Problem restoring session

[lynnettj@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-21)
Description
Opened chimerax session saved 2 days ago 

Log:
Startup Messages  
---  
warnings | 'clip' is a prefix of an existing command 'clipper'  
'rota' is a prefix of an existing command 'rotamers'  
  
UCSF ChimeraX version: 0.91 (2019-09-21)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/lynnettj/Documents/Grad School/Research/PyMOL and Chimera
sessions/1RTD_PuglisiLabColoring.cxs" format session

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2664, in
_update_graphics_if_needed  
s[i]._update_graphics_if_needed()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 314, in
_update_graphics_if_needed  
self._create_ring_graphics()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 500, in _create_ring_graphics  
atoms = ring.ordered_atoms  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 161, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 93, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'Ring' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "graphics update":  
AttributeError: 'Ring' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 93, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.3.9
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
File attachment: 1RTD_PuglisiLabColoring.cxs

1RTD_PuglisiLabColoring.cxs​

[lynnettj@…]

Added by email2trac

[Eric Pettersen]

Hi Lynette,

This problem was fixed a few weeks back, so if you download the latest release or the daily build then you will be able to open your session (I verified it works). Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[lynnettj@…]

Thank you for letting me know! When I tried to download and install the latest version, I received the following error. Have you seen this before too? Thank you for your time and help!
[cid:4A20654B-F3BE-4605-96C7-466FB53E5397@stanford.edu]
_________________________
Lynnette N. Jackson
Ph.D. Student, Puglisi Lab
Structural Biology Department

On Mar 27, 2020, at 1:35 PM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#2986: Problem restoring session
---------------------------------+----------------------------
         Reporter:  lynnettj@…  |      Owner:  Eric Pettersen
             Type:  defect      |     Status:  closed
         Priority:  normal      |  Milestone:
        Component:  Sessions    |    Version:
       Resolution:  duplicate   |   Keywords:
       Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
          Project:  ChimeraX    |
---------------------------------+----------------------------
Changes (by Eric Pettersen):

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


Comment:

Hi Lynette,
        This problem was fixed a few weeks back, so if you download the
latest release or the daily build then you will be able to open your
session (I verified it works).  Sorry for the inconvenience.

--Eric

        Eric Pettersen
        UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2986#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[lynnettj@…]

Added by email2trac

[Eric Pettersen]

Yes, Apple went to a stricter security protocol in Catalina, and we are working on getting ChimeraX (and Chimera) into compliance but are not quite there yet. Until then, the workaround is to right-click (or control-click) on the ChimeraX app icon. That will give you a popup menu, one of the entries of which will be "Open". Choose that and ChimeraX will open, and henceforward will open normally without having to use the popup menu.

--Eric