Context Navigation

← Previous Ticket
Next Ticket →

#6965 closed defect (duplicate)

sym: normalize_vector() takes 1 positional argument but 3 were given

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Higher-Order Structure	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.4.dev202202150901 (2022-02-15 09:01:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Data format provider 'ZDOCK' supplied unknown keywords with format
description: {'is_default': 'false'}  
  
UCSF ChimeraX version: 1.4.dev202202150901 (2022-02-15)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open pdb:6C53

6c53 title:  
Cryo-EM structure of the Type 1 pilus rod [more info...]  
  
Chain information for 6c53 #1  
---  
Chain | Description | UniProt  
A B C D E F G H I J K | Type-1 fimbrial protein, A chain | FIMA1_ECOLI  
  

> close all

> open
> F:/UVA/Data/Milano/Volumes/Tail_plate/Phenix_project/RealSpaceRefine_8/RSR_008-coot-1.pdb

Summary of feedback from opening
F:/UVA/Data/Milano/Volumes/Tail_plate/Phenix_project/RealSpaceRefine_8/RSR_008-coot-1.pdb  
---  
warning | Ignored bad PDB record found on line 20874  
  
Chain information for RSR_008-coot-1.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> hide atoms

> show cartoons

> open
> F:/UVA/Data/Milano/Volumes/Tail_plate/cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc

Opened cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc as #2, grid size
512,512,512, pixel 1.08, shown at level 0.238, step 2, values float32  

> volume zone #2 nearAtoms #1 range 6.48

> transparency 50

> sym #1 C6, 1

Expected a keyword  

> sym #1 C6 1

Expected a keyword  

> sym #1 C6

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!3.1 models

> hide #!3.2 models

> show #!3.1 models

> hide #!3 models

> show #!3 models

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 1 maps.  

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> sym clear #2

> sym clear #3

> sym clear #1

> show #!3.2 models

> show #!1 models

> hide #!2 target m

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 target m

> select clear

> hide #!2 target m

> hide #!1 models

> show #!2 models

> hide #!3 models

> hide #!3.1 models

> hide #!3.6 models

> hide #!3.5 models

> hide #!3.4 models

> hide #!3.3 models

> hide #!3.2 models

> show #!1 models

> transparency 0

> lighting simple

> volume #2 step 1

> open F:/UVA/Data/Milano/Volumes/Tail/rotaion_axis.pdb

Summary of feedback from opening
F:/UVA/Data/Milano/Volumes/Tail/rotaion_axis.pdb  
---  
warnings | Ignored bad PDB record found on line 5  
  
  
Ignored bad PDB record found on line 7  
  
  
Cannot find LINK/SSBOND residue mar (1 )  
Ignored bad PDB record found on line 9  
  
Chain information for rotaion_axis.pdb #4  
---  
Chain | Description  
kM | No description available  
  

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.  

> hide #!4 models

> volume zone #2 nearAtoms #1 range 6.48

> select add #1

20621 atoms, 21075 bonds, 1 pseudobond, 2708 residues, 2 models selected  

> select add #2

20621 atoms, 21075 bonds, 1 pseudobond, 2708 residues, 4 models selected  

> select clear

> clsoe #3

Unknown command: clsoe #3  

> close #3

> show #!4 models

> view clip false

> hide #!1 models

> hide #!2 models

> show #!1 models

> hide #!4 models

> select #1/H:17

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

> open
> F:/UVA/Data/Milano/Volumes/Tail_plate/Phenix_project/RealSpaceRefine_8/RSR_008-coot-1.pdb

Summary of feedback from opening
F:/UVA/Data/Milano/Volumes/Tail_plate/Phenix_project/RealSpaceRefine_8/RSR_008-coot-1.pdb  
---  
warning | Ignored bad PDB record found on line 20874  
  
Chain information for RSR_008-coot-1.pdb #3  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> hide #!1 models

> select #3/C:376@OD1

1 atom, 1 residue, 1 model selected  

> select clear

> hide #!3 atoms

> show #!3 cartoons

> select #3/H:33

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

> show #!2 models

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> transparency 50

> select #3/C:153

5 atoms, 4 bonds, 1 residue, 1 model selected  

> volume #2 region 0,0,0,511,511,511

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,62.985,0,1,0,-7.9884,0,0,1,5.956

> view matrix models #3,1,0,0,52.405,0,1,0,-15.969,0,0,1,23.085

> show #!1 models

> view matrix models #3,1,0,0,43.43,0,1,0,-14.415,0,0,1,25.083

> view matrix models
> #3,0.50547,-0.85767,-0.094414,16.697,0.85885,0.51062,-0.040526,5.0901,0.082968,-0.060602,0.99471,26.786

> view matrix models
> #3,-0.041414,-0.97886,0.20031,5.4124,0.98865,-0.011175,0.14979,7.381,-0.14439,0.20424,0.96821,22.316

> view matrix models
> #3,-0.041414,-0.97886,0.20031,0.32523,0.98865,-0.011175,0.14979,-21.777,-0.14439,0.20424,0.96821,23.622

> view matrix models
> #3,-0.041414,-0.97886,0.20031,8.8405,0.98865,-0.011175,0.14979,-33.292,-0.14439,0.20424,0.96821,19.53

> view matrix models
> #3,0.04105,-0.99889,-0.022955,6.1049,0.99914,0.040916,0.0062832,-35.6,-0.005337,-0.023193,0.99972,21.867

> view matrix models
> #3,0.43573,-0.88982,-0.13548,16.736,0.89442,0.41122,0.1758,-30.786,-0.10072,-0.19778,0.97506,16.463

> view matrix models
> #3,0.43573,-0.88982,-0.13548,7.3151,0.89442,0.41122,0.1758,-30.064,-0.10072,-0.19778,0.97506,10.446

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule RSR_008-coot-1.pdb (#3) to map
cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc (#2) using 20621 atoms  
average map value = 0.1089, steps = 264  
shifted from previous position = 24  
rotated from previous position = 10.4 degrees  
atoms outside contour = 16306, contour level = 0.23849  
  
Position of RSR_008-coot-1.pdb (#3) relative to
cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc (#2) coordinates:  
Matrix rotation and translation  
0.45146101 -0.88990992 -0.06514058 11.27737583  
0.89212144 0.45159341 0.01351828 -12.42958644  
0.01738701 -0.06421628 0.99778453 4.12081443  
Axis -0.04353331 -0.04621752 0.99798236  
Axis point 15.68733238 3.20811024 0.00000000  
Rotation angle (degrees) 63.22940004  
Shift along axis 4.19602334  
  

> hide #!1 models

> volume zone #2 nearAtoms sel & #3 range 6.48

> select add #3

20621 atoms, 21075 bonds, 1 pseudobond, 2708 residues, 2 models selected  

> volume zone #2 nearAtoms sel & #3 range 6.48

> view matrix models
> #3,0.45146,-0.88991,-0.065141,13.241,0.89212,0.45159,0.013518,-13.725,0.017387,-0.064216,0.99778,2.3185

> fitmap #3 inMap #2

Fit molecule RSR_008-coot-1.pdb (#3) to map
cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc (#2) using 20621 atoms  
average map value = 0.1089, steps = 60  
shifted from previous position = 3  
rotated from previous position = 0.0592 degrees  
atoms outside contour = 16326, contour level = 0.23849  
  
Position of RSR_008-coot-1.pdb (#3) relative to
cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc (#2) coordinates:  
Matrix rotation and translation  
0.45227047 -0.88952952 -0.06471988 11.30140160  
0.89172009 0.45237448 0.01387853 -12.41298991  
0.01693226 -0.06398886 0.99780696 4.13637847  
Axis -0.04362760 -0.04574812 0.99799987  
Axis point 15.69761504 3.24521871 0.00000000  
Rotation angle (degrees) 63.17763276  
Shift along axis 4.20292304  
  

> view matrix models
> #3,0.23069,-0.94318,-0.23915,0.097535,0.96872,0.24573,-0.034675,-13.508,0.091471,-0.22367,0.97036,3.9701

> select clear

> select #3/D:133

7 atoms, 6 bonds, 1 residue, 1 model selected  

> view matrix models
> #3,0.23069,-0.94318,-0.23915,-7.9594,0.96872,0.24573,-0.034675,-7.9744,0.091471,-0.22367,0.97036,2.1424

> view matrix models
> #3,0.13606,-0.96357,-0.23028,-10.849,0.9858,0.15477,-0.06515,-9.1679,0.098416,-0.21814,0.97094,2.4275

> fitmap #3 inMap #2

Fit molecule RSR_008-coot-1.pdb (#3) to map
cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc (#2) using 20621 atoms  
average map value = 0.1015, steps = 156  
shifted from previous position = 2.67  
rotated from previous position = 2.98 degrees  
atoms outside contour = 16700, contour level = 0.23849  
  
Position of RSR_008-coot-1.pdb (#3) relative to
cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc (#2) coordinates:  
Matrix rotation and translation  
0.18722027 -0.95609835 -0.22544295 -8.40906697  
0.97758300 0.20385120 -0.05268934 -6.23151799  
0.09633300 -0.21052468 0.97283057 4.41482011  
Axis -0.08025736 -0.16361917 0.98325354  
Axis point -0.81898264 -7.59234803 0.00000000  
Rotation angle (degrees) 79.51657823  
Shift along axis 6.03537284  
  

> view matrix models
> #3,0.46365,-0.88374,-0.063468,4.3837,0.88087,0.46748,-0.074322,-6.6602,0.095352,-0.021448,0.99521,7.0212

> view matrix models
> #3,0.46365,-0.88374,-0.063468,7.6838,0.88087,0.46748,-0.074322,-3.9829,0.095352,-0.021448,0.99521,4.2576

> fitmap #3 inMap #2

Fit molecule RSR_008-coot-1.pdb (#3) to map
cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc (#2) using 20621 atoms  
average map value = 0.4297, steps = 108  
shifted from previous position = 6.3  
rotated from previous position = 6.01 degrees  
atoms outside contour = 4192, contour level = 0.23849  
  
Position of RSR_008-coot-1.pdb (#3) relative to
cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc (#2) coordinates:  
Matrix rotation and translation  
0.50003806 -0.86600343 -0.00010019 16.23033157  
0.86600343 0.50003807 -0.00003500 -4.36440852  
0.00008040 -0.00006926 1.00000000 0.00450938  
Axis -0.00001978 -0.00010427 0.99999999  
Axis point 11.89504592 11.87438897 0.00000000  
Rotation angle (degrees) 59.99748172  
Shift along axis 0.00464333  
  

> volume zone #2 nearAtoms sel & #3 range 6.48

> select clear

> select add #3

20621 atoms, 21075 bonds, 1 pseudobond, 2708 residues, 2 models selected  

> volume zone #2 nearAtoms sel & #3 range 6.48

> volume zone #2 nearAtoms sel & #3 range 3

> select clear

> show #!1 models

> combine #1 #3

Remapping chain ID 'A' in RSR_008-coot-1.pdb #3 to 'I'  
Remapping chain ID 'B' in RSR_008-coot-1.pdb #3 to 'J'  
Remapping chain ID 'C' in RSR_008-coot-1.pdb #3 to 'K'  
Remapping chain ID 'D' in RSR_008-coot-1.pdb #3 to 'L'  
Remapping chain ID 'E' in RSR_008-coot-1.pdb #3 to 'M'  
Remapping chain ID 'F' in RSR_008-coot-1.pdb #3 to 'N'  
Remapping chain ID 'G' in RSR_008-coot-1.pdb #3 to 'O'  
Remapping chain ID 'H' in RSR_008-coot-1.pdb #3 to 'P'  

> hide #!2 models

> hide #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> show #!2 models

> volume zone #2 nearAtoms #5 range 6.48

> volume zone #2 nearAtoms #5 range 15

> transparency 0

> volume zone #2 nearAtoms #5 range 13

> transparency 50

> volume #2 color #d5d5d580

> color #1 #ff5500 transparency 0

> color #3 #00aa00 transparency 0

> show #!3 models

> show #!1 models

> hide #!5 models

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> select add #4

2 atoms, 1 pseudobond, 2 residues, 2 models selected  

> select add #5

41244 atoms, 42150 bonds, 3 pseudobonds, 5418 residues, 4 models selected  

> select subtract #4

41242 atoms, 42150 bonds, 2 pseudobonds, 5416 residues, 2 models selected  

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.  

> hide #!3 models

> hide #!1 models

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.  

> show #!5 models

> volume zone #2 nearAtoms sel & #5 range 6.48

> volume zone #2 nearAtoms sel & #5 range 12

> hide #!5 models

> show #!3 models

> show #!1 models

> measure rotation #2 toModel #4

Position of cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc #2 relative to
rotaion_axis.pdb #4 coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  
Rotation angle is near zero (0 degrees)  

> measure rotation #2 toModel #3

Position of cryosparc_P101_J248_003_volume_map_sharp_WIN512.mrc #2 relative to
RSR_008-coot-1.pdb #3 coordinates:  
Matrix rotation and translation  
0.50003806 0.86600342 0.00008040 -4.33619116  
-0.86600342 0.50003807 -0.00006926 16.23789332  
-0.00010019 -0.00003500 0.99999999 -0.00303607  
Axis 0.00001978 0.00010427 -0.99999999  
Axis point 11.89504583 11.87438889 0.00000000  
Rotation angle (degrees) 59.99748192  
Shift along axis 0.00464333  
  

> sym #2 C6

No structures specified.  

> measure rotation #1 toModel #3

Position of RSR_008-coot-1.pdb #1 relative to RSR_008-coot-1.pdb #3
coordinates:  
Matrix rotation and translation  
0.50003806 0.86600342 0.00008040 -4.33619116  
-0.86600342 0.50003807 -0.00006926 16.23789332  
-0.00010019 -0.00003500 0.99999999 -0.00303607  
Axis 0.00001978 0.00010427 -0.99999999  
Axis point 11.89504583 11.87438889 0.00000000  
Rotation angle (degrees) 59.99748192  
Shift along axis 0.00464333  
  

> hide #6 models

> hide #7 models

> show #7 models

> close #6

> hide #7 models

> show #7 models

> sym #1 C6 axis #7 center #7

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 302, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\std_commands\sym.py", line 87, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\atomic\args.py", line 428, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\atomic\args.py", line 447, in parse_symmetry  
tf = vector_rotation(axis, (0,0,1)) * tf  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\place.py", line 466, in vector_rotation  
return Place(m34.vector_rotation_transform(u, v))  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
  
See log for complete Python traceback.  
  

> sym #1 C6 axis #7

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 302, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\std_commands\sym.py", line 87, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\atomic\args.py", line 428, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\atomic\args.py", line 447, in parse_symmetry  
tf = vector_rotation(axis, (0,0,1)) * tf  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\place.py", line 466, in vector_rotation  
return Place(m34.vector_rotation_transform(u, v))  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
  
See log for complete Python traceback.  
  

> sym #1 C6

> close #6

> show #!1 models

> select #1/F

2970 atoms, 3034 bonds, 1 pseudobond, 385 residues, 2 models selected  

> select clear

> hide #7 models

> ui tool show "Side View"

> view clip false

> color #2 #fcfcfc80 models

> color #2 #ffffff80 models

> show #!5 models

> hide #!5 models

> show #!5 models

> view clip false

> sym #5 C3 axis #7

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 302, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\std_commands\sym.py", line 87, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\atomic\args.py", line 428, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\atomic\args.py", line 447, in parse_symmetry  
tf = vector_rotation(axis, (0,0,1)) * tf  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\place.py", line 466, in vector_rotation  
return Place(m34.vector_rotation_transform(u, v))  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
  
See log for complete Python traceback.  
  

> help sym

> show #7 models

> sym #5 C3 axis #7

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 302, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\std_commands\sym.py", line 87, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\atomic\args.py", line 428, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\atomic\args.py", line 447, in parse_symmetry  
tf = vector_rotation(axis, (0,0,1)) * tf  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\place.py", line 466, in vector_rotation  
return Place(m34.vector_rotation_transform(u, v))  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
File "C:\Program Files\ChimeraX 1.4.dev202202150901\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 511.79
OpenGL renderer: NVIDIA GeForce MX110/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Locale: en_IN.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: HP
Model: HP Laptop 15-da0xxx
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 17,090,756,608
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.5.2
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    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: 1.36.2
    ChimeraX-AtomicLibrary: 6.0.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    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-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202202150901
    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-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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.2
    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: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.7.7
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.1
    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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.0.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 3 years ago

Component:	Unassigned → Higher-Order Structure
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → sym: normalize_vector() takes 1 positional argument but 3 were given

comment:2 by Tom Goddard, 3 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Fixed this a few weeks ago.

Note: See TracTickets for help on using tickets.

Download in other formats: