<div dir="ltr">Thank you for this assistance and for identifying this bug. I am able to open .xyz files after restarting. </div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 23, 2022 at 12:08 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Hi Carina<div><span style="white-space:pre-wrap">        </span>Also, the fact that a restart is required is a bug.  I will open a ticket in the ChimeraX bug-tracking database with you and Tony on the recipient list so that you will be notified when it gets fixed.</div><div><br></div><div><div>--Eric</div><div><br></div><div><span style="white-space:pre-wrap">      </span>Eric Pettersen</div><div><span style="white-space:pre-wrap">   </span>UCSF Computer Graphics Lab</div></div><div><br><div><br><blockquote type="cite"><div>On Nov 23, 2022, at 8:17 AM, Anthony James Schaefer via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br><div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)">Carina,</div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)"><br></div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)">After installing a bundle, ChimeraX needs to be restarted before you can open its file formats. If this issue persists after restarting ChimeraX, submit a bug report through Help -> Report a Bug on the ChimeraX menu.</div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)"><br></div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)">Tony<br></div><div id="m_4895659627781426180m_-3681268503628900201appendonsend" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"></div><hr style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;display:inline-block;width:483.125px"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"></span><div id="m_4895659627781426180m_-3681268503628900201divRplyFwdMsg" dir="ltr" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span> </span>ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" target="_blank">chimerax-users-bounces@cgl.ucsf.edu</a>> on behalf of Carina Luo via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br><b>Sent:</b><span> </span>Wednesday, November 23, 2022 8:52 AM<br><b>To:</b><span> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a><span> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br><b>Subject:</b><span> </span>[chimerax-users] Opening .xyz file in ChimeraX</font><div> </div></div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><font color="BA0C2F">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]</font><br><br><div><div dir="ltr"><font face="arial, sans-serif">Hello,</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">I am trying to open an .xyz file in ChimeraX. I installed SEQCROW (1.5.9) as prompted, but ChimeraX still says "Opener for format 'XYZ file' is not installed; see log for more info."</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Here is the output I got when I installed SEQCROW (1.5.9):</font></div><div><font face="arial, sans-serif">Downloading bundle SEQCROW-1.5.9-py3-none-any.whl<br></font><div style="margin-top:0px;margin-bottom:0px"><font face="arial, sans-serif">Errors may have occurred when running pip:<br></font></div><div style="margin-top:0px;margin-bottom:0px"><font face="arial, sans-serif">pip standard error:<br>---<br><br>[notice] A new release of pip available: 22.2.2 -> 22.3.1<br>[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip<br>---<br></font></div><div style="margin-top:0px;margin-bottom:0px"><font face="arial, sans-serif">pip standard output:<br>---<br>Looking in indexes:<span> </span><a href="https://pypi.org/simple" target="_blank">https://pypi.org/simple</a>,<span> </span><a href="https://cxtoolshed.rbvi.ucsf.edu/pypi/" target="_blank">https://cxtoolshed.rbvi.ucsf.edu/pypi/</a><br>Processing c:\users\user\downloads\seqcrow-1.5.9-py3-none-any.whl<br>Requirement already satisfied: jinja2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (3.1.2)<br>Collecting Send2Trash<br>Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB)<br>Requirement already satisfied: ChimeraX-Core<=1.5,>=1.2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.5rc202210312311)<br>Requirement already satisfied: scipy in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.9.0)<br>Requirement already satisfied: psutil in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (5.9.1)<br>Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.5.9) (2.1.1)<br>Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.5.9) (1.23.1)<br>Installing collected packages: Send2Trash, SEQCROW<br>Successfully installed SEQCROW-1.5.9 Send2Trash-1.8.0</font></div><div style="margin-top:0px;margin-bottom:0px"><font face="arial, sans-serif"><br></font></div><div style="margin-top:0px;margin-bottom:0px"><font face="arial, sans-serif">Could you please help me figure out what I still need to do in order to successfully open .xyz files in ChimeraX?</font></div><div style="margin-top:0px;margin-bottom:0px">Sincerely,</div><div style="margin-top:0px;margin-bottom:0px">Carina</div></div></div></div></div><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">_______________________________________________</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">ChimeraX-users mailing list</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank">ChimeraX-users@cgl.ucsf.edu</a></span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Manage subscription:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></span></div></blockquote></div><br></div></div></blockquote></div>