<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hello,<div class="">Chimera and ChimeraX are two different programs. You cannot open that file in ChimeraX -- only Chimera knows how to open it. I know it is really confusing because the file is named .chimerax, but we chose that filetype name long before we decided to name the new program ChimeraX. </div><div class=""><br class=""></div><div class="">Actually you can open it Chimera, then export to another file that can be opened in ChimeraX, details below.</div><div class=""><br class=""></div><div class="">"chimerax" files that are really for Chimera:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html</a>></div><div class=""><br class=""></div><div class="">Example with image of how it looks in Chimera:</div><div class=""> <<a href="https://www.rbvi.ucsf.edu/chimera/consurf/consurf.html" class="">https://www.rbvi.ucsf.edu/chimera/consurf/consurf.html</a>></div><div class="">... that page includes a link to example .chimerax file:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/consurf/pdb1rtt_isd.chimerax" class="">https://www.rbvi.ucsf.edu/chimera/consurf/pdb1rtt_isd.chimerax</a>></div><div class=""><br class=""></div><div class="">When you try to open the .chimerax file in Chimera you will get a warning dialog "some files contain code [etc.] would you like to open this file in Chimera?" and you need to click Yes. Then it will show the structure and sequence alignment with color-coding, as in the image shown in the example page.</div><div class=""><br class=""></div><div class="">Then to export a file for ChimeraX, choose from the Chimera menu: File... Export Scene. In the export dialog choose File type "ChimeraX [.py]" and specify file name and location.</div><div class=""><br class=""></div><div class="">Then you can open the new exported .py file in ChimeraX and you will get the color-coded structure and sequence alignment. ChimeraX cannot yet show the phylogenetic tree to the left of the sequences, but all of the other stuff is exported. It made my ChimeraX window really really wide, but I was able to resize the windows and panels manually and then it looked like the attached image:</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""></div><div class=""><img apple-inline="yes" id="6DCAA867-C413-41F0-AE0E-FAF40450AA89" width="640" height="480" src="cid:A9A6A139-26BE-43B5-929B-081678FB5DA9" class=""></div><div class=""><br class=""></div><blockquote type="cite" class="">On Mar 2, 2022, at 7:41 PM, Shin, Yeonoh via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hello,<br class=""><br class="">I ran MSA in Consurf website, however I can not open the color-coded pdb result in Chimera or ChimeraX.<br class=""><br class="">When I click the link, attached error shows up.<br class=""><br class="">When I tried to open the link in chimeraX command line, another error shows up (attached).<br class=""><br class="">Could you tell me what I need to do to see the color-coded result in Chimera or X?<br class=""><br class="">Thank you.<br class="">Yeonoh<br class=""><span id="cid:7E9ED721-6ADC-4DA7-8B5D-A6D29637CB6E"><Screen Shot 2022-03-02 at 10.38.19 PM.png></span><span id="cid:E974C6C5-1AA5-445D-8AFE-7E59093553C2"><Screen Shot 2022-03-02 at 10.38.33 PM.png></span></blockquote></div></body></html>