[chimerax-users] Opening X3D?

[Aaron Lewis]

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 <goddard at sonic.net> 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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