Opened 4 years ago

Closed 4 years ago

#5453 closed defect (fixed)

Problem saving blast table info in session

Reported by: nishaj@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Eric Pettersen, Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.11.0-37-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3.dev202110140902 (2021-10-14 09:02:43 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202110140902 (2021-10-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold search
> EVDLGTGTRCVVLAEDKVREADVAERIAALKTQYGDSWHVDKEHPYRTWQYWGSYKTEATGSAASLINGVVKLLSWPWNAREDVVRMAMTDTTAFGQQRVFKEKVDTKAQEPQVGTKIIMRAVNDWIFERLAGKKTPRLCTREEFIAKVRSNAALGAWSDEQNRWPNAREAVEDPEFWRLVDEERERHLGGRCAQCVYNMMGKREKKLGEFGVAKGSRAIWYMWLGSRYLEFEALGFLNEDHWASRDLSGAGVEGTSLNYLGWHLKKLSELEGGLFYADDTAGWDTRITNADLEDEEQILRYLEGEHRTLAKTILEKAYHAKVVKVARPSSSGGCVMDIITRRDQRGSGQVVTYALNTLTNIKVQLIRMMEGEGVIGPSDSQDPRLLRVEAWLKEHGEERLTRMLVSGDDCVVRPIDDRFGKALYFLNDMAKVRKDIGEWEPSEGYSSWEEVPFCSHHFHELTMKDGRVIIVPCRDQDELVGRARVSPGCGWSVRETACLSKAYGQMWLLSYFHRRDLRTLGLAICSAVPIDWVPQGRTTWSIHASGAWMTTEDMLEVWNRVWILDNPFMGDKGKVREWRDIPYLPKSQDGLCSSLVGRRERAEWAKNIWGSVEKVRRMIGPERYADYLSCMDRH

ChimeraX REST job id: job_bfd3lbgs  
BlastProtein finished.  
Parsing BLAST results.  

BlastProtein returned no results  

> alphafold match
> EVDLGTGTRCVVLAEDKVREADVAERIAALKTQYGDSWHVDKEHPYRTWQYWGSYKTEATGSAASLINGVVKLLSWPWNAREDVVRMAMTDTTAFGQQRVFKEKVDTKAQEPQVGTKIIMRAVNDWIFERLAGKKTPRLCTREEFIAKVRSNAALGAWSDEQNRWPNAREAVEDPEFWRLVDEERERHLGGRCAQCVYNMMGKREKKLGEFGVAKGSRAIWYMWLGSRYLEFEALGFLNEDHWASRDLSGAGVEGTSLNYLGWHLKKLSELEGGLFYADDTAGWDTRITNADLEDEEQILRYLEGEHRTLAKTILEKAYHAKVVKVARPSSSGGCVMDIITRRDQRGSGQVVTYALNTLTNIKVQLIRMMEGEGVIGPSDSQDPRLLRVEAWLKEHGEERLTRMLVSGDDCVVRPIDDRFGKALYFLNDMAKVRKDIGEWEPSEGYSSWEEVPFCSHHFHELTMKDGRVIIVPCRDQDELVGRARVSPGCGWSVRETACLSKAYGQMWLLSYFHRRDLRTLGLAICSAVPIDWVPQGRTTWSIHASGAWMTTEDMLEVWNRVWILDNPFMGDKGKVREWRDIPYLPKSQDGLCSSLVGRRERAEWAKNIWGSVEKVRRMIGPERYADYLSCMDRH

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  

> alphafold predict
> EVDLGTGTRCVVLAEDKVREADVAERIAALKTQYGDSWHVDKEHPYRTWQYWGSYKTEATGSAASLINGVVKLLSWPWNAREDVVRMAMTDTTAFGQQRVFKEKVDTKAQEPQVGTKIIMRAVNDWIFERLAGKKTPRLCTREEFIAKVRSNAALGAWSDEQNRWPNAREAVEDPEFWRLVDEERERHLGGRCAQCVYNMMGKREKKLGEFGVAKGSRAIWYMWLGSRYLEFEALGFLNEDHWASRDLSGAGVEGTSLNYLGWHLKKLSELEGGLFYADDTAGWDTRITNADLEDEEQILRYLEGEHRTLAKTILEKAYHAKVVKVARPSSSGGCVMDIITRRDQRGSGQVVTYALNTLTNIKVQLIRMMEGEGVIGPSDSQDPRLLRVEAWLKEHGEERLTRMLVSGDDCVVRPIDDRFGKALYFLNDMAKVRKDIGEWEPSEGYSSWEEVPFCSHHFHELTMKDGRVIIVPCRDQDELVGRARVSPGCGWSVRETACLSKAYGQMWLLSYFHRRDLRTLGLAICSAVPIDWVPQGRTTWSIHASGAWMTTEDMLEVWNRVWILDNPFMGDKGKVREWRDIPYLPKSQDGLCSSLVGRRERAEWAKNIWGSVEKVRRMIGPERYADYLSCMDRH

Running AlphaFold prediction  
[Repeated 2 time(s)] Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in /home/nisha/Downloads/ChimeraX/AlphaFold/prediction_1  

> save /home/nisha/Pictures/shaswati-debasis/alphafold-str.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 133, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff14b354d90> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7ff11d2475b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, 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-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 133, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff14b354d90> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7ff11d2475b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /home/nisha/Pictures/shaswati-debasis/alphafold-kfdv.pdb relModel #1

> style stick

Changed 10122 atom styles  

> style sphere

Changed 10122 atom styles  

> style ball

Changed 10122 atom styles  

> color byhetero

> color bychain

> color byhetero

> style ball

Changed 10122 atom styles  

> style sphere

Changed 10122 atom styles  

> rainbow

> color bypolymer

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -20.12, mean
0.07, maximum 14.85  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "best_model.pdb_A SES surface": minimum -27.97, mean
-4.276, maximum 23  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp

Map values for surface "best_model.pdb_A SES surface": minimum -27.97, mean
-4.276, maximum 23  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -20.12, mean
0.07, maximum 14.85  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color bfactor

10122 atoms, 635 residues, 1 surfaces, atom bfactor range 26.6 to 98.8  

> hbonds reveal true

659 hydrogen bonds found  

> ~hbonds

> interfaces ~solvent

0 buried areas:  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> color bfactor

10122 atoms, 635 residues, 1 surfaces, atom bfactor range 26.6 to 98.8  

> rainbow

> mlp

Map values for surface "best_model.pdb_A SES surface": minimum -27.97, mean
-4.276, maximum 23  
To also show corresponding color key, enter the above mlp command and add key
true  

> color byhetero

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> show cartoons

> style stick

Changed 10122 atom styles  

> show surfaces

> style ball

Changed 10122 atom styles  

> color byhetero

> view

[Repeated 1 time(s)]

> view orient

> ui tool show "Side View"

> view orient

> view

[Repeated 1 time(s)]

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting full

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting simple

> set bgColor gray

> set bgColor white

> set bgColor black

> set bgColor white

> lighting shadows true

> lighting shadows false

> volume style surface

No volumes specified  

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> transparency 50

> transparency 0

> show atoms

> color byhetero

> rainbow

[Repeated 1 time(s)]

> color bychain

> color byhetero

> color bypolymer

> show atoms

> coulombic

Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -20.12, mean
0.07, maximum 14.85  
To also show corresponding color key, enter the above coulombic command and
add key true  

> cartoon

> style stick

Changed 10122 atom styles  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (single color)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "ghostly white"

Changed 10122 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "molecular surfaces" "chain id coloring (opaque)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color bychain targ s trans 0

  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> set bgColor white

> color red

> color hot pink

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> surface

> transparency 50

> surface hidePatches

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> style sphere

Changed 10122 atom styles  

> set bgColor black

> cartoon style xsection oval modeHelix default

> cartoon style xsection rectangle modeHelix default

> cartoon style coil xsection oval

> cartoon style xsection barbell modeHelix default

> cartoon style modeHelix tube sides 20

> cartoon style xsection oval modeHelix default

> preset cartoons/nucleotides ribbons/slabs

Changed 10122 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> rainbow

> set bgColor white

> save /home/nisha/Pictures/shaswati-debasis/session-kfdv_alphafold.cxs
> includeMaps true

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 133, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff14b354d90> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7ff11d2475b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, 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-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 133, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff14b354d90> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7ff11d2475b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /home/nisha/Pictures/shaswati-debasis/alphafold-kfdv-session.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 133, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff14b354d90> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7ff11d2475b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, 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-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 133, in take_snapshot  
, 'table_session': self.table.session_info()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 461, in session_info  
sort_info = (self.model().sortColumn(), int(self.model().sortOrder()))  
AttributeError: 'NoneType' object has no attribute 'sortColumn'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff14b354d90> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7ff11d2475b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff14b354d90> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff11d2475b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 21.0.3
OpenGL renderer: Mesa Intel(R) HD Graphics 530 (SKL GT2)
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 7040
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       5.3Gi       1.9Gi       1.0Gi       8.3Gi       8.9Gi
	Swap:         2.0Gi       131Mi       1.9Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 530 [8086:1912] (rev 06)	
	DeviceName: Intel HD Graphics	
	Subsystem: Dell HD Graphics 530 [1028:06b9]
Locale: ('en_IN', 'ISO8859-1')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110140902
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.3
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.2
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.6
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (4)

comment:1 by Eric Pettersen, 4 years ago

Cc: Zach Pearson added
Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Problem saving blast table info in session

comment:2 by Eric Pettersen, 4 years ago

Cc: Eric Pettersen Tom Goddard added; Zach Pearson removed
Owner: changed from Eric Pettersen to Zach Pearson
Status: accepted → assigned

I can reproduce this by just doing that first 'alphafold search' that returns no results. The blast results panel (should there really be one?) shows the blast parameters and a blank area underneath. It looks like the table is never fully initialized, but the session save of the Blast results tool tries to save the table state.

comment:3 by Tom Goddard, 4 years ago

This bug report is with the October 14, 2021 ChimeraX daily build.

When I test with October 19, 2021 running the alphafold search, getting no blast hits, then save a session, I get no error.

comment:4 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in the latest daily build.

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