Coordinates are NaN

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/1/A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/1/OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb

Chain information for
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/1/uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> graphics silhouettes true

> lighting soft

Drag select of 2006 residues  

> color sel cornflower blue

> ui tool show Matchmaker

> matchmaker #2-3 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
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 2352.5  
RMSD between 220 pruned atom pairs is 0.749 angstroms; (across all 658 pairs:
13.144)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3), sequence alignment score = 1587.7  
RMSD between 187 pruned atom pairs is 0.990 angstroms; (across all 655 pairs:
11.551)  
  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/2/A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/2/MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb

Chain information for
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/2/uvig_8948_18_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
uvig_8948_18_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #6  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> hide #2 models

> hide #3 models

Drag select of 2695 residues  

> ui tool show "Color Actions"

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel plum

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel thistle

> color sel plum

> select #5/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 2695 residues  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel thistle

> select #5/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> matchmaker #2-6 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
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 2352.5  
RMSD between 220 pruned atom pairs is 0.749 angstroms; (across all 658 pairs:
13.144)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3), sequence alignment score = 1587.7  
RMSD between 187 pruned atom pairs is 0.990 angstroms; (across all 655 pairs:
11.551)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4), sequence alignment score = 391.1  
RMSD between 54 pruned atom pairs is 1.167 angstroms; (across all 595 pairs:
57.112)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 162  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> matchmaker #1-5 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
uvig_8948_18_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#6) with
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1), sequence alignment score = 379.8  
RMSD between 64 pruned atom pairs is 1.250 angstroms; (across all 608 pairs:
57.549)  
  
Matchmaker
uvig_8948_18_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#6) with
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 354.5  
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 533 pairs:
39.420)  
  
Matchmaker
uvig_8948_18_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#6) with uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#3), sequence alignment score = 433.5  
RMSD between 54 pruned atom pairs is 1.096 angstroms; (across all 571 pairs:
47.332)  
  
Matchmaker
uvig_8948_18_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#6) with
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4), sequence alignment score = 2406.7  
RMSD between 477 pruned atom pairs is 1.303 angstroms; (across all 882 pairs:
4.736)  
  
Matchmaker
uvig_8948_18_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#6) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 1362  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> show #1 models

> show #2 models

> show #3 models

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/3/OP172649_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb

Chain information for
OP172649_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/3/uvig_138647_12_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
uvig_138647_12_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #8  
---  
Chain | Description  
A | No description available  
  

> select #5

6844 atoms, 7003 bonds, 894 residues, 1 model selected  

> ~select #5

Nothing selected  

> select #7

5011 atoms, 5101 bonds, 669 residues, 1 model selected  

> select #8

5842 atoms, 5932 bonds, 779 residues, 1 model selected  

> select #7

5011 atoms, 5101 bonds, 669 residues, 1 model selected  

> select #8

5842 atoms, 5932 bonds, 779 residues, 1 model selected  

> select #7

5011 atoms, 5101 bonds, 669 residues, 1 model selected  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel olive

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel deep sky blue

> color sel goldenrod

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

[Repeated 1 time(s)]

> color sel khaki

> color sel pale goldenrod

> color sel khaki

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel burly wood

> color sel khaki

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel yellow

> color sel pale goldenrod

> color sel khaki

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> select #8/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #7

5011 atoms, 5101 bonds, 669 residues, 1 model selected  

> select #8

5842 atoms, 5932 bonds, 779 residues, 1 model selected  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel khaki

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> matchmaker #2-8 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
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 2352.5  
RMSD between 220 pruned atom pairs is 0.749 angstroms; (across all 658 pairs:
13.144)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3), sequence alignment score = 1587.7  
RMSD between 187 pruned atom pairs is 0.990 angstroms; (across all 655 pairs:
11.551)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4), sequence alignment score = 391.1  
RMSD between 54 pruned atom pairs is 1.167 angstroms; (across all 595 pairs:
57.112)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 162  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> show #6 models

> show #5 models

> show #4 models

> show #1 models

> show #2 models

> show #3 models

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> show #7 models

> ~select #8

Nothing selected  

> matchmaker #6,8 to #7

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
OP172649_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#7) with uvig_8948_18_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#6), sequence alignment score = 376  
RMSD between 5 pruned atom pairs is 1.463 angstroms; (across all 601 pairs:
32.609)  
  
Matchmaker
OP172649_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#7) with
uvig_138647_12_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#8), sequence alignment score = 1431.3  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/4/uvig_2919_12_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
uvig_2919_12_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #9  
---  
Chain | Description  
A | No description available  
  

> hide #7 models

Drag select of 775 residues  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel dark sea green

> select clear

> hide #9 models

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/5/A_HM3_1_LOC_1_4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
A_HM3_1_LOC_1_4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #10  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/5/OP172643_00029_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
OP172643_00029_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #11  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/liuzhe/Desktop/project-X7D/paper/clade结构/5/OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb

Chain information for
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #12  
---  
Chain | Description  
A | No description available  
  
Drag select of 2382 residues  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> color sel indian red

> select clear

> matchmaker #1-11 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
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1), sequence alignment score = 1097.5  
RMSD between 139 pruned atom pairs is 0.877 angstroms; (across all 635 pairs:
13.902)  
  
Matchmaker
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 1063.9  
RMSD between 208 pruned atom pairs is 1.042 angstroms; (across all 649 pairs:
20.506)  
  
Matchmaker
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3), sequence alignment score = 1160.9  
RMSD between 300 pruned atom pairs is 1.118 angstroms; (across all 653 pairs:
15.817)  
  
Matchmaker
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4), sequence alignment score = 471.6  
RMSD between 12 pruned atom pairs is 1.211 angstroms; (across all 700 pairs:
37.730)  
  
Matchmaker
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 173.3  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> show #1 models

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> show #6 models

> show #7 models

> show #8 models

> show #9 models

> hide #9 models

> hide #8 models

> hide #7 models

> hide #6 models

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> hide #1 models

> hide #10 models

> hide #11 models

> hide #12 models

> show #11 models

> hide #11 models

> show #10 models

> matchmaker #9-11 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
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
uvig_2919_12_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#9), sequence alignment score = 1707.8  
RMSD between 111 pruned atom pairs is 0.784 angstroms; (across all 756 pairs:
21.823)  
  
Matchmaker
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
A_HM3_1_LOC_1_4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain
A (#10), sequence alignment score = 2477.6  
RMSD between 427 pruned atom pairs is 0.789 angstroms; (across all 765 pairs:
20.213)  
  
Matchmaker
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
OP172643_00029_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#11), sequence alignment score = 2717.5  
RMSD between 432 pruned atom pairs is 0.791 angstroms; (across all 784 pairs:
8.321)  
  

> show #11 models

> show #12 models

> hide #11 models

> hide #12 models

> hide #10 models

> show #11 models

> hide #11 models

> show #12 models

> hide #12 models

> show #11 models

> show #10 models

> hide #11 models

> save /Users/liuzhe/Desktop/image143.png supersample 3

> hide #10 models

> show #11 models

> save /Users/liuzhe/Desktop/image144.png supersample 3

> hide #11 models

> show #12 models

> save /Users/liuzhe/Desktop/image145.png supersample 3

> hide #12 models

> show #9 models

> save /Users/liuzhe/Desktop/image146.png supersample 3

> hide #9 models

> show #8 models

> show #7 models

> hide #8 models

> show #8 models

> matchmaker #8 to #7

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
OP172649_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#7) with
uvig_138647_12_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#8), sequence alignment score = 1431.3  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> matchmaker #7 to #8

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
uvig_138647_12_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#8) with
OP172649_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#7), sequence alignment score = 1431.3  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> matchmaker #7-8 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
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
OP172649_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#7), sequence alignment score = 1306  
RMSD between 109 pruned atom pairs is 1.045 angstroms; (across all 657 pairs:
24.282)  
  
Matchmaker
OP172693_00019_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#12) with
uvig_138647_12_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#8), sequence alignment score = 781.8  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> hide #8 models

> hide #7 models

> show #7 models

> show #8 models

> hide #8 models

> show #8 models

> hide #7 models

> show #6 models

> hide #6 models

> show #7 models

> hide #8 models

> hide #7 models

> show #8 models

> hide #8 models

> select #7

5011 atoms, 5101 bonds, 669 residues, 1 model selected  

> select #8

5842 atoms, 5932 bonds, 779 residues, 1 model selected  

> show #7 models

> show #8 models

> hide #8 models

> show #8 models

> ~select #8

Nothing selected  

> hide #8 models

> show #8 models

> hide #7 models

> show #6 models

> hide #6 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #4 models

> hide #4 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> hide #8 models

> show #1 models

> select add #1/A:660

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select clear

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> show #3 models

> hide #1 models

> save /Users/liuzhe/Desktop/image147.png supersample 3

> hide #3 models

> show #2 models

> save /Users/liuzhe/Desktop/image148.png supersample 3

> hide #2 models

> show #1 models

> save /Users/liuzhe/Desktop/image149.png supersample 3

> hide #1 models

> show #10 models

> hide #10 models

> show #4 models

> show #5 models

> show #6 models

> ui tool show Matchmaker

> matchmaker #5-6 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
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 2048.3  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> matchmaker #2-12 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
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 2352.5  
RMSD between 220 pruned atom pairs is 0.749 angstroms; (across all 658 pairs:
13.144)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3), sequence alignment score = 1587.7  
RMSD between 187 pruned atom pairs is 0.990 angstroms; (across all 655 pairs:
11.551)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4), sequence alignment score = 391.1  
RMSD between 54 pruned atom pairs is 1.167 angstroms; (across all 595 pairs:
57.112)  
  
Matchmaker
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 162  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> ui tool show Matchmaker

> matchmaker #1-8,10-12 to #9

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
uvig_2919_12_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#9) with
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1), sequence alignment score = 995  
RMSD between 47 pruned atom pairs is 1.003 angstroms; (across all 616 pairs:
27.160)  
  
Matchmaker
uvig_2919_12_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#9) with
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 842.6  
RMSD between 57 pruned atom pairs is 0.574 angstroms; (across all 611 pairs:
32.497)  
  
Matchmaker
uvig_2919_12_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#9) with uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#3), sequence alignment score = 880.7  
RMSD between 25 pruned atom pairs is 1.139 angstroms; (across all 639 pairs:
25.259)  
  
Matchmaker
uvig_2919_12_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#9) with
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4), sequence alignment score = 557  
RMSD between 39 pruned atom pairs is 0.847 angstroms; (across all 685 pairs:
43.723)  
  
Matchmaker
uvig_2919_12_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#9) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 317.5  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> matchmaker #1-2,4-12 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
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3) with
A_BL19_2_LOC_1_34_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1), sequence alignment score = 1587.7  
RMSD between 187 pruned atom pairs is 0.990 angstroms; (across all 655 pairs:
11.551)  
  
Matchmaker
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3) with
OP172723_00012_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 1721.9  
RMSD between 283 pruned atom pairs is 1.045 angstroms; (across all 663 pairs:
11.109)  
  
Matchmaker
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3) with
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4), sequence alignment score = 395.1  
RMSD between 39 pruned atom pairs is 1.048 angstroms; (across all 592 pairs:
48.309)  
  
Matchmaker
uvig_8948_19_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 131.7  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  

> save /Users/liuzhe/Desktop/project-X7D/paper/clade结构/compare.cxs

> close #7-12

> close #1-3

> ui tool show Matchmaker

> matchmaker #5-6 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
A_BL19_2_LOC_1_33_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#4) with
MT074135_00005_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 2048.3  
Traceback (most recent call last):  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 289, in run_matchmaker  
run(self.session, cmd)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 695, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 555, in match  
final_match, final_ref, rmsd, full_rmsd, xf = align.align(session,
initial_match, initial_ref,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 110, in align  
return align_atoms(patoms, pto_atoms, xyz_to, cutoff_distance,  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 126, in align_atoms  
tf, rmsd, indices = align_and_prune(xyz_from, xyz_to, cutoff_distance)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/align.py", line 153, in align_and_prune  
p, rms = align_points(axyz, ref_axyz)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/align.py", line 62, in align_points  
evals, evecs = linalg.eig(P) # eigenvectors are columns  
File "<__array_function__ internals>", line 5, in eig  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 1317, in eig  
_assert_finite(a)  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
numpy.linalg.LinAlgError: Array must not contain infs or NaNs  
  
File
"/Users/liuzhe/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 208, in _assert_finite  
raise LinAlgError("Array must not contain infs or NaNs")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.5.9
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 8 GB

Software:

    System Software Overview:

      System Version: macOS 11.3.1 (20E241)
      Kernel Version: Darwin 20.4.0
      Time since boot: 86 days 21:10

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 2880 x 1800
          UI Looks like: 1440 x 900 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

PDB reading has been revised to exclude this since then