Save .obj error

[TSkillman@…]

I loaded a pdb file (1j8h). Hid chains a,b,d. Saved as Wavefront .obj.  Got AttributeError: 'str' object has no attribute ‘all_drawings’ error.  Couldn’t find any additional documentation on how to create .obj.


Traceback (most recent call last):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/ui/gui.py", line 691, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess))
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/ui/gui.py", line 467, in file_save_cb
self.save_dialog.display(self, session)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/ui/save_dialog.py", line 133, in display
fmt.save(session, filename)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/ui/save_dialog.py", line 40, in save
return self._save(session, filename)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/ui/save_dialog.py", line 58, in <lambda>
None, None, lambda ses, fn, fmt=fmt: fmt.export_func(ses, fn, fmt.name))
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/wavefront_obj/__init__.py", line 37, in save_file
return obj.write_obj(session, path, models)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/wavefront_obj/obj.py", line 150, in write_obj
for d in m.all_drawings():
AttributeError: 'str' object has no attribute 'all_drawings'


AttributeError: 'str' object has no attribute 'all_drawings'

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/wavefront_obj/obj.py", line 150, in write_obj
for d in m.all_drawings():

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu<mailto:chimerax-bugs@cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log.

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[pett]

Reported by Tom Skillman

[Tom Goddard]

I don't any error doing the steps you describe. Can you give me the exact commands that produced this error? I suspect the trouble is with your syntax for the "save" command but I have not figure out a case that would produce your error.

I just added OBJ export at the end of last week. I see it makes enormous files for molecules showing atoms/bonds (300 Mbytes for your example). The "set subdivision" command before saving could reduce the file size.

[Tom Goddard]

By the way, the OBJ export does not save colors currently, so it may not be useful to you.

[TSkillman@…]

Tom,

Here are two screen captures that show the before and after save as Obj command.

I started ChimeraX, loaded 1J8H, and saved as Wavefront.

I was running on OS X MacBook with software all up to date.

Hope this helps.

Tom

[cid:30D37F11-9840-43A8-9AB4-4CCE7C38FCE6]



[cid:0B8FDFCB-B9E0-4DA6-9754-7DDB23486BF2]On Aug 29, 2017, at 12:59 PM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#814: Save .obj error
-----------------------------------+----------------------
         Reporter:  TSkillman@…   |      Owner:  goddard
             Type:  defect        |     Status:  assigned
         Priority:  normal        |  Milestone:  Alpha 3
        Component:  Input/Output  |    Version:
       Resolution:                |   Keywords:
       Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
          Project:  ChimeraX      |
-----------------------------------+----------------------

Comment (by goddard):

I don't any error doing the steps you describe.  Can you give me the exact
commands that produced this error?  I suspect the trouble is with your
syntax for the "save" command but I have not figure out a case that would
produce your error.

I just added OBJ export at the end of last week.  I see it makes enormous
files for molecules showing atoms/bonds (300 Mbytes for your example).
The "set subdivision" command before saving could reduce the file size.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/814#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

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[TSkillman@…]

Added by email2trac

[TSkillman@…]

Added by email2trac

[Tom Goddard]

Fixed.

The File / Save... menu dialog was broken due to some recent changes to the file export APIs. Fixed in tonight's build. The save command is working correctly ("save ~/Desktop/model.obj")

[TSkillman@…]

Update - Just realized that I can type the save command into the command window. That seems to be working. So the problem is just with using the Save dropdown menu item.


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[TSkillman@…]

Our last two messages crossed. Thanks for the fix.  -Tom


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[TSkillman@…]

All working great now.  The set subdivision really helps with file size.  I’ve been using 0.1 and the model still looks good. Generated a surface, stick, and ribbon models and loaded them into Meshlab without problem.  Cool.



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