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#5552 closed defect (duplicate)

morph same true: Execution of 'Structure' object's 'coordset_size' property raised AttributeError

Reported by:	am2837@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Structure Comparison	Version:
Keywords:		Cc:	Eric Pettersen
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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.  
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.  
  
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 "end 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 "end 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 "end 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 "end 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 "end 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.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1660/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: OriginPC
Model: NEURON
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 17,093,591,040
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9600K CPU @ 3.70GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Cc:	Eric Pettersen added
Component:	Unassigned → Structure Comparison
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → morph same true: Execution of 'Structure' object's 'coordset_size' property raised AttributeError

Reported by Arnold Muccini

comment:2 by Tom Goddard, 4 years ago

Resolution:	→ duplicate
Status:	assigned → closed

This error saving a session is fixed in the current ChimeraX 1.3 release candidate.

The problem is that your earlier commands like "morph #12,13 same true" gave an error because the two models had no residues with matching chain identifiers and residue numbers and that error left zombie morph models that later cause the session save to fail. In current ChimeraX such a morph reports that no residues matched and cleanup is properly done.

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