no 'self' in restore_snapshot

[kelvin.lau@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-07-07)
Description
tried to open session

Log:
UCSF ChimeraX version: 0.91 (2019-07-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/kelvinlau/Desktop/ralf dock model.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 629, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 540, in restore_snapshot  
match_map.mod_handler = match_map.triggers.add_handler('modified',
self._mmap_mod_cb)  
NameError: name 'self' is not defined  
  
opened ChimeraX session  

> open /Users/kelvinlau/Desktop/HOP2.pdb

Summary of feedback from opening /Users/kelvinlau/Desktop/HOP2.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2018-11-29 Time 22:41:04 CET +0100 (1543527664.81 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : 76_aimless32.mtz  
  
27 messages similar to the above omitted  
Cannot find LINK/SSBOND residue MAN (2099 )  
Cannot find LINK/SSBOND residue MAN (2221 )  
Cannot find LINK/SSBOND residue MAN (2229 )  
Cannot find LINK/SSBOND residue MAN (2220 )  
Cannot find LINK/SSBOND residue NAG (1109 )  
102 messages similar to the above omitted  
  
Chain information for HOP2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "/Users/kelvinlau/Desktop/ralf dock model.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 629, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 540, in restore_snapshot  
match_map.mod_handler = match_map.triggers.add_handler('modified',
self._mmap_mod_cb)  
NameError: name 'self' is not defined  
  
opened ChimeraX session  




OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
File attachment: ralf dock model.cxs

ralf dock model.cxs​

[kelvin.lau@…]

Added by email2trac

[pett]

Hi Kelvin,

Thanks for reporting this and providing a session I could test with. I've fixed the problem now and the fix will be in the next daily build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[kelvin.lau@…]

Thanks for the fix. I will try out the new daily build.

Great work with the new update!

Best

Kelvin


--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne<x-apple-data-detectors://0/0>
Switzerland<x-apple-data-detectors://0/0>
Email: kelvin.lau@epfl.ch<mailto:kelvin.lau@epfl.ch>
Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267>

On Jul 11, 2019, at 20:44, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#2194: no 'self' in restore_snapshot
-----------------------------------+--------------------
         Reporter:  kelvin.lau@…  |      Owner:  pett
             Type:  defect        |     Status:  closed
         Priority:  normal        |  Milestone:
        Component:  Sessions      |    Version:
       Resolution:  fixed         |   Keywords:
       Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
          Project:  ChimeraX      |
-----------------------------------+--------------------
Changes (by pett):

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


Comment:

Hi Kelvin,
        Thanks for reporting this and providing a session I could test
with.  I've fixed the problem now and the fix will be in the next daily
build.

--Eric

        Eric Pettersen
        UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2194#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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