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#3593 closed defect (fixed)

stepper.step_forward: index is out of bounds

Reported by:	chimerax-bug-report@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Error parsing
/Users/sconnell/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl:
No such file:
/Users/sconnell/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
File saved as
/Users/sconnell/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.12.1 ChimeraX-ISOLDE-1.0b5  
Installed ChimeraX-Clipper (0.12.1)  
Installed ChimeraX-ISOLDE (1.0b5)  

> open2
> /Users/sconnell/OneDrive/Documents/SyncPC/Refine3D-job103-run_class001.mrc

Opened Refine3D-job103-run_class001.mrc, grid size 300,300,300, pixel 1.05,
shown at level 0.0043, step 2, values float32  

> open2
> /Users/sconnell/OneDrive/Documents/SyncPC/vacant30S_head_270720_3_alnrefine103.pdb

Summary of feedback from opening <_io.textiowrapper
name="/Users/sconnell/OneDrive/Documents/SyncPC/vacant30S_head_270720_3_alnrefine103.pdb"
mode="rt" encoding="utf-8">  
---  
warning | Ignored bad PDB record found on line 18809  
END  
  
Chain information for vacant30S_head_270720_3_alnrefine103.pdb #2  
---  
Chain | Description  
1 | No description available  
B | No description available  
C | No description available  
G | No description available  
I | No description available  
J | No description available  
M | No description available  
N | No description available  
S | No description available  
  

> clipper associate #1 toModel #2

Chain information for vacant30S_head_270720_3_alnrefine103.pdb  
---  
Chain | Description  
1.2/1 | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/G | No description available  
1.2/I | No description available  
1.2/J | No description available  
1.2/M | No description available  
1.2/N | No description available  
1.2/S | No description available  
  

> set bgColor white

> isolde start

> set selectionWidth 4

Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> ui dockable false ISOLDE

> ui dockable true ISOLDE

> addh

Summary of feedback from adding hydrogens to
vacant30S_head_270720_3_alnrefine103.pdb #1.2  
---  
notes | No usable SEQRES records for vacant30S_head_270720_3_alnrefine103.pdb
(#1.2) chain 1; guessing termini instead  
No usable SEQRES records for vacant30S_head_270720_3_alnrefine103.pdb (#1.2)
chain B; guessing termini instead  
No usable SEQRES records for vacant30S_head_270720_3_alnrefine103.pdb (#1.2)
chain C; guessing termini instead  
No usable SEQRES records for vacant30S_head_270720_3_alnrefine103.pdb (#1.2)
chain G; guessing termini instead  
No usable SEQRES records for vacant30S_head_270720_3_alnrefine103.pdb (#1.2)
chain I; guessing termini instead  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /1 C 931, /B VAL 4, /C GLY
2, /G PRO 2, /I ASN 4, /J ASN 3, /M ALA 2, /N ALA 2, /S PRO 2  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /1 G 1386, /G ALA 152, /J LEU
102, /N TRP 101  
Chain-final residues that are not actual C termini: /B GLN 227, /C ALA 212, /I
ARG 130, /M ILE 116, /S ALA 84  
2005 hydrogen bonds  
/B GLN 227 is not terminus, removing H atom from 'C'  
/C ALA 212 is not terminus, removing H atom from 'C'  
/I ARG 130 is not terminus, removing H atom from 'C'  
/M ILE 116 is not terminus, removing H atom from 'C'  
/S ALA 84 is not terminus, removing H atom from 'C'  
14090 hydrogens added  
  

> hide HC

> isolde restrain ligands #1

> cview #1/1:1054

> select clear

> cview sel

> select #1

32672 atoms, 33913 bonds, 14 models selected  

QWidget::repaint: Recursive repaint detected  

> isolde sim start sel

No template found for residue 1931 (C)  

Excluding residue  

No template found for residue 1966 (2MG)  

Excluding residue  

No template found for residue 1967 (5MC)  

Excluding residue  

No template found for residue 11196 (A)  

Excluding residue  

No template found for residue 11207 (2MG)  

Excluding residue  

> volume #1.1.1.1 level 0.02257

> select clear

Traceback (most recent call last):  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2525, in _xtal_step_forward  
self._xtal_mask_to_atoms(sel, focus=False)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2561, in _xtal_mask_to_atoms  
atoms, 0, context, cutoff, focus=focus)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 972, in
isolate_and_cover_selection  
extra_padding=extra_padding)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/maps/map_mgr.py", line 358, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/maps/mask_handler.py", line 111, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2540, in _xtal_step_backward  
sel = sh.stepper.step_backward()  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 74, in step_backward  
return self._step(direction=self.BACKWARD)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2552, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2561, in _xtal_mask_to_atoms  
atoms, 0, context, cutoff, focus=focus)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 972, in
isolate_and_cover_selection  
extra_padding=extra_padding)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/maps/map_mgr.py", line 358, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/maps/mask_handler.py", line 111, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2524, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2524, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2524, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2524, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2524, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/sconnell/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.6.18
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.

Change History (3)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → stepper.step_forward: index is out of bounds

comment:2 by Tristan Croll, 5 years ago

Hmm... turns out I haven't tested this code on nucleic acid chains as well as I should have. To be honest, I'm thinking of retiring the whole method anyway - the new residue-by-residue step command is much nicer.

comment:3 by Tristan Croll, 3 years ago

Resolution:	→ fixed
Status:	assigned → closed

The offending code was retired some time ago. :)

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