KeyError matching selected regions

[m.hunter@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/m.hunter/OneDrive - Victor Chang Cardiac Research Institute
> Ltd/Documents/Our Structures/620T_highK/S620T300_3.pdb"

Chain information for S620T300_3.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> open "C:/Users/m.hunter/OneDrive - Victor Chang Cardiac Research Institute
> Ltd/Documents/Our
> Structures/588E_lowK/n588e3_0013_C4_TM_3_fixedABCD_real_space_refined_049.pdb"

Chain information for n588e3_0013_C4_TM_3_fixedABCD_real_space_refined_049.pdb
#2  
---  
Chain | Description  
A B C D | No description available  
  

> select add #2

19108 atoms, 19376 bonds, 12 pseudobonds, 1172 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99691,0.0051737,-0.078362,14.265,-0.0092541,0.99861,-0.051798,11.412,0.077985,0.052363,0.99558,-20.683

> view matrix models
> #2,0.99748,0.013453,-0.069688,11.188,-0.012214,0.99976,0.018174,-1.3334,0.069915,-0.017277,0.9974,-8.2011

> view matrix models
> #2,0.99859,0.0095339,0.052157,-11.065,-0.015437,0.99336,0.11398,-17.608,-0.050724,-0.11463,0.99211,28.754

> view matrix models
> #2,0.99933,0.011533,0.034835,-8.2861,-0.014854,0.99521,0.096637,-14.775,-0.033553,-0.097089,0.99471,22.543

> view matrix models
> #2,0.99358,0.0065354,0.11297,-21.08,-0.022369,0.98997,0.13947,-20.656,-0.11093,-0.1411,0.98376,44.612

> view matrix models
> #2,0.98481,0.0052474,0.17355,-30.715,-0.03997,0.97955,0.19719,-26.793,-0.16897,-0.20113,0.96488,67.615

> view matrix models
> #2,0.98756,0.0096767,0.15692,-28.8,-0.040908,0.97954,0.19704,-26.609,-0.15181,-0.20101,0.96776,64.227

> view matrix models
> #2,0.99907,0.032162,0.028608,-10.487,-0.036,0.98867,0.14574,-19.36,-0.023597,-0.14663,0.98891,30.156

> view matrix models
> #2,0.99585,0.02121,0.088551,-19.323,-0.029557,0.99513,0.094046,-11.852,-0.086125,-0.096272,0.99162,31.658

> view matrix models
> #2,0.99494,0.024813,0.097395,-21.416,-0.019632,0.99836,-0.053797,13.54,-0.09857,0.051613,0.99379,8.9054

> view matrix models
> #2,0.99206,0.024101,0.12341,-25.674,-0.027306,0.99933,0.02434,0.078002,-0.12274,-0.027517,0.99206,26.273

> view matrix models
> #2,0.95222,-0.28494,0.10991,34.409,0.27965,0.95815,0.061175,-50.642,-0.12274,-0.027517,0.99206,26.273

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.95222,-0.28494,0.10991,35.061,0.27965,0.95815,0.061175,-50.937,-0.12274,-0.027517,0.99206,23.843

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.89731,-0.42931,0.10264,69.297,0.42617,0.90316,0.051888,-64.307,-0.11498,-0.0028162,0.99336,18.244

> ui mousemode right "move picked models"

> view matrix models
> #2,0.89731,-0.42931,0.10264,70.4,0.42617,0.90316,0.051888,-60.427,-0.11498,-0.0028162,0.99336,18.021

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.92269,-0.37084,0.10546,56.039,0.36683,0.92861,0.055856,-55.576,-0.11865,-0.012851,0.99285,20.377

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.92269,-0.37084,0.10546,54.911,0.36683,0.92861,0.055856,-59.092,-0.11865,-0.012851,0.99285,20.601

> ui tool show Matchmaker

> matchmaker #!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 S620T300_3.pdb, chain A (#1) with
n588e3_0013_C4_TM_3_fixedABCD_real_space_refined_049.pdb, chain A (#2),
sequence alignment score = 1533.9  
RMSD between 285 pruned atom pairs is 0.537 angstroms; (across all 293 pairs:
0.671)  
  

> matchmaker #!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 S620T300_3.pdb, chain A (#1) with
n588e3_0013_C4_TM_3_fixedABCD_real_space_refined_049.pdb, chain A (#2),
sequence alignment score = 1533.9  
RMSD between 285 pruned atom pairs is 0.537 angstroms; (across all 293 pairs:
0.671)  
  

> select subtract #2

Nothing selected  

> select add #2

19108 atoms, 19376 bonds, 12 pseudobonds, 1172 residues, 2 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.30264,-0.95304,-0.011416,374.25,0.95301,-0.30276,0.010872,56.168,-0.013818,-0.0075891,0.99988,-0.48846

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.32634,-0.94522,-0.0080069,376.23,0.94517,-0.32641,0.010928,61.354,-0.012943,-0.0040018,0.99991,-1.2308

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.32634,-0.94522,-0.0080069,375.79,0.94517,-0.32641,0.010928,61.036,-0.012943,-0.0040018,0.99991,-1.1891

> view matrix models
> #2,-0.32634,-0.94522,-0.0080069,376.26,0.94517,-0.32641,0.010928,62.099,-0.012943,-0.0040018,0.99991,-0.588

> view matrix models
> #2,-0.32634,-0.94522,-0.0080069,375.74,0.94517,-0.32641,0.010928,61.233,-0.012943,-0.0040018,0.99991,-1.7273

> view matrix models
> #2,-0.32634,-0.94522,-0.0080069,375.24,0.94517,-0.32641,0.010928,60.566,-0.012943,-0.0040018,0.99991,-2.1635

> ui tool show Matchmaker

> matchmaker #!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 S620T300_3.pdb, chain A (#1) with
n588e3_0013_C4_TM_3_fixedABCD_real_space_refined_049.pdb, chain A (#2),
sequence alignment score = 1533.9  
RMSD between 285 pruned atom pairs is 0.537 angstroms; (across all 293 pairs:
0.671)  
  

> matchmaker #!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 S620T300_3.pdb, chain A (#1) with
n588e3_0013_C4_TM_3_fixedABCD_real_space_refined_049.pdb, chain A (#2),
sequence alignment score = 1533.9  
RMSD between 285 pruned atom pairs is 0.537 angstroms; (across all 293 pairs:
0.671)  
  

> mmaker #1/a,b,c,d:404-537 to #2/a,b,c,d:404-537 pair ss

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2918, in run  
result = ci.function(session, *args, optional=optional,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 3457, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 730, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at
0x000001D893433940>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.101.1692
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_AU.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7060
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 16,966,094,848
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
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    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-gltf: 1.0
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    ChimeraX-Hbonds: 2.4
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    ChimeraX-HKCage: 1.3
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    ChimeraX-Vive: 1.1
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    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[Eric Pettersen]

Hi Mark,

Thanks for reporting this problem. It is fixed in newer versions of ChimeraX, so if you upgrade your version then things will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab