"sequence chain" fails after chain lengthened

[ym337@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.4.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.91 (2019-12-17)
Description
I added a few aminoacids whist opening isolde. The sequence viewer was open by the time I added the amino acids. Then I closed the sequece viewer and tried to open the sequence again. The error message is attached. I couldn't save the ChimeraX session neither after that. Could you please have a look?

Log:
UCSF ChimeraX version: 0.91 (2019-12-17)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> select up

Nothing selected  

> select up

Nothing selected  

> open
> /nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job879/isolde/isolde_N_module_session_4.cxs
> format session

Summary of feedback from opening
/nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job879/isolde/isolde_N_module_session_4.cxs  
---  
warning | restore_snapshot for "RotamerRestraintMgr" returned None  
  
opened ChimeraX session  

> sequence chain /N

Alignment identifier is 1.1.N  

Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/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 "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1632, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/__init__.py", line 40, in run_provider  
return _start_seq_viewer(session, "Sequence Viewer", alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 684, in _start_seq_viewer  
return SequenceViewer(session, tool_name, alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 55, in __init__  
self._finalize_init(alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 174, in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 184, in __init__  
self.layout_alignment()  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 780, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1602, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2244, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2237, in _layout_line  
numberings[numbering] = self._make_numbering(line, numbering)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2329, in _make_numbering  
x, y = self.item_aux_info[line][-1]  
IndexError: list index out of range  
  

Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/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 "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1632, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/__init__.py", line 40, in run_provider  
return _start_seq_viewer(session, "Sequence Viewer", alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 684, in _start_seq_viewer  
return SequenceViewer(session, tool_name, alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 55, in __init__  
self._finalize_init(alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 174, in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 184, in __init__  
self.layout_alignment()  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 780, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1602, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2244, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2237, in _layout_line  
numberings[numbering] = self._make_numbering(line, numbering)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2329, 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 "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seqalign/cmd.py", line 141, in seqalign_chain  
auto_associate=None, intrinsic=True)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 244, in new_alignment  
alignment=alignment)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/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 "/usr/mbu/software/chimerax/chimerax-2019.12.17/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.  
  

> sequence chain /A

Alignment identifier is 1.1.A  

> sequence chain /N

Destroying pre-existing alignment with identifier 1.1.N  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seqalign/cmd.py", line 141, in seqalign_chain  
auto_associate=None, intrinsic=True)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 220, in new_alignment  
self.destroy_alignment(self._alignments[identify_as])  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 109, in destroy_alignment  
alignment._destroy()  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 501, in _destroy  
self._notify_observers("destroyed", None)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 541, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 459, in alignment_notification  
self.delete()  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 489, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 489, in delete  
self.region_browser.destroy()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.87.01
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: 89422800_196038681466979_538118797567983616_n.jpg

89422800_196038681466979_538118797567983616_n.jpg​

[ym337@…]

Added by email2trac

[Tristan Croll]

I've been trying to reproduce this on my Mac (using ChimeraX 0.92 release version) and so far failing. Will see if I have better luck using Yaikhomba's own model.

[Tristan Croll]

OK, I can reproduce. The bug arises specifically when you add a residue to the N-terminus of an existing chain (see below). The code for add_amino_acid_residue() is at ​https://github.com/tristanic/isolde/blob/977cf367d0e036305e1880f73466f01d7763c3b2/isolde/src/atomic/building/build_utils.py#L110.

from chimerax.core.commands import open as cxopen

m = cxopen.open(session, '3io0')[0]

from chimerax.isolde.atomic.building.build_utils import add_amino_acid_residue

add_amino_acid_residue(m, 'ALA', next_res=m.residues[0])
Out[4]: <chimerax.atomic.molobject.Residue at 0x1253fa8c0>

from chimerax.core.commands import run

run(session, 'sequence chain /A')
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-6-f4f907142508> in <module>
----> 1 run(session, 'sequence chain /A')

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/run.py in run(session, text, log, downgrade_errors)
     29     command = Command(session)
     30     try:
---> 31         results = command.run(text, log=log)
     32     except UserError as err:
     33         if downgrade_errors:

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py in run(self, text, log, log_only, _used_aliases)
   2843                 if not isinstance(ci.function, Alias):
   2844                     if not log_only:
-> 2845                         result = ci.function(session, **kw_args)
   2846                         results.append(result)
   2847                 else:

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seqalign/cmd.py in seqalign_chain(session, chains)
    139         ident = ".".join([str(part) for part in chain.structure.id]) + "." + chain.chain_id
    140         alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",
--> 141             auto_associate=None, intrinsic=True)
    142     else:
    143         # all chains have to have the same sequence, and they will all be associated with

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seqalign/manager.py in new_alignment(self, seqs, identify_as, attrs, markups, auto_destroy, align_viewer, seq_viewer, auto_associate, name, intrinsic)
    242         if viewer_text:
    243             self._installed_viewers[viewer_name].run_provider(self.session, viewer_name, self,
--> 244                 alignment=alignment)
    245         self.triggers.activate_trigger("new alignment", alignment)
    246         return alignment

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/toolshed/info.py in run_provider(self, session, name, mgr, **kw)
    451         """Supported API. Called by manager to invoke bundle provider."""
    452         api = self._get_api(session.logger)
--> 453         return api._api_caller.run_provider(api, session, name, mgr, **kw)
    454 
    455     def finish(self, session):

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/toolshed/__init__.py in run_provider(cls, api, session, name, mgr, **kw)
   1630     @classmethod
   1631     def run_provider(cls, api, session, name, mgr, **kw):
-> 1632         return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
   1633 
   1634     @classmethod

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/__init__.py in run_provider(session, name, manager, alignment)
     38         """Register sequence viewer with alignments manager"""
     39         from .tool import _start_seq_viewer
---> 40         return _start_seq_viewer(session, "Sequence Viewer", alignment)
     41 
     42 

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/tool.py in _start_seq_viewer(session, tool_name, alignment)
    691 
    692 def _start_seq_viewer(session, tool_name, alignment):
--> 693     return SequenceViewer(session, tool_name, alignment)
    694 

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/tool.py in __init__(self, session, tool_name, alignment)
     53         if alignment is None:
     54             return
---> 55         self._finalize_init(alignment)
     56 
     57     def _finalize_init(self, alignment):

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/tool.py in _finalize_init(self, alignment)
    172         """
    173         from .seq_canvas import SeqCanvas
--> 174         self.seq_canvas = SeqCanvas(parent, self, self.alignment)
    175         if self.alignment.associations:
    176             # There are pre-existing associations, show them

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py in __init__(self, parent, sv, alignment)
    182         #self._vdivider.hide()
    183         self.main_view.show()
--> 184         self.layout_alignment()
    185         """TODO
    186         self.mainCanvas.grid(row=1, column=2, sticky='nsew')

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py in layout_alignment(self)
    778             {}, lambda *args, **kw: self.sv.status(secondary=True, *args, **kw),
    779             self.show_ruler, None, self.show_numberings, self.sv.settings,
--> 780             self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())
    781 
    782     def letter_gaps(self):

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py in __init__(self, label_scene, main_scene, prev_block, font, emphasis_font, seq_offset, headers, alignment, line_width, label_bindings, status_func, show_ruler, tree_balloon, show_numberings, settings, label_width, font_pixels, numbering_widths, letter_gaps)
   1600         self.layout_ruler()
   1601         self.layout_lines(headers, self.header_label_color)
-> 1602         self.layout_lines(alignment.seqs, self.normal_label_color)
   1603 
   1604         if seq_offset + line_width >= len(alignment.seqs[0]):

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py in layout_lines(self, lines, label_color)
   2242         bli = self.base_layout_info()
   2243         for line in lines:
-> 2244             self._layout_line(line, label_color, bli, end)
   2245 
   2246     """TODO

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py in _layout_line(self, line, label_color, base_layout_info, end, line_index, adding)
   2235             for numbering in range(2):
   2236                 if self.show_numberings[numbering]:
-> 2237                     numberings[numbering] = self._make_numbering(line, numbering)
   2238         self.numbering_texts[line] = numberings
   2239 

/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py in _make_numbering(self, line, numbering)
   2327         fmt = "%d " if numbering == 0 else " %d"
   2328         item = self.main_scene.addSimpleText(fmt % n, font=self.font)
-> 2329         x, y = self.item_aux_info[line][-1]
   2330         rect = item.sceneBoundingRect()
   2331         if numbering == 0:

IndexError: list index out of range

[Tristan Croll]

Some more digging into this: the deeper (not necessarily the deep*est*) cause of the traceback is that for the affected chains, chain.characters now returns an empty string. This also appears to be messing up saving/loading in mmCIF format: all such chains get the same entity_id, and a bunch of residues simply get skipped when opening the file.

[Tristan Croll]

Surprisingly, chain.ungapped() still returns the correct sequence. If I do chain.characters = chain.ungapped()` then I can successfully save what looks to be a fully-valid mmCIF. The sequence viewer also no longer crashes, but it's still a bit borked for these chains: the residue letters aren't linked to the residues in the model, and for some reason the numbering up the left is reversed. But, if I save and reload the mmCIF then it looks to be back to fully operational.

[Tristan Croll]

Hi Yaikhomba,

This looks to be back in working order. You'll see from the emails on 
the ChimeraX bug tracker that this is a bona fide bug in ChimeraX - 
triggered when you add a residue to the N-terminus of a chain. I'm 
afraid at this stage the best thing for you to do will be to start a new 
session with the attached mmCIF (compressed with 7-zip) - I know that 
this may be a bit of a pain given all your restraints, but I don't see 
there's much that can be done about it.

The 'isolde restrain torsions' command has to be done chain-by-chain 
when restraining to a template. That is, each call should specify 
residues from exactly one chain for target, and one chain for template. 
For 'isolde restrain distances' you need to make sure that the order of 
chains in the target list is the same as the order in the template list, 
otherwise you'll get strange results.

Let me know how you get on.

Best regards,

Tristan

On 2020-03-13 17:17, ChimeraX wrote:

test.7z

[Tristan Croll]

Argh! Responded to the wrong email. Eric, that attachment is an 
unpublished model belonging to Yaikhomba, so would you mind deleting it 
when you see this? Doesn't look like I have the permissions.

On 2020-03-13 17:25, ChimeraX wrote:

[Eric Pettersen]

Okay, deleted the attachment. The code to update sequences/chains in the face of residue additions is (perhaps obviously) untested since ChimeraX itself has no capability yet to add residues to existing chains. Thanks for the detective work. I will look into fixing it soon.

--Eric

[Tristan Croll]

Would be good to know if there’s a short term workaround - e.g. would loading the full sequences of all chains from FASTA prior to editing help?
 

 

[Eric Pettersen]

No idea what a workaround might be since I haven't reproduced the problem!

I will be working on it today. Wish me luck. :-)

[Eric Pettersen]

Okay, I can now reproduce it with a hand-made script.

[Eric Pettersen]

I've fixed one problem. The sequence viewer now shows the sequence, but with no associations, as per your "a bit borked" comment above. Pushing out this fix and will work on tracking that one down...

[Eric Pettersen]

Okay, that's fixed too. Fixes in tomorrow's build. Unfortunately, ISOLDE doesn't yet work with 0.93, right?

You may be able to workaround it with, after you prepend a residue:

chain.bulk_set(chain.residues[int(len(chain.ungapped())):], chain.ungapped())

Of course, you would only want to do this for versions of ChimeraX that have the bug, so you might want to only execute that if:

len(chain.characters) == 0

[Tristan Croll]

Thanks! Yep - not quite caught up to 0.93 yet. Want to get an “official” release to match the 0.92 release first. Early next week, I think.
 

 

[Tristan Croll]

Just trying this out in ChimeraX 0.93. I'm afraid it still fails if the 
added residue is inside a chain break (same symptoms: chain.characters 
returns an empty string).

On 2020-03-13 21:17, ChimeraX wrote:

[Eric Pettersen]

Well, you did say "the bug arises specifically when you add a residue to the N-terminus of an existing chain" so that's what I tested. I will investigate the inside-a-chain-break case as time permits.

[Tristan Croll]

I know. Sorry for not testing that scenario previously.

On 2020-04-03 16:37, ChimeraX wrote:

[Eric Pettersen]

Hi Tristan,
I cannot replicate the add-residue-into-interior-gap being a problem (anymore). I've attached to this ticket the script I used to add a residue to the interior gap of 3fhr. I had to close and reopen the sequence viewer, but the reopened sequence viewer showed he new residue (and the rest of the sequence normally. Let me know if you can still replicate it, and if so give me a recipe.

--Eric