #18 models
Expected a keyword
> move x 10 models #18
> move x -100 models #18
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> move x -100 100 models #18
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> move x -100 1 models #18
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> move x -10 100 models #18
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> move x -10 25 models #18
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> select ::name="GTP"
172 atoms, 180 bonds, 4 residues, 4 models selected
> show sel & #18#!15 atoms
> select clear
> hide #9 models
> show #9 models
> hide #18 models
> show #18 models
> hide #18 models
> hide #!15 models
> select ::name="GDP"
196 atoms, 210 bonds, 7 residues, 7 models selected
> show sel & #9 atoms
> hide #9 models
> select clear
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #11 models
> show #18 cartoons
> show #18 ::name="GTP"
> move x 10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #!15 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> show #18 models
> hide #18 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 cartoons
> show #18 ::name="GTP"
> move x 10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #9 models
> show #6 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 cartoons
> show #18 ::name="GTP"
> move x 10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> show #18 cartoons
> show #18 ::name="GTP"
> move x 10 25 models #18
> wait
> show #18 models
> show #18 ::name="GTP"
> move x 10 25 models #18
> wait
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> hide #18 models
> show #18 models
> show #18 ::name="GTP"
> move x 10 25 models #18
> wait
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> hide #18 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> show #!15 models
> hide #!15 models
> hide #9 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 cartoons
> show #18 ::name="GTP"
> move x -10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #9 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> show #18 ::name="GTP"
> move x -10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #9 models
> show #6 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> hide #18 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 cartoons
> show #18 ::name="GTP"
> move x -10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> show #18 models
> hide #18 models
> show #18 cartoons
> show #18 models
> hide #18 models
> hide #9 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> move x -10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #9 models
> show #6 models
> hide #6 models
> show #1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> ui mousemode right "play map series"
> hide #!2 models
> hide #1 models
> show #!3 models
> hide #18 models
> select #3/A:780
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B
Alignment identifier is 1
> select #2
19922 atoms, 20242 bonds, 44 pseudobonds, 2483 residues, 2 models selected
> ~select #2
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #3/A #3/B
Alignment identifier is 1
> select clear
Drag select of 7 residues
> color (#!3 & sel) #aa0000ff
> select clear
> zoom 10 10
> zoom -10 100
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\std_commands\zoom.py", line 46, in zoom
ff = math.pow(factor, 1/frames)
ValueError: math domain error
ValueError: math domain error
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\zoom.py", line 46, in zoom
ff = math.pow(factor, 1/frames)
See log for complete Python traceback.
> zoom -10
> zoom 0.01
> zoom 10
> zoom 0.01
> zoom 100
> view orient
> view
> view orient
> turn x 180
> turn x -90 20
> turn x 1 90 20
Expected a keyword
> turn x 1-90 20
Expected a number or a keyword
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 90 1
> turn x 270 360
> turn x 90
> turn x 180
> turn x -1 90
> turn y 90
> view orient
> turn x90
Expected an axis vector or a keyword
> turn x 90
> turn x 90
> turn x 1 90
> turn y 1 90
> view
> view orient
> turn x 90
> turn x 90
> turn x -1 90
> turn y 1 90
> view orient
> turn x -1 90
> turn y 1 90
> zoom 2
> turn z 20
> turn
> turn
> view orient
> turn x 180
> turn x -1 90
> turn y -1 90
> move x 10
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 1
> move x -10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #9 models
> hide #18 models
> show #6 models
> mmaker #18 to 11
> matchmaker #18 to 11
Invalid "to" argument: invalid atoms specifier
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 1
> move x -10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #9 models
> show #6 models
> hide #18 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 5
> move x -10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> hide #18 models
> hide #9 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 5
> move x -10 25 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #18 models
> hide #9 models
> show #6 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 10
> move x -10 35 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #18 models
> hide #9 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 3
> move x -5 30 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 3
> move x -5 30 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #18 models
> hide #9 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 3
> move x -5 30 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #18 models
> hide #9 models
> show #6 models
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 728.4
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 165 pairs:
4.525)
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 3
> move x -5 30 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> mmaker #18 to #11
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 - complex-morph.pdb, chain C (#11) with 2KSQ-7.pdb, chain A
(#18), sequence alignment score = 828
RMSD between 165 pruned atom pairs is 0.001 angstroms; (across all 165 pairs:
0.001)
> hide #18 models
> hide #9 models
> show #6 models
> movie record
> show #6 ::name="GDP"
> coordset #6 1,21
> wait 21
> hide #6 ::name="GDP"
> show #9 models
> coordset #9 1,21
> hide #6 models
> show #3/C cartoons
> coordset #3 1,21
> wait 21
> hide #3/C cartoons
> show #11 models
> show #15 models
> coordset #15 21,1
> wait 21
> coordset #11 1,21
> wait 21
> hide #!11 models
> hide #15 models
> show #18 models
> wait 3
> move x -5 30 models #18
> wait
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/moprh.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 69, in <lambda>
lambda *args, qual=ses_func: self._ses_call(qual)))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1792, in _ses_call
f(self._c_pointer)
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 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute '_c_pointer'
Error processing trigger "begin save session":
AttributeError: 'Structure' object has no attribute '_c_pointer'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 69, in <lambda>
lambda *args, qual=ses_func: self._ses_call(qual)))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1792, in _ses_call
f(self._c_pointer)
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 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute '_c_pointer'
Error processing trigger "begin save session":
AttributeError: 'Structure' object has no attribute '_c_pointer'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 69, in <lambda>
lambda *args, qual=ses_func: self._ses_call(qual)))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1792, in _ses_call
f(self._c_pointer)
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 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute '_c_pointer'
Error processing trigger "begin save session":
AttributeError: 'Structure' object has no attribute '_c_pointer'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 69, in <lambda>
lambda *args, qual=ses_func: self._ses_call(qual)))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1792, in _ses_call
f(self._c_pointer)
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 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute '_c_pointer'
Error processing trigger "begin save session":
AttributeError: 'Structure' object has no attribute '_c_pointer'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 69, in <lambda>
lambda *args, qual=ses_func: self._ses_call(qual)))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1792, in _ses_call
f(self._c_pointer)
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 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute '_c_pointer'
Error processing trigger "begin save session":
AttributeError: 'Structure' object has no attribute '_c_pointer'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
opened ChimeraX session
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2KSQ-7_modified.pdb
Chain information for 2KSQ-7_modified.pdb #20
---
Chain | Description
A | No description available
> 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
Drag select of 10 atoms, 11 bonds
Drag select of 12 atoms, 12 bonds
> delete atoms sel
> delete bonds sel
> select clear
Drag select of 12 atoms, 12 bonds
> delete atoms sel
> delete bonds sel
Drag select of 12 atoms, 12 bonds
> delete atoms sel
> delete bonds sel
Drag select of 6 atoms, 6 bonds
Drag select of 9 atoms, 10 bonds
> delete atoms sel
> delete bonds sel
Drag select of 2 atoms
Drag select of 3 atoms, 1 bonds
> delete atoms sel
> delete bonds sel
Drag select of 5 atoms, 5 bonds
> delete atoms sel
> delete bonds sel
Drag select of 7 atoms, 6 bonds
> delete atoms sel
> delete bonds sel
> undo
Undo failed, probably because structures have been modified.
> select clear
Drag select of 9 atoms, 9 bonds
> delete atoms sel
> delete bonds sel
Drag select of 5 atoms, 4 bonds
> delete atoms sel
> delete bonds sel
Drag select of 1 atoms
> delete atoms sel
> delete bonds sel
> lighting soft
> hide #!3 models
> show #!3 models
> mmaker #20 to #3
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 C (#3) with
2KSQ-7_modified.pdb, chain A (#20), sequence alignment score = 623.6
RMSD between 112 pruned atom pairs is 1.104 angstroms; (across all 160 pairs:
4.482)
> show #4 models
> hide #!3 models
> hide #4 models
> hide #9 models
> hide #18 models
> hide #!20 models
> show #18 models
> hide #18 models
> show #19 models
> hide #19 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!11 models
> show #12 models
> hide #12 models
> hide #!11 models
> show #6 models
> hide #6 models
> show #9 models
> hide #9 models
> show #!10 models
> show #!20 models
> morph #10,20 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 #10,20
Computed 21 frame morph #21
> coordset #21 1,21
> morph #10,20 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 #10,20 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.
> select #20 ::name="GTP"
43 atoms, 45 bonds, 1 residue, 1 model selected
> delete atoms #21
> delete bonds #21
> show #!20 models
> close #20
> show #19 models
> select #19
2810 atoms, 2837 bonds, 180 residues, 1 model selected
> ~select #19
Nothing selected
> hide #19 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2KSQ-7_modified.pdb
Chain information for 2KSQ-7_modified.pdb #20
---
Chain | Description
A | No description available
> show #!3 models
> mmaker #20 to #3
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 C (#3) with
2KSQ-7_modified.pdb, chain A (#20), sequence alignment score = 623.6
RMSD between 112 pruned atom pairs is 1.104 angstroms; (across all 160 pairs:
4.482)
> hide #!3 models
> select ::name="SO3"
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #5
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> ~select #5
Nothing selected
> select ::name="MTN"
405 atoms, 405 bonds, 15 residues, 3 models selected
> delete atoms (#20 & sel)
> delete bonds (#20 & sel)
> select #20 ::name="MYR"
42 atoms, 41 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #20 ::name="GTP"
43 atoms, 45 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #9 models
> hide #9 models
> show #8 models
> hide #8 models
> show #!10 models
> morph #10,20 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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Arnold,
--Eric
duplicate of #5552