[chimerax-users] Opening X3D?

[Tom Goddard]

Hi Aaron,

  Greg Pintilie who wrote Segger is going to move it from SourceForge to GitHub hopefully in the next few weeks.  Then I will do an initial port from the current Chimera 1 code to ChimeraX that will be just a command based interface.  Optimistically I might have that a month from now, more likely 3 months from now.  It is going to take a few years to get ChimeraX doing most of the things Chimera 1 does now, on top of the new features we are constantly adding to ChimeraX.

	Tom


> On Feb 16, 2017, at 1:03 PM, Aaron Lewis wrote:
> 
> Hi Tom,
> 
> Thanks for the explanation. You have guessed my use case exactly, regarding both the Regions / Color Density Map and the motive being to render with ambient occlusion. That would be quite handy; I and those else I know who work with EM maps rely on Segger to annotate them.
> 
> Thanks again,
> Aaron
> 
> On Thu, Feb 16, 2017 at 8:07 PM Tom Goddard  wrote:
> Hi Aaron,
> 
>   ChimeraX is not able to read X3D, it can only write it.  A mistake in the code caused it to claim it could read it and that got into the documentation.  I've fixed that.   I'll also make it give a clear error message instead of a traceback.
> 
>   When you say view maps colored with Chimera 1 and Segger do you mean you use the Chimera 1 Segger menu entry Regions / Color Density Map, and you want to see that result in ChimeraX (probably for the nicer ambient occlusion lighting)?  I'll take a look at how hard it would be to put Segger into ChimeraX.
> 
>         Tom
> 
> 
> > On Feb 16, 2017, at 4:26 AM, Aaron Lewis wrote:
> >
> > Dear x-users,
> >
> > I've tried to open x3d files using recent Mac and Linux dailies, but without any success. This would be useful as a way to view maps colored in Chimera 1 & Segger. I take it from docs/user/commands/open.html that the following usage should be supported:
> >
> > open ~/Desktop/color.x3d format x3d
> >
> > but I only get the error below.  Any suggestions would be welcome.
> >
> > Aaron
> >
> > --
> > Traceback (most recent call last):
> > File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/tool.py", line 158, in execute
> > cmd.run(cmd_text)
> > File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2257, in run
> > result = ci.function(session, **kw_args)
> > File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 108, in open
> > models = session.models.open(paths, format=format, name=name, **kw)
> > File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py", line 351, in open
> > session, filenames, format=format, name=name, **kw)
> > File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 368, in open_multiple_data
> > models, status = open_data(session, fspec, format=format, name=name, **kw)
> > File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 298, in open_data
> > open_func = fmt.open_func
> > AttributeError: 'NoneType' object has no attribute 'open_func'
> >
> >
> >
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