problem opening solid state NMR structures (7K3G)

[J.Procter@…]

Another buglet!

Opening 7K3G leads to unhappiness:

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 676, in customEvent
    func(*args, **kw)
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/rest_server/server.py", line 203, in f
    ret_val = run(session, cmd, log=False, return_json=json, return_list=True)
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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 "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856, in run
    result = ci.function(session, **kw_args)
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/std_commands/setattr.py", line 137, in set_attr
    if attr_name not in type_attrs(class_):
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/attributes.py", line 35, in type_attrs
    attrs.extend(t._attr_registration.reg_attr_info.keys())
AttributeError: type object 'Model' has no attribute '_attr_registration'

AttributeError: type object 'Model' has no attribute '_attr_registration'

File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/attributes.py", line 35, in type_attrs
attrs.extend(t._attr_registration.reg_attr_info.keys())

See log for complete Python traceback.


The University of Dundee is a registered Scottish Charity, No: SC015096

[Eric Pettersen]

Hi Jim,

I am having trouble reproducing this. If I use ChimeraX 1.3 and start a REST server with "remotecontrol rest start" and then use the URL that remotecontrol provides in the log to get an interface to the server (which for some reason takes about a minute on my machine), I can use that interface to execute "open 7k3g" with any errors. So I guess I need more of a recipe. This happened via Jalview? What do I need to do to reproduce it?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[J.Procter@…]

Found the issue - Jalview imports 7K3G as an anonymised mmCIF, and renames:

setattr #1 models name 7K3G

That's what's causing the issue - not a bug I guess - we need to fix Jalview to insert #1.* rather than #1 there I guess. I don't seem to be able to rename the parent model, however. Is there a way ?

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 17 March 2022 21:23
Cc: James Procter (Staff) <J.Procter@dundee.ac.uk>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #6401: problem opening solid state NMR structures (7K3G)


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#6401: problem opening solid state NMR structures (7K3G)
-----------------------------------+----------------------
          Reporter:  J.Procter@…   |      Owner:  pett
              Type:  defect        |     Status:  feedback
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi Jim,
         I am having trouble reproducing this.  If I use ChimeraX 1.3 and
 start a REST server with "remotecontrol rest start" and then use the URL
 that remotecontrol provides in the log to get an interface to the server
 (which for some reason takes about a minute on my machine), I can use that
 interface to execute "open 7k3g" with any errors.  So I guess I need more
 of a recipe.  This happened via Jalview?  What do I need to do to
 reproduce it?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6401#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

The University of Dundee is a registered Scottish Charity, No: SC015096

[Eric Pettersen]

Hi Jim,

The command to rename the parent model that will work is "rename #1 7K3G". Nonetheless, the command you tried should not result in a traceback, so I'm keeping this ticket open -- though it might be awhile before I get to it since there is a viable workaround.

--Eric