Opened 7 years ago

Closed 7 years ago

Last modified 7 years ago

#1667 closed defect (fixed)

Session-restore failure: KeyError: 'rotations'

Reported by: shiwei.zhu@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

Dear Chimera experts,


When I open session file, I met the error as shown in the below,


Unable to restore session, resetting.

Traceback (most recent call last):
File "/home/szhu/chimerax/lib/python3.6/site-packages/chimerax/core/session.py", line 581, in restore
obj = sm.restore_snapshot(self, data)
File "/home/szhu/chimerax/lib/python3.6/site-packages/chimerax/atomic/bond_rot/manager.py", line 158, in restore_snapshot
mgr._ses_restore(data)
File "/home/szhu/chimerax/lib/python3.6/site-packages/chimerax/atomic/bond_rot/manager.py", line 172, in _ses_restore
self.bond_rotations = data['rotations']
KeyError: 'rotations'


Do you know what is the possible reason for this issue and how can I fix it?


Thank you in advance.

Shiwei


Shiwei Zhu (Postdoc associate)
Liu Lab
Department of Microbial Pathogenesis
Microbial Sciences Institute
Yale School of Medicine

ABC211B, 840 West Campus Drive

West Haven, CT 06516

Phone:203-737-3110

Email: shiwei.zhu@yale.edu

www.cryoet.org<http://www.cryoet.org>

Change History (6)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: report erroes → Session-restore failure: KeyError: 'rotations'

comment:2 by Eric Pettersen, 7 years ago

Resolution: → fixed
Status: accepted → closed

Hi Shiwei,

This problem was fixed on December 17th, so if you download a version of ChimeraX newer than that then you should be able to restore your session. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by shiwei.zhu@…, 7 years ago 

Hi Eric,

Thank you for your nice suggestions.

I have downloaded a newer version after Dec-17th.

However, when I open it, I always have the errors like below:

Traceback (most recent call last):
  File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__
    self.init_available_from_cache(logger)
  File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 445, in
init_available_from_cache
    abc.load_from_cache()
  File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache
    b = _build_bundle(d)
  File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle
    keywords = _extract_extra_keywords(keywords)
  File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/installed.py", line 270, in
_extract_extra_keywords
    all_kwds = [k.strip() for k in kwds.split(',')]
AttributeError: 'list' object has no attribute 'split'


Could you suggest me how to fix it?

Thanks. Shiwei
Shiwei Zhu (Postdoc associate)
Liu Lab
Department of Microbial Pathogenesis
Microbial Sciences Institute
Yale School of Medicine

ABC211B, 840 West Campus Drive

West Haven, CT 06516

Phone:203-737-3110

Email: shiwei.zhu@yale.edu

www.cryoet.org<http://www.cryoet.org>



________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, January 31, 2019 1:39 PM
Cc: pett@cgl.ucsf.edu; Zhu, Shiwei
Subject: Re: [ChimeraX] #1667: Session-restore failure: KeyError: 'rotations'

#1667: Session-restore failure: KeyError: 'rotations'
----------------------------------------+--------------------
          Reporter:  shiwei.zhu@…       |      Owner:  pett
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  fixed              |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+--------------------
Changes (by pett):

 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 Hi Shiwei,
         This problem was fixed on December 17th, so if you download a
 version of ChimeraX newer than that then you should be able to restore
 your session.  Sorry for the inconvenience.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
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ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 7 years ago

Could you try the command 'toolshed reload', then restart ChimeraX and see if the error goes away. Please let me know. Also, even if it doesn't I don't think the error isn't actually harmful, so you should be able to continue using ChimeraX anyway.

Thanks!

--Eric

in reply to:  5 ; comment:5 by shiwei.zhu@…, 7 years ago 

Hi Eric,

I tried again as you suggested. The errors are still there like the below.

NOTE: Traceback (most recent call last):
 File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__
   self.init_available_from_cache(logger)
 File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 445, in
init_available_from_cache
   abc.load_from_cache()
 File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache
   b = _build_bundle(d)
 File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle
   keywords = _extract_extra_keywords(keywords)
 File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/installed.py", line 270, in
_extract_extra_keywords
   all_kwds = [k.strip() for k in kwds.split(',')]
AttributeError: 'list' object has no attribute 'split'


BUG: Error preloading available bundles:
AttributeError: 'list' object has no attribute 'split'

File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/installed.py", line 270, in
_extract_extra_keywords
all_kwds = [k.strip() for k in kwds.split(',')]

 _See log for complete Python traceback._

Yes, I can use chimeraX.

Thank you again.

Shiwei


Shiwei Zhu (Postdoc associate)
Liu Lab
Department of Microbial Pathogenesis
Microbial Sciences Institute
Yale School of Medicine

ABC211B, 840 West Campus Drive

West Haven, CT 06516

Phone:203-737-3110

Email: shiwei.zhu@yale.edu

www.cryoet.org<http://www.cryoet.org>



________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, February 28, 2019 8:10 PM
Cc: pett@cgl.ucsf.edu; Zhu, Shiwei
Subject: Re: [ChimeraX] #1667: Session-restore failure: KeyError: 'rotations'

#1667: Session-restore failure: KeyError: 'rotations'
----------------------------------------+--------------------
          Reporter:  shiwei.zhu@…       |      Owner:  pett
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  fixed              |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+--------------------

Comment (by pett):

 Could you try the command 'toolshed reload', then restart ChimeraX and see
 if the error goes away.  Please let me know.  Also, even if it doesn't I
 don't think the error isn't actually harmful, so you should be able to
 continue using ChimeraX anyway.

 Thanks!

 --Eric

--
Ticket URL: <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F1667%23comment%3A4&amp;data=02%7C01%7Cshiwei.zhu%40yale.edu%7C0e36efa67a1d4a3e415008d69de2b701%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636869994395304894&amp;sdata=EQZFun4eDs%2BTGVUFC2XICCdNPDCgcx0XyQKU4CnMcTc%3D&amp;reserved=0>
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ChimeraX Issue Tracker

comment:6 by Eric Pettersen, 7 years ago

We have a separate ticket open for this particular problem. I will add you to the recipient list for that ticket.

--Eric

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