Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#3100 closed defect (duplicate)

IndexError during ribbon pick

Reported by: karim.rafie@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-96-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.94 (2020-04-21)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.94.dev202004210536 (2020-04-21)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2
> /media/karim/Storage/karim/Ad41_Phenix/ModelBuilding/Coot7/ad41_asu_coot7_complete.pdb

Summary of feedback from opening
/media/karim/Storage/karim/Ad41_Phenix/ModelBuilding/Coot7/ad41_asu_coot7_complete.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
969 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 9 9 HYP A 455 ILE A 460
1 6  
Start residue of secondary structure not found: HELIX 48 48 HYP C 455 ILE C
460 1 6  
Start residue of secondary structure not found: HELIX 203 203 HYP J 455 ILE J
460 1 6  
Start residue of secondary structure not found: HELIX 224 224 HYP K 455 ILE K
460 1 6  
Start residue of secondary structure not found: HELIX 270 270 ASP O 15 GLN O
25 1 11  
5 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 74 2 PRO H 132 LYS H 136
0  
Start residue of secondary structure not found: SHEET 2 74 2 ILE H 141 GLY H
145 -1 N ARG H 144 O CYS H 133  
  
Chain information for ad41_asu_coot7_complete.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 8 9 | No description available  
7 | No description available  
A | No description available  
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  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
V W | No description available  
X | No description available  
Y | No description available  
  

> hide atoms

> show cartoons

> set bgColor white

> hide ~#1/A,B,C,K,L,J cartoons

> hide #1/J atoms

> hide ~#1/K,C cartoons

> lighting shadows false

> show #1/K:663-667 atoms

> show atoms

> hide atoms

> show #1/K atoms

> style ball

Changed 176109 atom styles  

> hide ~#1/K:699-702 atoms

> color #1 byelement

> show #1/C atoms

> show #1/C@H* atoms

> show #1/C@H* atoms

> hide #1/C@H* atoms

> hide #1@H* atoms

> ui mousemode rightMode distance

> distance /K:700@OG /C:643@CZ

Distance between /K SER 700 OG and /C ARG 643 CZ: 4.629Å  

> ui mousemode rightMode distance

> ui mousemode rightMode distance

> show #1/K atoms

> hide #1@H* atoms

> ui mousemode rightMode distance

> distance /C:642@CB /K:639@OG

Distance between /C SER 642 CB and /K SER 639 OG: 4.988Å  

> distance /K:713@CG /C:318@OG1

Distance between /K PRO 713 CG and /C THR 318 OG1: 9.227Å  

> distance /K:722@CB /C:318@CA

Distance between /K VAL 722 CB and /C THR 318 CA: 7.288Å  

> show #1/J cartoons

> hide #1/K all

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

> hide #1/K atoms

> hide #1/K cartoons

> show #1/J atoms

> hide #1@H* atoms

> ui mousemode rightMode distance

> distance /K:723@CB /C:329@CA

Distance between /K ASP 723 CB and /C SER 329 CA: 22.504Å  

> distance /J:66@CD2 /C:329@CB

Distance between /J LEU 66 CD2 and /C SER 329 CB: 4.936Å  

> distance /C:72@CA /J:73@CZ

Distance between /C ASP 72 CA and /J ARG 73 CZ: 5.874Å  

> distance /C:72@CG /J:73@CZ

Distance between /C ASP 72 CG and /J ARG 73 CZ: 4.483Å  

> distance /J:104@CZ /C:74@OE1

Distance between /J ARG 104 CZ and /C GLU 74 OE1: 5.940Å  

> distance /J:67@CZ /C:74@OE2

Distance between /J ARG 67 CZ and /C GLU 74 OE2: 9.660Å  

> distance /J:585@OG /C:74@CG

Distance between /J SER 585 OG and /C GLU 74 CG: 7.122Å  

> distance /C:76@CA /C:75@CB

Distance between /C THR 76 CA and ASP 75 CB: 4.212Å  

> distance /C:75@CB /J:582@CZ

Distance between /C ASP 75 CB and /J ARG 582 CZ: 10.054Å  

> hide

> hide cartoons

> show #1/A,B,C,J,K,L cartoons

> show #1/A,B,C,D,E,F cartoons

> show #1/A,B,C,D,E,F,G,H,I cartoons

> show
> #1/A,B,C,D,E,F,G,H,I:699-702,642-646,916-920,637-639,641-642,66-69,327-331,71-73,582-587,71-76
> atoms

> show #1/F atoms

> show #1/J atoms

> show #1@H*

> hide #1@H*

> hide

> hide ~#1/E,F,J cartoons

> show #1/E,F,J atoms

> hide #1@H*

> distance /J:74@CD /E:67@CZ

Distance between /J GLU 74 CD and /E ARG 67 CZ: 4.455Å  

> hide

> hide cartoons

> show #1/M,A,B,C,O

> show #1/M,A,B,C,O cartoons

> hide atoms

> open2
> /media/karim/Storage/karim/Ad41_PentonBase_LocRec/ModelBuilding/ApplyNCS_10/Ad41_PB_LocRec_apply_ncs_10.pdb

Summary of feedback from opening
/media/karim/Storage/karim/Ad41_PentonBase_LocRec/ModelBuilding/ApplyNCS_10/Ad41_PB_LocRec_apply_ncs_10.pdb  
---  
warnings | Ignored bad PDB record found on line 4219  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4211 messages similar to the above omitted  
Ignored bad PDB record found on line 8437  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4211 messages similar to the above omitted  
Ignored bad PDB record found on line 12655  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4211 messages similar to the above omitted  
Ignored bad PDB record found on line 16873  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4211 messages similar to the above omitted  
Ignored bad PDB record found on line 21091  
  
  
Ignored bad PDB record found on line 21092  
  
Chain information for Ad41_PB_LocRec_apply_ncs_10.pdb #3  
---  
Chain | Description  
A B C D O | No description available  
  

> mmaker #2 to #1/O

No molecules/chains to match specified  

> mmaker #2/O to #1/O

No molecules/chains to match specified  

> mmaker #3/O to #1/O

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 ad41_asu_coot7_complete.pdb, chain O (#1) with
Ad41_PB_LocRec_apply_ncs_10.pdb, chain O (#3), sequence alignment score =
1224.4  
RMSD between 263 pruned atom pairs is 0.587 angstroms; (across all 266 pairs:
0.664)  
  

> hide atoms

> show cartoons

> hide ~#1/M cartoons

> show #3 cartoons

> show #3/D atoms

> style ball

Changed 197189 atom styles  

> show #3/C atoms

> show #1/M atoms

> hide #!3 models

> show #1/A atoms

> show #1/A cartoons

> hide #1@H*

> show #1/A,B,C cartoons

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 279, in mouse_drag  
self._rotate(axis, angle)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 330, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 927, in rotate  
center = self.center_of_rotation  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 654, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 681, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 749, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 759, in _front_center_point  
exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 774, in first_intercept  
p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude,
beyond=beyond)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 3018 is out of bounds for axis 0 with size 2849  
  
IndexError: index 3018 is out of bounds for axis 0 with size 2849  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 279, in mouse_drag  
self._rotate(axis, angle)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 330, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 927, in rotate  
center = self.center_of_rotation  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 654, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 681, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 749, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 759, in _front_center_point  
exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 774, in first_intercept  
p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude,
beyond=beyond)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 3013 is out of bounds for axis 0 with size 2849  
  
IndexError: index 3013 is out of bounds for axis 0 with size 2849  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 279, in mouse_drag  
self._rotate(axis, angle)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 330, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 927, in rotate  
center = self.center_of_rotation  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 654, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 681, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 749, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 759, in _front_center_point  
exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 774, in first_intercept  
p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude,
beyond=beyond)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 3042 is out of bounds for axis 0 with size 2849  
  
IndexError: index 3042 is out of bounds for axis 0 with size 2849  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 279, in mouse_drag  
self._rotate(axis, angle)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 330, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 927, in rotate  
center = self.center_of_rotation  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 654, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 681, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 749, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 759, in _front_center_point  
exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 774, in first_intercept  
p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude,
beyond=beyond)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 3018 is out of bounds for axis 0 with size 2849  
  
IndexError: index 3018 is out of bounds for axis 0 with size 2849  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 279, in mouse_drag  
self._rotate(axis, angle)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 330, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 927, in rotate  
center = self.center_of_rotation  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 654, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 681, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 749, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 759, in _front_center_point  
exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 774, in first_intercept  
p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude,
beyond=beyond)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 3018 is out of bounds for axis 0 with size 2849  
  
IndexError: index 3018 is out of bounds for axis 0 with size 2849  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 279, in mouse_drag  
self._rotate(axis, angle)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 330, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 927, in rotate  
center = self.center_of_rotation  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 654, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 681, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 749, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 759, in _front_center_point  
exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 774, in first_intercept  
p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude,
beyond=beyond)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 3019 is out of bounds for axis 0 with size 2849  
  
IndexError: index 3019 is out of bounds for axis 0 with size 2849  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 279, in mouse_drag  
self._rotate(axis, angle)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 330, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 927, in rotate  
center = self.center_of_rotation  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 654, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 681, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 749, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 759, in _front_center_point  
exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 774, in first_intercept  
p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude,
beyond=beyond)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 3013 is out of bounds for axis 0 with size 2849  
  
IndexError: index 3013 is out of bounds for axis 0 with size 2849  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 279, in mouse_drag  
self._rotate(axis, angle)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 330, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 927, in rotate  
center = self.center_of_rotation  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 654, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 681, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 749, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 759, in _front_center_point  
exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 774, in first_intercept  
p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude,
beyond=beyond)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 3015 is out of bounds for axis 0 with size 2849  
  
IndexError: index 3015 is out of bounds for axis 0 with size 2849  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 683, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 384.145
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: Z10PE-D8 WS
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 48 Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
Cache Size: 30720 KB
Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)
	Subsystem: ASUSTeK Computer Inc. Device [1043:85aa]
	Kernel driver in use: nvidia

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → IndexError during ribbon pick

comment:2 by Eric Pettersen, 6 years ago

Resolution: → duplicate
Status: assigned → closed

Hi Karim,

Thanks for reporting this problem. It was fixed just a couple of days ago, so if you get the very latest daily build it shouldn't happen again. Sorry for the hassle!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by karim.rafie@…, 6 years ago 

Hi Eric,

Grand, thanks for the quick response. I'll make sure to update it

Best,
K

Get Outlook for Android<https://aka.ms/ghei36>

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, April 23, 2020 6:56:47 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; karim.rafie@umu.se <karim.rafie@umu.se>
Subject: Re: [ChimeraX] #3100: IndexError during ribbon pick

#3100: IndexError during ribbon pick
------------------------------------+-------------------------
          Reporter:  karim.rafie@…  |      Owner:  Tom Goddard
              Type:  defect         |     Status:  closed
          Priority:  normal         |  Milestone:
         Component:  Graphics       |    Version:
        Resolution:  duplicate      |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------
Changes (by Eric Pettersen):

 * status:  assigned => closed
 * resolution:   => duplicate


Comment:

 Hi Karim,
         Thanks for reporting this problem.  It was fixed just a couple of
 days ago, so if you get the very latest daily build it shouldn't happen
 again.  Sorry for the hassle!

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3100#comment:2>
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