Attribute specifier with string instead of number gives traceback

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-20.5.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/hhpred-3.pdb"

Chain information for hhpred-3.pdb #1  
---  
Chain | Description  
X | No description available  
  

> apbs

Unknown command: apbs  
Drag select of 77 residues  

> apbs

Unknown command: apbs  

> open /Users/amirbasis/Downloads/eeq4i6b1m4-pot.dx

Opened eeq4i6b1m4-pot.dx, grid size 161,129,129, pixel 0.466,0.455,0.473,
shown at level -14.5,14.5, step 1, values float32  

> apbs

Unknown command: apbs  

> apbs #2

Unknown command: apbs #2  

> APBS

Unknown command: APBS  

> select #1

625 atoms, 641 bonds, 77 residues, 1 model selected  

> ~select #1

Nothing selected  

> select #2

3 models selected  

> close #1

> coulombic

> coulombic

> undo

> undo

> undo

> undo

Undo failed, probably because structures have been modified.  

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/hhpred-3.pdb"

Chain information for hhpred-3.pdb #1  
---  
Chain | Description  
X | No description available  
  

> hide #!2 models

> coulombic

> mlp

Map values for surface "hhpred-3.pdb_X SES surface": minimum -24.68, mean
-2.552, maximum 21.85  

> show ribbons

> style stick

Changed 625 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> show cartoons

> hide surfaces

> mlp

Map values for surface "hhpred-3.pdb_X SES surface": minimum -24.68, mean
-2.552, maximum 21.85  

> mlp

Map values for surface "hhpred-3.pdb_X SES surface": minimum -24.68, mean
-2.552, maximum 21.85  

> hide surfaces

> mlp

Map values for surface "hhpred-3.pdb_X SES surface": minimum -24.68, mean
-2.552, maximum 21.85  

> coulombic

> pdb2pqr

Unknown command: pdb2pqr  
Drag select of hhpred-3.pdb_X SES surface, 104699 of 113030 triangles, 75
residues  
Drag select of hhpred-3.pdb_X SES surface, 77 residues  

> pdb2pqr

Unknown command: pdb2pqr  

> open /Users/amirbasis/Downloads/eeq4i6b1m4.pqr

Chain information for eeq4i6b1m4.pqr #3  
---  
Chain | Description  
| No description available  
  

> hide #3 models

> show #3 models

> hide #3 models

> hide #!1 models

> select #1

625 atoms, 641 bonds, 77 residues, 1 model selected  

> show #3 models

> show bfactor

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> bfactor

Unknown command: bfactor  

> coulombic #3

Atoms with non-standard names found in standard residues: eeq4i6b1m4.pqr #3
MET 1 H. Try deleting all hydrogens first.  
Drag select of 29 residues  
Drag select of 77 residues  

> coulombic sel

Atoms with non-standard names found in standard residues: eeq4i6b1m4.pqr #3
MET 1 H. Try deleting all hydrogens first.  

> hide H

> coulombic sel

Atoms with non-standard names found in standard residues: eeq4i6b1m4.pqr #3
MET 1 H. Try deleting all hydrogens first.  

> delete h

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete @h

> coulombic sel

> mkp

Unknown command: mkp  

> mlp

Map values for surface "hhpred-3.pdb_X SES surface": minimum -24.68, mean
-2.552, maximum 21.85  
Map values for surface "eeq4i6b1m4.pqr_ SES surface": minimum -29.19, mean
-2.975, maximum 21.46  

> hide surfaces

> close

> open hhpred-3-electro

'hhpred-3-electro' has no suffix  

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/hhpred-3-electro.pqr"

Chain information for hhpred-3-electro.pqr #1  
---  
Chain | Description  
| No description available  
  

> rainbow

> pdb2pqr

Unknown command: pdb2pqr  

> coulombic

Atoms with non-standard names found in standard residues: MET 1 H. Try
deleting all hydrogens first.  

> delete @h

> coulombic

> open hhpred-3.pdb

No such file/path: hhpred-3.pdb  

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/hhpred-3.pdb"

Chain information for hhpred-3.pdb #2  
---  
Chain | Description  
X | No description available  
  

> show #2

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> move x10 #2

Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms  

> move x 10 #2

Expected an integer >= 1 or a keyword  

> move x #2 10

Expected a number or a keyword  

> move x 10 models #2

> move x 10 models #2

> move x 10 models #2

> move x 10 models #2

> surface #2

> coulombic

> hide #!2 models

> mlp 31

Expected an atoms specifier or a keyword  

> mlp #1

Map values for surface "hhpred-3-electro.pqr_ SES surface": minimum -27.73,
mean -2.663, maximum 22.32  

> hide #!1 models

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/hhpred-6.pdb"

Chain information for hhpred-6.pdb #3  
---  
Chain | Description  
X | No description available  
  

> select #3

860 atoms, 885 bonds, 103 residues, 1 model selected  

> ~select #3

Nothing selected  

> show #3

> select #3

860 atoms, 885 bonds, 103 residues, 1 model selected  

> hide #3 models

> show #3 models

> coulombic sel

> center #3

Unknown command: center #3  

> show #!3 target m

> view #!3 clip false

> mlp

Map values for surface "hhpred-3-electro.pqr_ SES surface": minimum -27.73,
mean -2.663, maximum 22.32  
Map values for surface "hhpred-3.pdb_X SES surface": minimum -24.68, mean
-2.552, maximum 21.85  
Map values for surface "hhpred-6.pdb_X SES surface": minimum -25.23, mean
-1.776, maximum 22.4  

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/hhpred-7.pdb"

Chain information for hhpred-7.pdb #4  
---  
Chain | Description  
X | No description available  
  

> view #4

> move x 10 models #4

> move x 10 models #4

> hide surfaces

> ribbon

> show ribbons

> show sel atoms

> hide sel atoms

> mmaker #3 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 hhpred-7.pdb, chain X (#4) with hhpred-6.pdb, chain X (#3),
sequence alignment score = 418.2  
RMSD between 27 pruned atom pairs is 1.116 angstroms; (across all 85 pairs:
6.097)  
  

> mmaker #3 to #4 to #2

> matchmaker #3 to #4 to #2

Repeated keyword argument "to"  

> mmaker #3 to #4, #2

> matchmaker #3 to #4, #2

Invalid "to" argument: only initial part "#4" of atom specifier valid  

> mmaker #3 to #4, 2

Specify a single 'to' model only  

> mmaker #3 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 hhpred-3.pdb, chain X (#2) with hhpred-6.pdb, chain X (#3),
sequence alignment score = 340.9  
RMSD between 9 pruned atom pairs is 1.364 angstroms; (across all 74 pairs:
12.592)  
  

> show #2

> view #2

> view #3

> show #!2 models

> hide #4 models

> show #4 models

> view #4 clip false

> hide #4 models

> hide #!3 models

> ~select #3

1 model selected  

> hide #!2 models

> show #!2 models

> show #!3 models

> show #4 models

> show #!2 target m

> show #!3 target m

> show #4 target m

> view #2,3,4

> mmaker #4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker hhpred-6.pdb, chain X (#3) with hhpred-7.pdb, chain X (#4),
sequence alignment score = 418.2  
RMSD between 27 pruned atom pairs is 1.116 angstroms; (across all 85 pairs:
6.097)  
  
Drag select of 332 atoms, 257 residues, 285 bonds  
Drag select of 394 atoms, 265 residues, 338 bonds  

> hide sel atoms

> move x 10 models #2

> move x 10 models #2

> move x 10 models #2

> move x 10 models #2

> move x 10 models #2

> ~select all

2 models selected  

> mmaker #2 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker hhpred-6.pdb, chain X (#3) with hhpred-3.pdb, chain X (#2),
sequence alignment score = 340.9  
RMSD between 9 pruned atom pairs is 1.364 angstroms; (across all 74 pairs:
12.592)  
  

> close all

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/hhpred-7.pdb"

Chain information for hhpred-7.pdb #1  
---  
Chain | Description  
X | No description available  
  

> color rainbow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> rainbow

> coulombic

> mlp

Map values for surface "hhpred-7.pdb_X SES surface": minimum -22.34, mean
-1.47, maximum 22.26  

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/ttroseta.pdb"

Chain information for ttroseta.pdb #2  
---  
Chain | Description  
A | No description available  
  

> view #2

> view #2,1

> 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 hhpred-7.pdb, chain X (#1) with ttroseta.pdb, chain A (#2),
sequence alignment score = 369.6  
RMSD between 20 pruned atom pairs is 1.337 angstroms; (across all 85 pairs:
10.989)  
  

> center all

Unknown command: center all  

> select all

2583 atoms, 2628 bonds, 199 residues, 2 models selected  

> hide serf

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide surfaces

> undo

> undo

> undo

> undo

> undo

> show #2

> move x 0 models #2

> move x 0 models #2

> move x 0 models #2

> move x 0 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move x -10 models #1

> move y -10 models #1

> move y -10 models #1

> move y -10 models #1

> move y -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z -10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

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> move z 10 models #1

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> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #1

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

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> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

> move z 10 models #2

Drag select of 85 residues  

> select all

2583 atoms, 2628 bonds, 199 residues, 2 models selected  

> hide surfaces

> hide @

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide sel atoms

> 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 hhpred-7.pdb, chain X (#1) with ttroseta.pdb, chain A (#2),
sequence alignment score = 369.6  
RMSD between 20 pruned atom pairs is 1.337 angstroms; (across all 85 pairs:
10.989)  
  

> hide #2 models

> hide #!1 models

> show #2 models

> coulombic

Atoms with non-standard names found in standard residues: ttroseta.pdb #2/A
ASP 31 1HB, ttroseta.pdb #2/A ASP 31 2HB, ttroseta.pdb #2/A PRO 45 1HB,
ttroseta.pdb #2/A PRO 45 2HG, ttroseta.pdb #2/A PRO 45 2HB, and 545 other
atoms. Try deleting all hydrogens first.  

> delete @h

> coulombic

Atoms with non-standard names found in standard residues: ttroseta.pdb #2/A
ASP 31 1HB, ttroseta.pdb #2/A ASP 31 2HB, ttroseta.pdb #2/A PRO 45 1HB,
ttroseta.pdb #2/A PRO 45 2HG, ttroseta.pdb #2/A PRO 45 2HB, and 545 other
atoms. Try deleting all hydrogens first.  

> coulombic sel & #2

Atoms with non-standard names found in standard residues: ttroseta.pdb #2/A
ASP 31 1HB, ttroseta.pdb #2/A ASP 31 2HB, ttroseta.pdb #2/A PRO 45 1HB,
ttroseta.pdb #2/A PRO 45 2HG, ttroseta.pdb #2/A PRO 45 2HB, and 545 other
atoms. Try deleting all hydrogens first.  

> delete @h

> coulombic sel & #2

Atoms with non-standard names found in standard residues: ttroseta.pdb #2/A
ASP 31 1HB, ttroseta.pdb #2/A ASP 31 2HB, ttroseta.pdb #2/A PRO 45 1HB,
ttroseta.pdb #2/A PRO 45 2HG, ttroseta.pdb #2/A PRO 45 2HB, and 545 other
atoms. Try deleting all hydrogens first.  

> mlp sel & #2

Map values for surface "ttroseta.pdb_A SES surface": minimum -26.17, mean
-1.852, maximum 26.15  

> coulombic

Atoms with non-standard names found in standard residues: ttroseta.pdb #2/A
ASP 31 1HB, ttroseta.pdb #2/A ASP 31 2HB, ttroseta.pdb #2/A PRO 45 1HB,
ttroseta.pdb #2/A PRO 45 2HG, ttroseta.pdb #2/A PRO 45 2HB, and 545 other
atoms. Try deleting all hydrogens first.  

> hide #!2 models

> ~select #2

730 atoms, 749 bonds, 85 residues, 3 models selected  

> ~select #1

1 model selected  

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/rtrosetta-electro.pqr"

Chain information for rtrosetta-electro.pqr #3  
---  
Chain | Description  
| No description available  
  

> view #3 clip false

> coulombic

Atoms with non-standard names found in standard residues: ttroseta.pdb #2/A
ASP 31 1HB, ttroseta.pdb #2/A ASP 31 2HB, ttroseta.pdb #2/A PRO 45 1HB,
ttroseta.pdb #2/A PRO 45 2HG, ttroseta.pdb #2/A PRO 45 2HB, and 546 other
atoms. Try deleting all hydrogens first.  

> delete @h

Drag select of 114 residues  

> delete @h

> coulombic sel

> hide #!3 models

> show #!2 models

> view #!2 clip false

> view #!3 clip false

> show #!3 models

> view #!2 clip false

> view #2,3

> mmaker #2 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker rtrosetta-electro.pqr, chain (blank) (#3) with ttroseta.pdb, chain
A (#2), sequence alignment score = 623.1  
RMSD between 114 pruned atom pairs is 0.000 angstroms; (across all 114 pairs:
0.000)  
  

> hide #!3 target m

> hide #!2 target m

> show #!3 models

> move x y z 0models #3

Expected a number or a keyword  

> move x y z 0 models #3

Expected a number or a keyword  

> move x y z 0 models #3

Expected a number or a keyword  

> move x,y,z 0 models #3

Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms  

> center #3

Unknown command: center #3  

> hide #!3 models

> select #3

1744 atoms, 1770 bonds, 114 residues, 1 model selected  

> ~select #3

1 model selected  

> hide #!3 target m

> hide #!2 target m

> hide #!1 target m

> show #!3 models

> hide #!3 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/amirbasis/Desktop/movie1.mp4

Movie saved to /Users/amirbasis/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/amirbasis/Desktop/movie2.mp4

Movie saved to /Users/amirbasis/Desktop/movie2.mp4  
  

> show #!3 models

> close #1

> close #2

> close #3

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/ttroseta.pdb" "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/rtrosetta-electro.pqr"

Chain information for ttroseta.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for rtrosetta-electro.pqr #2  
---  
Chain | Description  
| No description available  
  

> mmaker #1 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 rtrosetta-electro.pqr, chain (blank) (#2) with ttroseta.pdb, chain
A (#1), sequence alignment score = 623.1  
RMSD between 114 pruned atom pairs is 0.000 angstroms; (across all 114 pairs:
0.000)  
  

> select #1

1853 atoms, 1879 bonds, 114 residues, 1 model selected  

> select #2

1853 atoms, 1879 bonds, 114 residues, 1 model selected  

> ~select #2

Nothing selected  

> view #2 clip false

> view #1 clip false

> show #1 target m

> show #2 target m

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> move x 10 models #1

> move x 10 models #1

> move x 10 models #1

> select #1

1853 atoms, 1879 bonds, 114 residues, 1 model selected  

> coulombic

Atoms with non-standard names found in standard residues: rtrosetta-
electro.pqr #2 MET 1 H, ttroseta.pdb #1/A CYS 18 1HB, ttroseta.pdb #1/A CYS 18
2HB, ttroseta.pdb #1/A ALA 37 3HB, ttroseta.pdb #1/A ALA 37 1HB, and 546 other
atoms. Try deleting all hydrogens first.  

> delete @h

> coulombic

Atoms with non-standard names found in standard residues: ttroseta.pdb #1/A
CYS 18 1HB, ttroseta.pdb #1/A CYS 18 2HB, ttroseta.pdb #1/A ALA 37 3HB,
ttroseta.pdb #1/A ALA 37 1HB, ttroseta.pdb #1/A ALA 37 2HB, and 545 other
atoms. Try deleting all hydrogens first.  

> plm

Unknown command: plm  

> mlp

Map values for surface "ttroseta.pdb_A SES surface": minimum -25.98, mean
-1.848, maximum 26.08  
Map values for surface "rtrosetta-electro.pqr_ SES surface": minimum -27.06,
mean -2.65, maximum 23.06  

> select #2

1744 atoms, 1770 bonds, 114 residues, 1 model selected  

> delete @h

> coulomboc

Unknown command: coulomboc  

> coulombic

Atoms with non-standard names found in standard residues: ttroseta.pdb #1/A
CYS 18 1HB, ttroseta.pdb #1/A CYS 18 2HB, ttroseta.pdb #1/A ALA 37 3HB,
ttroseta.pdb #1/A ALA 37 1HB, ttroseta.pdb #1/A ALA 37 2HB, and 545 other
atoms. Try deleting all hydrogens first.  

> coulombic sel

> close

> open /Users/amirbasis/Downloads/1A07A_with_Conservation_Scores.pdb

1A07A_with_Conservation_Scores.pdb title:  
C-SRC (SH2 domain) complexed with ace-malonyl tyr-glu-(N,N-dipentyl amine)
[more info...]  
  
Chain information for 1A07A_with_Conservation_Scores.pdb #1  
---  
Chain | Description  
A B | C-SRC tyrosine kinase  
C D | ace-malonyl tyr-glu-(N,N-dipentyl amine)  
  
Non-standard residues in 1A07A_with_Conservation_Scores.pdb #1  
---  
ACE — acetyl group  
DIP — dipentylamine  
  

> color bfactor

2282 atoms, 267 residues, atom bfactor range -1.59 to 83.1  

> color bfactor(-10,10)

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> bfactor key 2 blue 30 red 50 yellow

Unknown command: bfactor key 2 blue 30 red 50 yellow  
Drag select of 192 atoms, 208 residues, 177 bonds  
Drag select of 192 atoms, 209 residues, 177 bonds  

> bfactor key 2 blue 30 red 50 yellow

Unknown command: bfactor key 2 blue 30 red 50 yellow  

> bfactor key 2 blue 30 red

Unknown command: bfactor key 2 blue 30 red  

> rangecolor bfactor key 2 blue 30 red 50 yellow

Unknown command: rangecolor bfactor key 2 blue 30 red 50 yellow  

> rangecolor bfactor

Unknown command: rangecolor bfactor  

> rangecolor

Unknown command: rangecolor  

> color key

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> close

> open "/Users/amirbasis/Desktop/medcine
> MD/phd/מעבדה/ביואינפורמטקיה/ttroseta_pdb_With_Conservation_Scores.pdb"

Chain information for ttroseta_pdb_With_Conservation_Scores.pdb #1  
---  
Chain | Description  
A | No description available  
  

> color bfactor

1853 atoms, 114 residues, atom bfactor range -1.62 to 2.8  

> show surfaces

> color bfactor

1853 atoms, 114 residues, 1 surfaces, atom bfactor range -1.62 to 2.8  

> colrange -10 to 10

Unknown command: colrange -10 to 10  

> toolshed show

> ui tool show "Color Actions"

> rangecol bfactor,s key min blue 20 white 40 red

Unknown command: rangecol bfactor,s key min blue 20 white 40 red  

> rangecol bfactor key min blue 20 white 40 red

Unknown command: rangecol bfactor key min blue 20 white 40 red  

> rangecol bfactor

Unknown command: rangecol bfactor  

> rangecol

Unknown command: rangecol  

> colrange

Unknown command: colrange  

> ui tool show "Volume Viewer"

> undo

> undo

> undo

> undo

Undo failed, probably because structures have been modified.  

> color bfactor

1853 atoms, 114 residues, 1 surfaces, atom bfactor range -1.62 to 2.8  

> color bfactor

1853 atoms, 114 residues, 1 surfaces, atom bfactor range -1.62 to 2.8  

> ui tool show "Volume Viewer"

> undo

> undo

> undo

Undo failed, probably because structures have been modified.  

> color bfactor

1853 atoms, 114 residues, 1 surfaces, atom bfactor range -1.62 to 2.8  

> color bfactor

1853 atoms, 114 residues, 1 surfaces, atom bfactor range -1.62 to 2.8  

> color bfactor -.62 to 2.8

> color byattribute bfactor -.62 to 2.8

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color bfactor -1.62 to 2.8

> color byattribute bfactor -1.62 to 2.8

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color bfactor -2 to 2.8

> color byattribute bfactor -2 to 2.8

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> display @@bfactor <"10"

Traceback (most recent call last):  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2822, in run  
_used_aliases=used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 3352, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2767, in run  
prev_annos = self._process_positional_arguments()  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2550, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2413, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 888, in parse  
return anno.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 1248, in parse  
objects = aspec.evaluate(session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1043, in evaluate  
session, models, top=False, ordered=order_implicit_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 431, in find_matches  
model_spec.find_matches(session, model_list, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 592, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 612, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 537, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 556, in _filter_parts  
None, self.my_attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 805, in atomspec_filter  
return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 893, in _atomspec_filter_atom  
selected = self._atomspec_attr_filter(atoms, selected, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 845, in _atomspec_attr_filter  
s = numpy.vectorize(choose)(objects)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2091, in __call__  
return self._vectorize_call(func=func, args=vargs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2161, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2121, in _get_ufunc_and_otypes  
outputs = func(*inputs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
TypeError: '<' not supported between instances of 'float' and 'str'  
  
TypeError: '  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
  
See log for complete Python traceback.  
  

> display @@bfactor <"1"

Traceback (most recent call last):  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2822, in run  
_used_aliases=used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 3352, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2767, in run  
prev_annos = self._process_positional_arguments()  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2550, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2413, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 888, in parse  
return anno.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 1248, in parse  
objects = aspec.evaluate(session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1043, in evaluate  
session, models, top=False, ordered=order_implicit_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 431, in find_matches  
model_spec.find_matches(session, model_list, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 592, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 612, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 537, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 556, in _filter_parts  
None, self.my_attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 805, in atomspec_filter  
return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 893, in _atomspec_filter_atom  
selected = self._atomspec_attr_filter(atoms, selected, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 845, in _atomspec_attr_filter  
s = numpy.vectorize(choose)(objects)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2091, in __call__  
return self._vectorize_call(func=func, args=vargs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2161, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2121, in _get_ufunc_and_otypes  
outputs = func(*inputs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
TypeError: '<' not supported between instances of 'float' and 'str'  
  
TypeError: '  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
  
See log for complete Python traceback.  
  

> select #1

1853 atoms, 1879 bonds, 114 residues, 1 model selected  

> display @@bfactor <"1"

Traceback (most recent call last):  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2822, in run  
_used_aliases=used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 3352, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2767, in run  
prev_annos = self._process_positional_arguments()  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2550, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2413, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 888, in parse  
return anno.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 1248, in parse  
objects = aspec.evaluate(session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1043, in evaluate  
session, models, top=False, ordered=order_implicit_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 431, in find_matches  
model_spec.find_matches(session, model_list, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 592, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 612, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 537, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 556, in _filter_parts  
None, self.my_attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 805, in atomspec_filter  
return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 893, in _atomspec_filter_atom  
selected = self._atomspec_attr_filter(atoms, selected, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 845, in _atomspec_attr_filter  
s = numpy.vectorize(choose)(objects)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2091, in __call__  
return self._vectorize_call(func=func, args=vargs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2161, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2121, in _get_ufunc_and_otypes  
outputs = func(*inputs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
TypeError: '<' not supported between instances of 'float' and 'str'  
  
TypeError: '  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
  
See log for complete Python traceback.  
  

> display @@bfactor <""

Traceback (most recent call last):  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2822, in run  
_used_aliases=used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 3352, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2767, in run  
prev_annos = self._process_positional_arguments()  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2550, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2413, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 888, in parse  
return anno.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 1248, in parse  
objects = aspec.evaluate(session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1043, in evaluate  
session, models, top=False, ordered=order_implicit_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 431, in find_matches  
model_spec.find_matches(session, model_list, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 592, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 612, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 537, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 556, in _filter_parts  
None, self.my_attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 805, in atomspec_filter  
return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 893, in _atomspec_filter_atom  
selected = self._atomspec_attr_filter(atoms, selected, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 845, in _atomspec_attr_filter  
s = numpy.vectorize(choose)(objects)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2091, in __call__  
return self._vectorize_call(func=func, args=vargs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2161, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2121, in _get_ufunc_and_otypes  
outputs = func(*inputs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
TypeError: '<' not supported between instances of 'float' and 'str'  
  
TypeError: '  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
  
See log for complete Python traceback.  
  

> display @@bfactor < "1"

Traceback (most recent call last):  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2822, in run  
_used_aliases=used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 3352, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2767, in run  
prev_annos = self._process_positional_arguments()  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2550, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2413, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 888, in parse  
return anno.parse(text, session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 1248, in parse  
objects = aspec.evaluate(session)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1043, in evaluate  
session, models, top=False, ordered=order_implicit_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 431, in find_matches  
model_spec.find_matches(session, model_list, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 592, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 612, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 548, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 537, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 556, in _filter_parts  
None, self.my_attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 805, in atomspec_filter  
return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 893, in _atomspec_filter_atom  
selected = self._atomspec_attr_filter(atoms, selected, attrs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 845, in _atomspec_attr_filter  
s = numpy.vectorize(choose)(objects)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2091, in __call__  
return self._vectorize_call(func=func, args=vargs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2161, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/function_base.py", line 2121, in _get_ufunc_and_otypes  
outputs = func(*inputs)  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
TypeError: '<' not supported between instances of 'float' and 'str'  
  
TypeError: '  
File
"/Users/amirbasis/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 884, in matcher  
return op(v, attr_value)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.4.5
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 427.0.0.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 16 days 20:15

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

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
    appnope: 0.1.0
    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: 1.1.1
    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
    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
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    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
    ptyprocess: 0.6.0
    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
    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

[Tom Goddard]

User specified a string instead of a number with in an attribute specifier and it gave a traceback

display @@bfactor <"1"

User error of course, but our code should be catching this and give a simple error message, not a traceback.