Opened 5 years ago

Closed 5 years ago

#4400 closed defect (can't reproduce)

Session trying to directly save alignment header

Reported by: elinteppa@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-70-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs
> format session

Log from Wed Mar 24 14:45:38 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home_pers/teppa/dEEPEN/data/UbiL/Brucella/UbiL1_Bruc_WP_008503541.1.B99990013.pdb

Chain information for UbiL1_Bruc_WP_008503541.1.B99990013.pdb #1  
---  
Chain | Description  
| No description available  
  

> set bgColor white

> style ligand ball

Changed 0 atom styles  

> close session

> open
> /home_pers/teppa/dEEPEN/data/UbiL/Brucella/UbiL1_Bruc_WP_008503541.1.B99990013.pdb

Chain information for UbiL1_Bruc_WP_008503541.1.B99990013.pdb #1  
---  
Chain | Description  
| No description available  
  

> clear

Unknown command: clear  

> open 1pbe

1pbe title:  
Crystal structure of the P-hydroxybenzoate hydroxylase-substrate complex
refined At 1.9 angstroms resolution. Analysis of the enzyme-substrate and
enzyme-product complexes [more info...]  
  
Chain information for 1pbe #2  
---  
Chain | Description  
A | P-hydroxybenzoate hydroxylase  
  
Non-standard residues in 1pbe #2  
---  
FAD — flavin-adenine dinucleotide  
PHB — P-hydroxybenzoic acid  
  
1pbe mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> mmaker #2 to #1

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 UbiL1_Bruc_WP_008503541.1.B99990013.pdb, chain (blank) (#1) with
1pbe, chain A (#2), sequence alignment score = 293.6  
RMSD between 135 pruned atom pairs is 0.937 angstroms; (across all 365 pairs:
6.261)  
  

> select #2/A:38

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

42 atoms, 43 bonds, 5 residues, 1 model selected  

> select up

3491 atoms, 3231 bonds, 723 residues, 1 model selected  

> hide sel target a

> hide sel cartoons

> open
> /home_pers/teppa/dEEPEN/data/UbiL/Brucella/UbiL1_Bruc_WP_008503541.1.B99990013.pdb

Chain information for UbiL1_Bruc_WP_008503541.1.B99990013.pdb #3  
---  
Chain | Description  
| No description available  
  

> close #3

> open /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1.aln

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/parse.py", line 31, in open_file  
seqs, file_attrs, file_markups = ns['read'](session, stream)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/io/readALN.py", line 33, in read  
raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")  
chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
with 'CLUSTAL'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/__init__.py", line 63, in open  
format_name=name.upper(), **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file  
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))  
OSError: Syntax error in ALN file 'ubiL1.aln': First non-blank line does not
start with 'CLUSTAL'  
  
OSError: Syntax error in ALN file 'ubiL1.aln': First non-blank line does not
start with 'CLUSTAL'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file  
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))  
  
See log for complete Python traceback.  
  

> open /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1.aln

Summary of feedback from opening
/home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1.aln  
---  
notes | Alignment identifier is ubiL1.aln  
Associated UbiL1_Bruc_WP_008503541.1.B99990013.pdb chain (blank) to
WP_008503541.1 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment ubiL1.aln  
  
Opened 761 sequences from ubiL1.aln  

> color byattribute seq_conservation

6655 atoms, 1137 residues, atom seq_conservation range -1.24 to 3.29  

> hide #1 models

> select #2

3491 atoms, 3231 bonds, 723 residues, 1 model selected  

> show #1 models

> hide #1 models

> show sel cartoons

> select ::name="FAD"

53 atoms, 58 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #2 models

> show #1 models

> show #2 models

> select #2/A:262

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

> select up

58 atoms, 58 bonds, 8 residues, 1 model selected  

> select up

3491 atoms, 3231 bonds, 723 residues, 1 model selected  

> hide sel cartoons

> color byattribute seq_conservation palette blue:red:yellow

6655 atoms, 1137 residues, atom seq_conservation range -1.24 to 3.29  

> color byattribute seq_conservation palette cyanmaroon

6655 atoms, 1137 residues, atom seq_conservation range -1.24 to 3.29  

> show sel atoms

> hide sel atoms

> show sel target ab

> hide sel target ab

> show sel target ab

> hide sel target ab

> select clear

> show sel atoms

> style sel stick

Changed 7 atom styles  

> style sel stick

Changed 7 atom styles  

> style sel ball

Changed 7 atom styles  

> hide sel cartoons

> show sel atoms

> style sel stick

Changed 7 atom styles  

> style sel sphere

Changed 7 atom styles  

> style sel ball

Changed 7 atom styles  

> style sel ball

Changed 15 atom styles  

> hide sel cartoons

> style sel ball

Changed 15 atom styles  

> show sel atoms

> show sel cartoons

> hide sel atoms

> style sel sphere

Changed 20 atom styles  

> hide sel atoms

> style sel sphere

Changed 20 atom styles  

> show sel atoms

> style sel ball

Changed 20 atom styles  

> style sel stick

Changed 20 atom styles  

> style sel ball

Changed 20 atom styles  

> hide sel atoms

> show sel cartoons

> hide #2 models

> show #2 models

> select #1:78

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

> select up

63 atoms, 65 bonds, 7 residues, 1 model selected  

> show sel atoms

Drag select of 25 residues  

> show sel atoms

> select clear

> show sel atoms

> style sel ball

Changed 15 atom styles  

> style sel stick

Changed 15 atom styles  

> style sel sphere

Changed 15 atom styles  

> style sel stick

Changed 15 atom styles  

> show sel atoms

> select clear

> select #1:52

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

> select up

108 atoms, 111 bonds, 15 residues, 1 model selected  

> select up

3164 atoms, 3228 bonds, 414 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 3164 atom styles  

> style sel sphere

Changed 3164 atom styles  

> style sel ball

Changed 3164 atom styles  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select clear

> select ::name="FAD"

53 atoms, 58 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 53 atom styles  

> style sel stick

Changed 53 atom styles  

> show sel atoms

> hide sel atoms

> show sel atoms

> style sel sphere

Changed 53 atom styles  

> style sel ball

Changed 53 atom styles  

> select up

3491 atoms, 3231 bonds, 723 residues, 1 model selected  

> style sel stick

Changed 3491 atom styles  

> style sel sphere

Changed 3491 atom styles  

> style sel ball

Changed 3491 atom styles  

> show sel cartoons

> hide sel cartoons

> style sel ball

Changed 3491 atom styles  

> style sel sphere

Changed 3491 atom styles  

> style sel stick

Changed 3491 atom styles  

> select #1:277

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

> style sel ball

Changed 5 atom styles  

> show sel atoms

> select #1:236

14 atoms, 15 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 14 atom styles  

> show sel atoms

> select #1:221

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

> style sel ball

Changed 7 atom styles  

> show sel atoms

> select #1:226

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

> show sel atoms

> select #1:223

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

> show sel atoms

> show sel atoms

> show sel atoms

> show sel atoms

> save /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs

opened ChimeraX session  

> select ::name="FAD"

53 atoms, 58 bonds, 1 residue, 1 model selected  

> hide sel target a

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> show sel target ab

> show sel target ab

> style sel ball

Changed 60 atom styles  

> select up

68 atoms, 73 bonds, 3 residues, 2 models selected  

> select up

99 atoms, 106 bonds, 7 residues, 2 models selected  

> select up

6655 atoms, 6459 bonds, 1137 residues, 2 models selected  

> style sel ball

Changed 6655 atom styles  

> show sel target ab

> hide sel target a

> select clear

> show sel target ab

> select #1:397

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

> select up

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select up

174 atoms, 177 bonds, 24 residues, 1 model selected  

> select up

3164 atoms, 3228 bonds, 414 residues, 1 model selected  

> style sel stick

Changed 3164 atom styles  

> show sel atoms

> hide sel atoms

> show sel target ab

> hide sel atoms

> select clear

> show sel target ab

> show sel target ab

> label sel attribute label_one_letter_code

> select clear

> select ::name="PHB"

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select ::name="FAD"

53 atoms, 58 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1:310

4 atoms, 3 bonds, 1 residue, 1 model selected  

> color byattribute seq_conservation palette cyanmaroon -1.24 to 1.24

Expected a keyword  

> color byattribute seq_conservation palette cyanmaroon range -1.24 to 1.24
> novalue yellow

Invalid "range" argument: Need exactly 2 ','-separated numbers  

> color byattribute seq_conservation palette cyanmaroon range -1.24 ,1.24
> noValueColor yellow

6655 atoms, 1137 residues, atom seq_conservation range -1.24 to 3.29  

> select clear

> select #1:317

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

> select clear

> select clear

> select #1:197

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

48 atoms, 47 bonds, 7 residues, 1 model selected  

> select up

3164 atoms, 3228 bonds, 414 residues, 1 model selected  

> hide sel atoms

> show ::seq_conservation>1.8

> ~label sel residues

> label ::seq_conservation>1.8

> label height 1.3

> preset pub

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select clear

> label delete

> surface

> colr fromatoms

Unknown command: colr fromatoms  

> color fromatoms

> present inter

Unknown command: present inter  

> preset inter

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> set bgColor white

> hide #!2 models

> select ::name="FAD"

53 atoms, 58 bonds, 1 residue, 1 model selected  

> show #1 target ab

> show #!2 models

> hide #2.1 models

> transparency sel 50

> select clear

> select #1:187@CB

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

81 atoms, 83 bonds, 10 residues, 2 models selected  

> select up

3164 atoms, 3228 bonds, 414 residues, 2 models selected  

> transparency (#!1 & sel) 50

> hide sel atoms

> select clear

> transparency #1#!2 80

> transparency #1#!2 30

> save /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

53 atoms, 58 bonds, 1 residue, 1 model selected  

> color sel byelement

> color byattribute seq_conservation palette cyanmaroon range -1.24 ,1.24
> noValueColor gray

6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to
3.29  

> show ::seq_conservation>2

> surface hidePatches sel

> select clear

> select #1:286@CZ

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

105 atoms, 106 bonds, 13 residues, 2 models selected  

> select up

3164 atoms, 3228 bonds, 414 residues, 2 models selected  

> surface hidePatches (#!1 & sel)

> size stickRadius .5

Changed 6459 bond radii  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

53 atoms, 58 bonds, 1 residue, 1 model selected  

> size stickRadius .1

Changed 6459 bond radii  

> size stickRadius .2

Changed 6459 bond radii  

> select clear

> show ::seq_conservation>2

> size stickRadius .5

Changed 6459 bond radii  

> select clear

> select #2/A:395@N6A

1 atom, 1 residue, 1 model selected  

> select up

53 atoms, 58 bonds, 1 residue, 1 model selected  

> size stickRadius .3

Changed 6459 bond radii  

> color ligand byhetero

> lighting soft

> sequence header conservation setting style "identity histogram"

> select ~::seq_conservation

3491 atoms, 3231 bonds, 723 residues, 1 model selected  

> color byattribute seq_conservation

6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range 0.0342 to 1  

> select #1:32

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

> sequence header conservation setting style AL2CO

> color byattribute seq_conservation palette cyanmaroon range -2,3
> noValueColor yellow

6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to
3.29  

> lighting flat

> graphics silhouettes depthJump 0.03

> graphics silhouettes depthJump 0.06

> graphics silhouettes depthJump 0.1

> graphics silhouettes depthJump 0.01

> 0.5

Unknown command: 0.5  

> graphics silhouettes depthJump 0.5

> graphics silhouettes depthJump 0.01

> lighting simple

> lighting soft

> lighting full

> lighting full

> lighting flat

> lighting flat

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting flat

> lighting flat

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting simple

> lighting simple

> graphics silhouettes false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> color byattribute seq_conservation palette cyanmaroon range -2,3
> noValueColor gray

6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to
3.29  

> lighting soft

> set bgColor gray

> set bgColor black

> set bgColor gray

> color byattribute seq_conservation palette cyanmaroon range -2,3
> noValueColor yellow

6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to
3.29  

> select #2/A:395@N6A

1 atom, 1 residue, 1 model selected  

> select up

53 atoms, 58 bonds, 1 residue, 1 model selected  

> select up

63 atoms, 68 bonds, 2 residues, 1 model selected  

> color sel byelement

> set bgColor white

> : set bg steelblue

Unknown command: : set bg steelblue  

> set bgColor steelblue

> select clear

> set bgColor gray

> color byattribute seq_conservation palette cyanmaroon range -2,3
> noValueColor yellow

6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to
3.29  

> 2dlabels text "UbiL-1 conservation" color white

> ui mousemode right "move label"

> ui mousemode right "move label"

> 2dlabels #3.1 xpos 0.526 ypos 0.787

> 2dlabels #3.1 xpos 0.539 ypos 0.953

> 2dlabels #3.1 xpos 0.495 ypos 0.947

> ui mousemode right "move label"

> 2dlabels #3.1 xpos 0.475 ypos 0.942

> 2dlabels text "UbiL-1 conservation" color white size 26

> ui mousemode right "move label"

> 2dlabels #3.2 xpos 0.064 ypos 0.593

> hide #3.2 models

> show #3.2 models

> close #3.2

> color byattribute seq_conservation palette cyanmaroon range -1.24 ,1.24
> noValueColor gray

6655 atoms, 1137 residues, 2 surfaces, atom seq_conservation range -1.24 to
3.29  

> set bgColor white

> graphics silhouettes true

> lighting simple

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting soft

> lighting full

> lighting full

> lighting full

> lighting flat

> lighting flat

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> save /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 215, in copy_state  
return _copy(data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 210, in _copy  
return data.__class__(items)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/conservation.py", line 42, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f04a8b48ed0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f03cb2b1a90>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 215, in copy_state  
return _copy(data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/state.py", line 210, in _copy  
return data.__class__(items)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/conservation.py", line 42, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f04a8b48ed0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f03cb2b1a90>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.27.04
OpenGL renderer: Quadro M5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 16 Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        6.1G        117G        199M        1.7G        118G
	Swap:          8.0G          0B        8.0G

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM204GL [Quadro M5000] [10de:13f0] (rev a1)	
	Subsystem: NVIDIA Corporation GM204GL [Quadro M5000] [10de:1152]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (5)

comment:1 by Eric Pettersen, 5 years ago

Cc: Eric Pettersen added
Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Session trying to directly save alignment header

comment:2 by Eric Pettersen, 5 years ago

Status: assigned → feedback

Hi Elin,

We have seen this problem a few times now but have never been able to reproduce it. It there any chance you could provide the /home_pers/teppa/dEEPEN/data/UbiL/Brucella/ubiL1_conservation.cxs session file? That would help us a lot in tracking this down.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by elinteppa@…, 5 years ago 

Hi Eric,
Please find the link below to the session file.

Have a nice day, Elin.
 ubiL1_conservation.cxs
<https://drive.google.com/file/d/10crWw8xeJLCPQAHRzm-2vPUuKywMKh4g/view?usp=drive_web>

Elin Teppa, PhD

Molecular Modelling & Design/Catalysis & Enzyme Engineering

INSA - Toulouse Biotechnology Institute


El mié, 24 mar 2021 a las 16:48, ChimeraX (<ChimeraX-bugs-admin@cgl.ucsf.edu>)
escribió:

comment:4 by Eric Pettersen, 5 years ago

Status: feedback → accepted

Thanks for providing that!

comment:5 by Eric Pettersen, 5 years ago

Resolution: → can't reproduce
Status: accepted → closed

Unfortunately, using your session and then running through all the commands you issued afterward in both the 1.1 release and daily build did not produce the error that you encountered. This was on my home Mac and not a Linux box, but I can't see any reason that would make a difference.

So reproducing this remains "the great white whale" for us. Operations on your large alignment are incredibly slow. I'll see if there's anything I can do about that.

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