<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Junha,<div class=""><br class=""></div><div class=""> Glad to hear you are trying VR with ChimeraX.</div><div class=""><br class=""></div><div class=""> Per-model clipping in ChimeraX is done with the clip command, or with the clipping mouse modes, atom radii are set with the size command, visibility is set with the show/hide commands, color is set with the color command, there are volume tracer mouse modes, and saving marker files should work, although you hit some bug and should press the Report a Bug… button when you get that traceback. ChimeraX does not have the selection inspector window yet. ChimeraX uses a different window toolkit Qt while Chimera used Tk so it requires all new code to move any graphical user interface from Chimera to ChimeraX. ChimeraX is a completely new program, modernizing every component of the 20-year-old design of Chimera so even moving commands from Chimera to ChimeraX requires substantial work.</div><div class=""><br class=""></div><div class=""> If you don’t find ChimeraX ready for your use, of course you should continue to use Chimera. We expect ChimeraX to replace Chimera in a few years. You might want to spend an hour skimming Elaine’s thorough ChimeraX documentation to understand what is in ChimeraX, including many new features like virtual reality that are not in Chimera.</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=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 26, 2019, at 2:03 AM, Jun Ha Song wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="gmail_default" style="font-size:small">Tom,</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">I recently got HTC Vive, and therefore started using ChimeraX. I have to say; the VR functionality is amazing. The ability to VR alone is sufficient reason for me to move over to ChimeraX.</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">However, I noticed that key, crucial, irreplaceable features are (as far as I am aware) non-existent on ChimeraX. Below are function/tools that exist in Chimera that I use (literally) everyday, and I am wondering if these function/tools can also be implemented on ChimeraX or not.</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">- per-model clipping (mclip)</div><div class="gmail_default" style="font-size:small">- inspect selection (ability to change atom/bond/surface radius, visibility, color)</div><div class="gmail_default" style="font-size:small">- volume tracer (ability to save markerset or atom/bond as .cmm)</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">If the circumstance is so that implementing these onto ChimeraX is not feasible, then I must remain with Chimera until similar tools become available on ChimeraX.<br class=""></div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">Also, is there any particular reason why all the tools of Chimera are not copied onto ChimeraX? Is ChimeraX trying to be another program that is different from Chimera?</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">As for "ability to save .cmm", I tried saving atom/link using command</div><div class="gmail_default" style="font-size:small"><i class=""><br class=""></i></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote"><i class="">save E:\LBNL\Stereocilia\ChimeraX_Markerset.cmm format markers models #1</i></blockquote><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">but I got error saying that</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small"><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">NotImplementedError: Slices are not implemented.<br class="">File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\markers\cmmfiles.py", line 39, in markerset_as_xml<br class="">rgb = tuple(r/255 for r in m.color[:3])<br class=""><span style="font-style:italic" class="">See log for complete Python traceback.</span></blockquote></div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">is this a simple bug during development, or have I typed wrong command?</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">Best,</div><div class="gmail_default" style="font-size:small">Junha Song.</div></div></div>
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