<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Aaron,<div class=""><br class=""></div><div class=""> 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.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On Feb 16, 2017, at 1:03 PM, Aaron Lewis wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class="gmail_msg">Hi Tom,<div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">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.</div><div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">Thanks again,</div><div class="gmail_msg">Aaron</div></div><br class="gmail_msg"><div class="gmail_quote gmail_msg"><div dir="ltr" class="gmail_msg">On Thu, Feb 16, 2017 at 8:07 PM Tom Goddard wrote:<br class="gmail_msg"></div><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Aaron,<br class="gmail_msg">
<br class="gmail_msg">
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.<br class="gmail_msg">
<br class="gmail_msg">
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.<br class="gmail_msg">
<br class="gmail_msg">
Tom<br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
> On Feb 16, 2017, at 4:26 AM, Aaron Lewis wrote:<br class="gmail_msg">
><br class="gmail_msg">
> Dear x-users,<br class="gmail_msg">
><br class="gmail_msg">
> 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:<br class="gmail_msg">
><br class="gmail_msg">
> open ~/Desktop/color.x3d format x3d<br class="gmail_msg">
><br class="gmail_msg">
> but I only get the error below. Any suggestions would be welcome.<br class="gmail_msg">
><br class="gmail_msg">
> Aaron<br class="gmail_msg">
><br class="gmail_msg">
> --<br class="gmail_msg">
> Traceback (most recent call last):<br class="gmail_msg">
> 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<br class="gmail_msg">
> cmd.run(cmd_text)<br class="gmail_msg">
> 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<br class="gmail_msg">
> result = ci.function(session, **kw_args)<br class="gmail_msg">
> 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<br class="gmail_msg">
> models = session.models.open(paths, format=format, name=name, **kw)<br class="gmail_msg">
> 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<br class="gmail_msg">
> session, filenames, format=format, name=name, **kw)<br class="gmail_msg">
> 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<br class="gmail_msg">
> models, status = open_data(session, fspec, format=format, name=name, **kw)<br class="gmail_msg">
> 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<br class="gmail_msg">
> open_func = fmt.open_func<br class="gmail_msg">
> AttributeError: 'NoneType' object has no attribute 'open_func'<br class="gmail_msg">
><br class="gmail_msg">
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><br class="gmail_msg">
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