Sequence viewer fails on edited chain

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-4.20.8-200.fc29.x86_64-x86_64-with-fedora-29-Twenty_Nine
ChimeraX Version: 0.91 (2019-09-17)
Description
Sequence view fails after adding residues to the chain (inside a chain break, in case it makes a difference)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-09-17)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open MyD88_refine_5.pdb

Summary of feedback from opening MyD88_refine_5.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-09-17 Time 22:41:57 CEST +0200 (1568752917.06 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/home/tic20/structure_dump/aus/brisbane/kobe/myd88_ED/MyD88_20190813.mtz  
  
56 messages similar to the above omitted  
  
Chain information for MyD88_refine_5.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open ../MyD88_20190813.mtz structureModel #1

Summary of feedback from opening ../MyD88_20190813.mtz  
---  
warnings | Missing or corrupted CRYST1 card found in the PDB file. This model
will be treated as a cryo-EM model until associated with an MTZ file
containing symmetry information.  
WARNING: This MTZ file contains data from multiple crystals. Only the data
from the first crystal will be used. If you wish to use the other data, please
split your MTZ file into individual datasets (you can do this using tools from
the PHENIX or CCP suites).  
notes | MTZ file either contains multiple crystal datasets or is a mini-MTZ
file. Checking...  
(CLIPPER) NOTE: No symmetry information found in model. Using symmetry from
MTZ file.  
  
Opened crystallographic dataset from ../MyD88_20190813.mtz  
Generated maps:  
Reflection Data  
Any unwanted maps may be safely closed via the Model panel.  
Chain information for MyD88_refine_5.pdb  
---  
Chain | Description  
1.3/A | No description available  
  

> close #1

Deleting Crystallographic maps (MyD88_20190813.mtz)  

> open MyD88_*.pdb

Summary of feedback from opening MyD88_refine_5.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-09-17 Time 22:41:57 CEST +0200 (1568752917.06 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/home/tic20/structure_dump/aus/brisbane/kobe/myd88_ED/MyD88_20190813.mtz  
  
56 messages similar to the above omitted  
  
Chain information for MyD88_refine_5.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open ../reflections.mtz structureModel #1

Summary of feedback from opening ../reflections.mtz  
---  
warning | Missing or corrupted CRYST1 card found in the PDB file. This model
will be treated as a cryo-EM model until associated with an MTZ file
containing symmetry information.  
notes | (CLIPPER) NOTE: No symmetry information found in model. Using symmetry
from MTZ file.  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Opened crystallographic dataset from ../reflections.mtz  
Found experimental reflection data:  
(dataset) IMEAN, SIGIMEAN  
Rwork: 0.3076; Rfree: 0.3534  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_sharp_29  
Any unwanted maps may be safely closed via the Model panel.  
Chain information for MyD88_refine_5.pdb  
---  
Chain | Description  
1.3/A | No description available  
  

> addh

Summary of feedback from adding hydrogens to MyD88_refine_5.pdb #1.3  
---  
notes | No usable SEQRES records for MyD88_refine_5.pdb (#1.3) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 159  
Chain-initial residues that are not actual N termini: /A ARG 251  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LEU 295, /A SER 242  
115 hydrogen bonds  
Adding 'H' to /A ARG 251  
/A LEU 295 is not terminus, removing H atom from 'C'  
/A SER 242 is not terminus, removing H atom from 'C'  
1089 hydrogens added  
  

> hide HC

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select #1

2157 atoms, 2179 bonds, 1 pseudobond, 25 models selected  

> select clear

> toolshed show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> pwd

Current working directory is:
/home/tic20/structure_dump/aus/brisbane/kobe/myd88_ED/Refine_5  

> save working.pdb #1

QWidget::repaint: Recursive repaint detected  

> sequence chain /A

Alignment identifier is 1.3.A  

> toolshed show Shell

> color sel bychain

> color sel byhetero

> color sel bychain

> color sel byhetero

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> color sel bychain

> color sel byhetero

> color sel bychain

> color sel byhetero

> select #1

2196 atoms, 2218 bonds, 1 pseudobond, 30 models selected  

> select clear

> color sel bychain

> color sel byhetero

> color sel bychain

> color sel byhetero

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select up

19 atoms, 18 bonds, 1 model selected  

> select up

2215 atoms, 2237 bonds, 1 model selected  

> select up

17 atoms, 16 bonds, 1 model selected  

> set bgColor white

> view :173

> cofr centerOfView

> select #1

2215 atoms, 2237 bonds, 1 pseudobond, 30 models selected  

> view :276

> cofr centerOfView

> view :258

> cofr centerOfView

> select #1

2215 atoms, 2237 bonds, 1 pseudobond, 30 models selected  

> view :159

> cofr centerOfView

> sequence chain /A

Alignment identifier is 1.3.A  

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1594, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/__init__.py", line 40, in run_provider  
return _start_seq_viewer(session, "Sequence Viewer", alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 690, in _start_seq_viewer  
return SequenceViewer(session, tool_name, alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 55, in __init__  
self._finalize_init(alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 174, in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 184, in __init__  
self.layout_alignment()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 787, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 1601, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2243, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2236, in _layout_line  
numberings[numbering] = self._make_numbering(line, numbering)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2328, in _make_numbering  
x, y = self.item_aux_info[line][-1]  
IndexError: list index out of range  
  

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1594, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/__init__.py", line 40, in run_provider  
return _start_seq_viewer(session, "Sequence Viewer", alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 690, in _start_seq_viewer  
return SequenceViewer(session, tool_name, alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 55, in __init__  
self._finalize_init(alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 174, in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 184, in __init__  
self.layout_alignment()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 787, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 1601, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2243, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2236, in _layout_line  
numberings[numbering] = self._make_numbering(line, numbering)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/seq-
view/seq_canvas.py", line 2328, in _make_numbering  
x, y = self.item_aux_info[line][-1]  
IndexError: list index out of range  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2737, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/seqalign/cmd.py", line 141, in seqalign_chain  
auto_associate=None, intrinsic=True)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 248, in new_alignment  
alignment=alignment)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 459, in run_provider  
"run_provider() failed in bundle %s:\n%s" % (self.name, str(e)))  
chimerax.core.toolshed.ToolshedError: run_provider() failed in bundle
ChimeraX-SeqView:  
list index out of range  
  
chimerax.core.toolshed.ToolshedError: run_provider() failed in bundle
ChimeraX-SeqView:  
list index out of range  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 459, in run_provider  
"run_provider() failed in bundle %s:\n%s" % (self.name, str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 410.93
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

I have a question somewhat related to this: is it currently possible for the user to assign sequences to their model from a fasta file? Ideally what I want to have is a “add the next residue here” button, without the need for the user to have to specify the *name* of that residue every time. From what I’ve seen the API for this is essentially there, but I haven’t explored it in detail yet.
 

 

[pett]

Sort of. The user can open a FASTA file and if the sequence is "similar enough" to a chain in an open structure then the chain will "associate" with the appropriate sequence from the file. The session.alignments manager can be queried for the residue-to-position correspondences of the sequence association. I'm glossing over a lot of details obviously, but at a high level that's how it works.

[pett]

Another functional duplicate of #2919