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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