Opened 4 years ago

Closed 4 years ago

#4934 closed defect (can't reproduce)

Crash computing clashes

Reported by: macbas@… Owned by: pett
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Fatal Python error: Aborted

Thread 0x00001eec (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 306 in wait
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 558 in wait
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 1252 in run
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 932 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 890 in _bootstrap

Current thread 0x000005c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 1015 in 
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 194 in _run_module_as_main


Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\Maciek\\\Desktop\\\FinO_proteins.cxs

Log from Thu Jul 22 11:19:18 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\Maciek\\\Desktop\\\FinO_proteins.cxs

Log from Wed Jul 21 14:22:07 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\Maciek\\\Desktop\\\FinO_proteins.cxs

Log from Tue Jul 20 15:35:07 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "F:/Roboczy_folder/PyMol data/ProQ_czyste.pse"

Unrecognized file suffix '.pse'  

> open
> C:\Users\Maciek\Desktop\Data.copy\\#Studia_doktoranckie_Zakład_Biochemii_zrzut_21.11.19\granty\Preludium\Preludium_2021\robocze_pliki\Structural_alignments\Complete_FopA_strucutre\model1.pdb
> format pdb

Chain information for model1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:1

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

> select /A:1-83

1362 atoms, 1378 bonds, 83 residues, 1 model selected  

> delete :1-83

> open
> F:/Roboczy_folder/Projekt_domeny_FinO/FinO_proteins_strucural_analysis/ProQ.cif

Summary of feedback from opening
F:/Roboczy_folder/Projekt_domeny_FinO/FinO_proteins_strucural_analysis/ProQ.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for MET /A:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for ProQ.cif #2  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

Drag select of 4 residues  
Drag select of 4 residues  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,12.942,0,1,0,28.822,0,0,1,53.637

> view matrix models #2,1,0,0,6.3703,0,1,0,11.783,0,0,1,23.71

> select clear

> select #1/A:141

14 atoms, 13 bonds, 1 residue, 1 model selected  

> view matrix models #1,1,0,0,-93.527,0,1,0,-56.182,0,0,1,-31.873

Drag select of 8 residues  

> view matrix models #1,1,0,0,-104.36,0,1,0,-51.316,0,0,1,-29.654

> select clear

> select #2/A:39

20 atoms, 20 bonds, 1 residue, 1 model selected  

> view matrix models #2,1,0,0,7.8377,0,1,0,19.276,0,0,1,20.375

> show surfaces

> select clear

> select #2/A:62@CG

1 atom, 1 residue, 1 model selected  

> view matrix models #2,1,0,0,30.309,0,1,0,44.846,0,0,1,0.51203

Drag select of model1.pdb_A SES surface, 470 of 149100 triangles, 3 residues  
Drag select of model1.pdb_A SES surface, 1204 of 149100 triangles, 4 residues  

> view matrix models #1,1,0,0,-84.088,0,1,0,-32.763,0,0,1,-24.099

> view matrix models #1,1,0,0,-84.038,0,1,0,-32.357,0,0,1,-23.877

> select #1/A:110@CG2

1 atom, 1 residue, 1 model selected  

> view matrix models #1,1,0,0,-81.56,0,1,0,-33.393,0,0,1,-25.464

> view matrix models #1,1,0,0,-82.188,0,1,0,-35.326,0,0,1,-26.368

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.75178,0.31072,0.58162,-126.55,-0.045219,0.90424,-0.42463,3.4339,-0.65787,0.29293,0.69383,19.179

> select #2/A:36@HB

1 atom, 1 residue, 1 model selected  

> view matrix models
> #2,0.73253,-0.45298,0.50815,29.443,0.23577,0.86909,0.43485,45.548,-0.6386,-0.19873,0.74343,-1.4536

> view matrix models
> #2,0.70446,-0.44583,0.55224,29.368,0.23318,0.88028,0.41321,45.541,-0.67034,-0.16232,0.72408,-1.5369

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #2,0.70446,-0.44583,0.55224,27.052,0.23318,0.88028,0.41321,43.636,-0.67034,-0.16232,0.72408,0.93157

> view matrix models
> #1,0.75178,0.31072,0.58162,-124.32,-0.045219,0.90424,-0.42463,2.407,-0.65787,0.29293,0.69383,16.982

> select clear

> save C:/Users/Maciek/Desktop/FinO_proteins.cxs

> open 1dvo

1dvo title:  
The X-ray crystal structure of fino, A repressor of bacterial conjugation
[more info...]  
  
Chain information for 1dvo #3  
---  
Chain | Description  
A | fertility inhibition protein O  
  

> show surfaces

> view matrix models #3,1,0,0,-35.537,0,1,0,48.703,0,0,1,33.157

> view matrix models #3,1,0,0,-36.024,0,1,0,44.538,0,0,1,33.904

> tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> delete #3:33-72

> reneame #1 FopA

Unknown command: reneame #1 FopA  

> rename #1 FopA

> rename #3 FinO

> rename #2 ProQ

> ui mousemode right "rotate selected models"

> select #1/A:193@CB

1 atom, 1 residue, 1 model selected  

> view matrix models
> #1,0.73395,0.10374,0.67124,-112.7,-0.072924,0.99459,-0.073976,-25.703,-0.67528,0.0053447,0.73754,37.907

> select #3/A:130@CB

1 atom, 1 residue, 1 model selected  

> view matrix models
> #3,0.51046,0.62568,-0.58988,3.4568,0.54159,-0.76676,-0.34462,67.578,-0.66792,-0.14356,-0.73026,149.69

> ui mousemode right "move picked models"

> view matrix models
> #3,0.51046,0.62568,-0.58988,-5.364,0.54159,-0.76676,-0.34462,81.751,-0.66792,-0.14356,-0.73026,144.86

> view matrix models
> #3,0.51046,0.62568,-0.58988,-18.44,0.54159,-0.76676,-0.34462,63.762,-0.66792,-0.14356,-0.73026,125.94

> select #3/A:128@CG2

1 atom, 1 residue, 1 model selected  

> view matrix models
> #3,0.51046,0.62568,-0.58988,-18.209,0.54159,-0.76676,-0.34462,64.187,-0.66792,-0.14356,-0.73026,125.51

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.61278,0.23475,-0.75458,-7.4367,0.75613,-0.45173,0.4735,9.5112,-0.22971,-0.86072,-0.45431,106.47

> ui mousemode right "move picked models"

> view matrix models
> #3,0.61278,0.23475,-0.75458,-8.2744,0.75613,-0.45173,0.4735,7.5345,-0.22971,-0.86072,-0.45431,108.32

> save C:/Users/Maciek/Desktop/FinO_proteins.cxs

> open 3mw6

3mw6 title:  
Crystal structure of NMB1681 from Neisseria meningitidis MC58, a FinO-like RNA
chaperone [more info...]  
  
Chain information for 3mw6 #4  
---  
Chain | Description  
A B C D E F | uncharacterized protein NMB1681  
  
Non-standard residues in 3mw6 #4  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
3mw6 mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
4| software_defined_assembly  
  

> delete #4/B-F

> delete solvent

> style #4 cartoon

Expected a keyword  

> style #4 cartoon atoms

Expected a keyword  

> style #4 atoms cartoon

Expected a keyword  

> usage style

style [objects] [atomStyle] [dashes an integer] [ringFill ringFill]  
— change atom and bond depiction  
objects: an objects specifier or nothing  
atomStyle: one of ball, sphere, or stick or nothing  
ringFill: one of off, on, thick, or thin  

> style #4 cartoon

Expected a keyword  

> style #4

> style #4 ball off

Expected a keyword  

> style #4 sphere FALSE

Expected a keyword  

> style #4 sphere False

Expected a keyword  

> style #4 sphere false

Expected a keyword  

> style #4 sphere off

Expected a keyword  

> hide :4 sphere

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

> hide :4 atoms sphere

Expected ',' or a keyword  

> hide :4 spehe atoms

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

> style sel sphere

Changed 1 atom style  

> select #4/A:49@N

1 atom, 1 residue, 1 model selected  

> select #4

959 atoms, 975 bonds, 122 residues, 1 model selected  

> style sel sphere

Changed 959 atom styles  

> style sel stick

Changed 959 atom styles  

> style sel stick

Changed 959 atom styles  

> style sel sphere

Changed 959 atom styles  

> style sel ball

Changed 959 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 959 atom styles  

> style sel sphere

Changed 959 atom styles  

> style sel ball

Changed 959 atom styles  

> style sel sphere

Changed 959 atom styles  

> show sel atoms

> show sel atoms

> show sel atoms

> show sel cartoons

> show sel cartoons

> hide sel atoms

> show sel surfaces

> select #4/A:45@O

1 atom, 1 residue, 1 model selected  

> view matrix models #4,1,0,0,-83.513,0,1,0,6.3887,0,0,1,91.272

> view matrix models #4,1,0,0,-62.355,0,1,0,44.93,0,0,1,110.07

> view matrix models #4,1,0,0,-75.954,0,1,0,34.991,0,0,1,133.14

> view matrix models #4,1,0,0,-78.076,0,1,0,34.692,0,0,1,135.32

> view matrix models #4,1,0,0,-77.818,0,1,0,35.594,0,0,1,134.07

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.93355,-0.20658,0.29295,-70.557,0.26346,0.94959,-0.16994,34.041,-0.24307,0.23582,0.94091,129.57

> view matrix models
> #4,0.99972,-0.015582,0.018014,-77.327,0.015825,0.99978,-0.013415,35.412,-0.017801,0.013696,0.99975,133.85

> view matrix models
> #4,0.99964,0.017743,-0.019926,-78.37,-0.017438,0.99973,0.015361,35.81,0.020193,-0.015008,0.99968,134.3

> view matrix models
> #4,0.96546,0.18607,-0.18237,-83.237,-0.15651,0.9738,0.16498,38.275,0.20829,-0.13074,0.96929,135.69

> ui mousemode right "move picked models"

> view matrix models
> #4,0.96546,0.18607,-0.18237,-87.712,-0.15651,0.9738,0.16498,41.86,0.20829,-0.13074,0.96929,135.46

> view matrix models
> #4,0.96546,0.18607,-0.18237,-85.578,-0.15651,0.9738,0.16498,38.781,0.20829,-0.13074,0.96929,137.13

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.94083,0.24764,-0.23132,-87.214,-0.197,0.95511,0.22124,39.847,0.27573,-0.16258,0.94739,137.33

> view matrix models
> #4,0.94293,0.24291,-0.22775,-87.091,-0.19407,0.95671,0.2169,39.763,0.27058,-0.16032,0.94925,137.32

> view matrix models
> #4,0.98444,0.12235,-0.1261,-83.807,-0.10904,0.9882,0.10758,37.765,0.13777,-0.092161,0.98617,136.76

> view matrix models
> #4,-0.2608,0.057686,-0.96367,-115.51,0.91335,-0.30856,-0.26566,42.55,-0.31267,-0.94945,0.027786,112.17

> view matrix models
> #4,-0.6873,-0.58226,-0.43427,-104.28,0.49988,0.054608,-0.86437,22.859,0.52701,-0.81116,0.25353,124.93

> view matrix models
> #4,-0.094145,0.14375,-0.98513,-114.79,0.89513,-0.42089,-0.14696,45.672,-0.43576,-0.89565,-0.089048,108

> view matrix models
> #4,-0.25112,0.063529,-0.96587,-115.49,0.91322,-0.31524,-0.25817,42.755,-0.32088,-0.94688,0.021148,111.93

> view matrix models
> #4,-0.648,-0.35412,-0.67431,-110.57,0.72345,-0.0093688,-0.69031,29.39,0.23813,-0.93515,0.26226,122.92

> view matrix models
> #4,0.087728,-0.75589,-0.6488,-101.78,0.81837,-0.31666,0.47958,59.912,-0.56796,-0.57303,0.59082,122.27

> view matrix models
> #4,-0.26659,-0.80893,-0.52398,-101.81,0.89723,-0.40686,0.17162,53.426,-0.35201,-0.42438,0.83426,129.69

> view matrix models
> #4,-0.60755,0.36193,0.70703,-78.933,0.48619,0.87336,-0.029296,40.296,-0.62809,0.32595,-0.70658,86.906

> view matrix models
> #4,-0.64999,0.59008,0.47887,-85.688,0.65851,0.75186,-0.032642,42.221,-0.37931,0.29412,-0.87728,85.135

> view matrix models
> #4,-0.62122,0.60071,0.50323,-84.865,0.6661,0.74305,-0.064716,41.538,-0.4128,0.295,-0.86173,85.204

> view matrix models
> #4,-0.46323,0.64899,0.60352,-81.129,0.68141,0.69624,-0.22568,37.909,-0.56666,0.3067,-0.76474,86.117

> view matrix models
> #4,-0.64319,0.59265,0.48484,-85.489,0.66047,0.74977,-0.040316,42.059,-0.38741,0.29429,-0.87368,85.148

> view matrix models
> #4,-0.63571,0.59544,0.49124,-85.273,0.6625,0.74748,-0.048688,41.881,-0.39619,0.2945,-0.86966,85.165

> view matrix models
> #4,-0.74021,0.55139,0.38478,-88.683,0.62075,0.78032,0.075946,44.428,-0.25837,0.29507,-0.91988,85.204

> view matrix models
> #4,-0.82652,0.50219,0.25432,-92.494,0.55278,0.80943,0.19814,46.687,-0.10635,0.30435,-0.94661,85.918

> view matrix models
> #4,-0.78393,0.52857,0.32567,-90.451,0.59182,0.79474,0.13469,45.547,-0.18763,0.29832,-0.93584,85.453

> view matrix models
> #4,-0.68947,0.57427,0.44141,-86.912,0.64491,0.76414,0.013192,43.173,-0.32973,0.29377,-0.89721,85.106

> view matrix models
> #4,-0.74019,0.55141,0.38481,-88.682,0.62077,0.78031,0.075916,44.428,-0.25841,0.29507,-0.91987,85.204

> view matrix models
> #4,0.52789,0.34594,-0.77567,-104.65,-0.8045,0.49643,-0.32611,22.475,0.27225,0.79617,0.54036,124.03

> view matrix models
> #4,0.069514,0.23518,-0.96946,-113.22,-0.77239,0.62771,0.096889,32.65,0.63133,0.74207,0.22528,119.82

> view matrix models
> #4,-0.66525,0.58415,0.46499,-86.147,0.65372,0.75658,-0.015198,42.587,-0.36068,0.29386,-0.88519,85.114

> view matrix models
> #4,-0.78943,0.52544,0.31736,-90.693,0.58748,0.7966,0.14247,45.691,-0.17795,0.29891,-0.93754,85.499

> view matrix models
> #4,-0.67516,0.58018,0.45558,-86.455,0.6503,0.75967,-0.0036843,42.826,-0.34822,0.29377,-0.89019,85.107

> view matrix models
> #4,-0.031842,0.99322,-0.1118,-95.829,0.97538,0.0553,0.21349,53.566,0.21822,-0.10225,-0.97053,89.729

> ui mousemode right "move picked models"

> view matrix models
> #4,-0.031842,0.99322,-0.1118,-101.54,0.97538,0.0553,0.21349,59.332,0.21822,-0.10225,-0.97053,88.087

> save C:/Users/Maciek/Desktop/FinO_proteins.cxs

> transparncy 60

Unknown command: transparncy 60  

> transparency 60

> open
> F:/Roboczy_folder/Projekt_domeny_FinO/FinO_proteins_strucural_analysis/chimeraX/4_proteins.aln

Summary of feedback from opening
F:/Roboczy_folder/Projekt_domeny_FinO/FinO_proteins_strucural_analysis/chimeraX/4_proteins.aln  
---  
notes | Alignment identifier is 4_proteins.aln  
Associated FopA chain A to FopA/1-200 with 0 mismatches  
Associated ProQ chain A to Ec_ProQ/1-232 with 0 mismatches  
Associated FinO chain A to Ec_FinO/1-186 with 1 mismatch  
Associated 3mw6 chain A to Nm_ProQ/1-141 with 3 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4_proteins.aln  
  
Opened 4 sequences from 4_proteins.aln  

> select #3/A:143

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:143 #1/A:157 #2/A:80 #4/A:87

70 atoms, 66 bonds, 4 residues, 4 models selected  
Seqview [ID: 4_proteins.aln] region Ec_FinO/1-186..Nm_ProQ/1-141 [161] RMSD:
103.636  
  

> show sel atoms

> color sel blue

> save C:/Users/Maciek/Desktop/FinO_proteins.cxs

> style sel sphere off

Expected a keyword  

> style sel stick

Changed 70 atom styles  

> select clear

> save C:\Users\Maciek\Desktop\image1.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Maciek\Desktop\movie1.mp4

Movie saved to \C:Users\\...\Desktop\movie1.mp4  
  

> 2dlabels text "concave side - ProQ R80 and homologous positions"

> view matrix models
> #1,0.73395,0.10374,0.67124,-118.56,-0.072924,0.99459,-0.073976,-27.168,-0.67528,0.0053447,0.73754,44.176

> undo

> ui mousemode right "move label"

> 2dlabels #5.1 xpos 0.026 ypos 0.905

> save C:/Users/Maciek/Desktop/FinO_proteins.cxs

——— End of log from Tue Jul 20 15:35:07 2021 ———

opened ChimeraX session  

> ui tool show Rotamers

> select #3/A:151@CA

1 atom, 1 residue, 1 model selected  

> select #3/A:151@CA

1 atom, 1 residue, 1 model selected  

> select #3/A:144@CE1

1 atom, 1 residue, 1 model selected  

> select #3/A:95@CB

1 atom, 1 residue, 1 model selected  

> select #3/A:144@CE1

1 atom, 1 residue, 1 model selected  

> select #3/A:95@CD1

1 atom, 1 residue, 1 model selected  

> select #3/A:144@CE1

1 atom, 1 residue, 1 model selected  

> select #3/A:143

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:143 #1/A:157 #2/A:80 #4/A:87

70 atoms, 66 bonds, 4 residues, 4 models selected  
Seqview [ID: 4_proteins.aln] region Ec_FinO/1-186..Nm_ProQ/1-141 [161] RMSD:
103.636  
  

> style sel sticks

Expected a keyword  

> hide sel atoms

> show sel atoms

> style sel stick

Changed 70 atom styles  

> style sel stick

Changed 70 atom styles  

> style sel ringFill off

Changed 4 residue ring styles  

> select clear

> select #3/A:143

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:143 #1/A:157 #2/A:80 #4/A:87

70 atoms, 66 bonds, 4 residues, 4 models selected  
Seqview [ID: 4_proteins.aln] region Ec_FinO/1-186..Nm_ProQ/1-141 [161] RMSD:
103.636  
  

> style sel ball

Changed 70 atom styles  

> style sel ball

Changed 70 atom styles  

> style sel sphere

Changed 70 atom styles  

> style sel sphere

Changed 70 atom styles  

> style sel stick

Changed 70 atom styles  

> hide sel @H

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

> hide sel @hydrogens

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

> hide sel @hydrogens atoms

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

> hide hydrogen

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

> hide hydrogen atoms

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

> hide @hydrogen atoms

> hide atoms @hydrogen

Expected ',' or a keyword  

> hide atoms hydro

Expected ',' or a keyword  

> delete H

> save C:/Users/Maciek/Desktop/FinO_proteins.cxs

——— End of log from Wed Jul 21 14:22:07 2021 ———

opened ChimeraX session  

> delete 2dlabels

Missing or invalid "atoms" argument: invalid atoms specifier  

> 2dlabels delete

> mmaker #1 #2 #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 3mw6, chain A (#4) with FopA, chain A (#1), sequence alignment
score = 139.1  
RMSD between 47 pruned atom pairs is 1.091 angstroms; (across all 101 pairs:
7.497)  
  
Matchmaker 3mw6, chain A (#4) with ProQ, chain A (#2), sequence alignment
score = 70.4  
RMSD between 34 pruned atom pairs is 1.090 angstroms; (across all 101 pairs:
7.560)  
  
Matchmaker 3mw6, chain A (#4) with FinO, chain A (#3), sequence alignment
score = 106.7  
RMSD between 56 pruned atom pairs is 1.012 angstroms; (across all 97 pairs:
8.039)  
  

> select clear

> hide surfaces

> hide cartoons

> undo

> hide cartoons

> select #3/A:143 #1/A:157 #2/A:80 #4/A:87

44 atoms, 40 bonds, 4 residues, 4 models selected  

> select #2/A:80

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:80

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide śel

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

> hide ~sel

> save C:/Users/Maciek/Desktop/FinO_proteins.cxs

——— End of log from Thu Jul 22 11:19:18 2021 ———

opened ChimeraX session  




OpenGL version: 3.3.0 - Build 27.20.100.8935
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 8,361,283,584
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
OSLanguage: pl-PL
Locale: ('pl_PL', 'cp1250')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (9)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Unknown crash

comment:2 by pett, 4 years ago

Status: accepted → feedback

Hi Maciek,

Do you remember what was going on when this crash happened? Was it at ChimeraX startup, or later while you were doing something?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by mmaciej.basczok@…, 4 years ago 

Hi Eric,
It was during rotametrs investigation - I had selected several rotametrs from the library and run the clashes calculation. Instanteniulsy crash happened.

Kind regards,

Maciej

Pobierz aplikację Outlook dla systemu Android<https://aka.ms/AAb9ysg>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, July 22, 2021 5:52:49 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Maciej Basczok <mmaciej.basczok@amu.edu.pl>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #4934: Unknown crash

#4934: Unknown crash
-------------------------------+----------------------------
          Reporter:  macbas@…  |      Owner:  Eric Pettersen
              Type:  defect    |     Status:  feedback
          Priority:  normal    |  Milestone:
         Component:  Core      |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Hi Maciek,
         Do you remember what was going on when this crash happened?  Was
 it at ChimeraX startup, or later while you were doing something?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F4934%23comment%3A2&amp;data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C399c2eeac04e4f73f9af08d94d28c67f%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637625659807939713%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=1%2B9sPF14vkSVASoIriTfnz%2BcMzvqO%2B3YgHEp6rY%2B3Oc%3D&amp;reserved=0>
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comment:4 by pett, 4 years ago

Component: Core → Structure Analysis
Status: feedback → accepted
Summary: Unknown crash → Crash computing clashes

comment:5 by pett, 4 years ago

Status: accepted → feedback

Hi Maciej,

Thanks for that info. I assume the crash happened after the secondary dialog that asks for the clash parameters came up and you clicked OK on that. That calculation works the vast majority of the time, and it works for me in some test cases I just tried. Do you know if that crash is at all reproducible for you? If it is, then there's some hope of fixing it...

--Eric

in reply to:  6 ; comment:6 by mmaciej.basczok@…, 4 years ago 

Hi Eric,

unfortunately it happened on my PC at work, and I have my vacation from tomorrow till the end of next week (at the moment I am already at home and I had some troubles to install ChimeraX on my Linux distro, so I cannot test the problem at home). I will be able to check if this persists after I am back on the 2nd August. If you think that after such time it is reasonable to check it again, please let me know - I will surely do it. Thank you for maintaining such a great tool as ChimeraX is!

Kind regards,

Maciek
________________________________
Od: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Wysłane: czwartek, 22 lipca 2021 19:51
DW: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Maciej Basczok <mmaciej.basczok@amu.edu.pl>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Temat: Re: [ChimeraX] #4934: Crash computing clashes

#4934: Crash computing clashes
-----------------------------------------+----------------------------
          Reporter:  macbas@…            |      Owner:  Eric Pettersen
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Hi Maciej,
         Thanks for that info.  I assume the crash happened after the
 secondary dialog that asks for the clash parameters came up and you
 clicked OK on that.  That calculation works the vast majority of the time,
 and it works for me in some test cases I just tried.  Do you know if that
 crash is at all reproducible for you?  If it is, then there's some hope of
 fixing it...

 --Eric

--
Ticket URL: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F4934%23comment%3A5&amp;data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C064ee54475f84a664dd508d94d39699d%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637625731266700207%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=r4GBzJZV0bXyvbNRLmo709iz3va1F5HD%2FGky%2FWKfF%2Fc%3D&amp;reserved=0>
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comment:7 by pett, 4 years ago

Anytime you can manage to test it would be fine. For my part, I should try testing on a Windows machine (I used a Mac), but that will have to wait for the next time I physically go into work, which is kind of the same timeframe as you (start of August). Glad you like ChimeraX despite these problems!

--Eric

in reply to:  8 ; comment:8 by mmaciej.basczok@…, 4 years ago 

Hi Eric,

I have just tried to repeat the crash situation. Apparently, it was an incidental issue since now everything is looking perfectly fine. Anyway, if such a crash occurs again, I will surely let you know. Hope you had a good vacation.

Best,

Maciek
________________________________
Od: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Wysłane: czwartek, 22 lipca 2021 20:31
DW: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Maciej Basczok <mmaciej.basczok@amu.edu.pl>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Temat: Re: [ChimeraX] #4934: Crash computing clashes

#4934: Crash computing clashes
-----------------------------------------+----------------------------
          Reporter:  macbas@…            |      Owner:  Eric Pettersen
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------------

Comment (by Eric Pettersen):

 Anytime you can manage to test it would be fine.  For my part, I should
 try testing on a Windows machine (I used a Mac), but that will have to
 wait for the next time I physically go into work, which is kind of the
 same timeframe as you (start of August).  Glad you like ChimeraX despite
 these problems!

 --Eric

--
Ticket URL: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F4934%23comment%3A7&amp;data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C7dd5288b1f594224d2bf08d94d3f000d%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637625755258291342%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=xtvrakGMIcKaZAWxYgjqPaxNfyYIy6NoCBYWN99jHKg%3D&amp;reserved=0>
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comment:9 by pett, 4 years ago

Resolution: → can't reproduce
Status: feedback → closed

Hi Maciek,

Thanks for the info. Without a reproducible test case, it will be terribly hard to track down this problem, or to be assured that any fix actually works. So I'm closing this ticket. Nonetheless, the info you provided is valuable in case any other reports come in.

--Eric

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