<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=""><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class="">Hi Atanas,</p><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The MOLE plugin is trying to write some settings into the "current directory". When you start Chimera by double-clicking the icon, the "current directory" is some system directory that you don't have permission to write into. So, before you start the MOLE plugin you should change Chimera's current directory with the "cd" command (Favorites→Command Line). Specifically "cd ~" will make your home directory the current directory. The plugin should work after that.</p><p style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class="">--Eric<br class=""></p><blockquote style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px;" class=""><p class="">Eric Pettersen<br class="">UCSF Computer Graphics Lab</p></blockquote><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 8, 2019, at 1:35 PM, Radkov, Atanas <<a href="mailto:Atanas.Radkov@ucsf.edu" class="">Atanas.Radkov@ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">Hello,</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""><br class=""></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">My name is Atanas Radkov, postdoc in Seemay Chou's lab at UCSF. I was wondering if you could help me set up Mole on Chimera. I installed it, as well as Mono, but I keep seeing the error below. Could you please let me know if there is a way to address this error? Thank you so much for your time and help!</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""><br class=""></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">Best wishes,</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">Atanas</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""><br class=""></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""><br class=""></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""><br class=""></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""><br class=""></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">Traceback (most recent call last):</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> File "/Applications/Chimera.app/Contents/Resources/share/chimera/toolbar.py", line 26, in _guard</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> func()</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 954, in <lambda></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None)</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> File "/Applications/Chimera.app/Contents/Resources/share/chimera/dialogs.py", line 76, in display</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> dialog = find(name, create=1)</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> File "/Applications/Chimera.app/Contents/Resources/share/chimera/dialogs.py", line 61, in find</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> return d()</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 353, in __init__</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> with open(CONFIGFILE, 'w') as f:</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt'</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">Error in toolbar callback:</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt'</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""><br class=""></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 353, in __init__</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""> with open(CONFIGFILE, 'w') as f:</div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class=""><br class=""></div><div style="font-family: -webkit-standard; caret-color: rgb(0, 0, 0);" class="">See reply log for Python traceback.</div><br class=""></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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Atanas Radkov, PhD</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Postdoctoral Scholar</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Adviser: Professor Seemay Chou</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Biophysics and Biochemistry Department</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">University of California - San Francisco</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Genentech Hall</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">600 16th str</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">San Francisco, CA 94158</div></div></div><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></body></html>