<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">It seems that you have the IDLE shell set to autostart, which unsurprisingly fails in nogui mode. It’s harmless — you can ignore it.<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 12, 2017, at 2:30 PM, hy liao <<a href="mailto:hl_random@yahoo.com" class="">hl_random@yahoo.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><div style="background-color: rgb(255, 255, 255); font-family: 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 16px;" class=""><div id="yui_3_16_0_ym19_1_1492028541676_6492" class="">Thank you, Eric! but I get this error, will it cause later malfunctions?</div><div id="yui_3_16_0_ym19_1_1492028541676_6492" dir="ltr" class=""><br class=""></div><div id="yui_3_16_0_ym19_1_1492028541676_6492" dir="ltr" class="">> chimera/bin/chimera --nogui --script "chimera/bin/pip install scipy"<br class=""></div><div id="yui_3_16_0_ym19_1_1492028541676_7610" class="">Starting extension 'IDLE' failed </div><div id="yui_3_16_0_ym19_1_1492028541676_7610" class="">(and then blah...)</div><div id="yui_3_16_0_ym19_1_1492028541676_7610" class=""><br class=""></div><div id="yui_3_16_0_ym19_1_1492028541676_7610" class="">Thanks again,</div><div id="yui_3_16_0_ym19_1_1492028541676_7610" class="">SL</div><div dir="ltr" id="yui_3_16_0_ym19_1_1492028541676_7611" class=""><br id="yui_3_16_0_ym19_1_1492028541676_7612" class=""></div><div dir="ltr" id="yui_3_16_0_ym19_1_1492028541676_7611" class=""><br class=""></div> <div class="qtdSeparateBR" id="yui_3_16_0_ym19_1_1492028541676_7737"><br class=""><br class=""></div><div class="yahoo_quoted" id="yui_3_16_0_ym19_1_1492028541676_7219" style="display: block;"> <div style="font-family: Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;" id="yui_3_16_0_ym19_1_1492028541676_7218" class=""> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;" id="yui_3_16_0_ym19_1_1492028541676_7217" class=""> <div dir="ltr" class=""><font size="2" face="Arial" class=""> On Tuesday, April 11, 2017 1:28 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></font></div> <br class=""><br class=""> <div class="y_msg_container" id="yui_3_16_0_ym19_1_1492028541676_7216"><div id="yiv1366939342" class=""><div id="yui_3_16_0_ym19_1_1492028541676_7215" class="">You type that to the Unix shell, the same way you started Chimera. So:<div class="yiv1366939342" id="yui_3_16_0_ym19_1_1492028541676_7285"><br clear="none" class="yiv1366939342"></div><div class="yiv1366939342" id="yui_3_16_0_ym19_1_1492028541676_7287"><span class="yiv1366939342Apple-tab-span" style="white-space:pre;"> </span><whatever command you use to start Chimera> --nogui --script get-pip.py</div><div class="yiv1366939342" id="yui_3_16_0_ym19_1_1492028541676_7283"><br clear="none" class="yiv1366939342"></div><div class="yiv1366939342" id="yui_3_16_0_ym19_1_1492028541676_7281">—Eric</div><div class="yiv1366939342" id="yui_3_16_0_ym19_1_1492028541676_7214"><br clear="none" class="yiv1366939342"><div class="yiv1366939342">
<div class="yiv1366939342" style="letter-spacing: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"><div class="yiv1366939342"><span class="yiv1366939342Apple-tab-span" style="white-space:pre;"> </span>Eric Pettersen</div><div class="yiv1366939342"><span class="yiv1366939342Apple-tab-span" style="white-space:pre;"> </span>UCSF Computer Graphics Lab</div></div><br clear="none" class="yiv1366939342Apple-interchange-newline">
</div>
<br clear="none" class="yiv1366939342"><div id="yui_3_16_0_ym19_1_1492028541676_7298" class=""><blockquote class="yiv1366939342" type="cite" id="yui_3_16_0_ym19_1_1492028541676_7297"><div class="yiv1366939342yqt5056269139" id="yiv1366939342yqt21607"><div class="yiv1366939342">On Apr 10, 2017, at 6:23 PM, hy liao <<a rel="nofollow" shape="rect" class="yiv1366939342" ymailto="mailto:hl_random@yahoo.com" target="_blank" href="mailto:hl_random@yahoo.com">hl_random@yahoo.com</a>> wrote:</div><br clear="none" class="yiv1366939342Apple-interchange-newline"><div class="yiv1366939342" id="yui_3_16_0_ym19_1_1492028541676_7296"><div class="yiv1366939342" id="yui_3_16_0_ym19_1_1492028541676_7295"><div class="yiv1366939342" style="background-color:rgb(255, 255, 255);font-family:'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;font-size:16px;" id="yui_3_16_0_ym19_1_1492028541676_7294"><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_26173">Hi, this was posted here, but where exactly do I invoke the said chimera command? I open chimera with IDLE; a python shell opens with the following</div><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_26173"><br clear="none" class="yiv1366939342"></div><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34913">Python 2.7.10 (default, May 4 2016, 01:09:35) </div><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34914">[GCC 4.6.2] on linux2</div><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34915">Type "copyright", "credits" or "license()" for more information.</div><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34916">==== No Subprocess ====</div><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34917">>>> </div><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34918">>>> import chimera</div><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34919">>>></div><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34919"><br clear="none" class="yiv1366939342"></div><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34919">I tried what the posting said, but got an error</div><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_36689">>>> <span class="yiv1366939342" style="font-family:'Courier New';white-space:pre-wrap;">chimera --nogui --script get-pip.py</span></div><pre class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_40156" style="word-wrap:break-word;"><span class="yiv1366939342" style="font-family:'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;">Traceback (most recent call last):</span><br clear="none" class="yiv1366939342"></pre><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_36691"> File "<pyshell#3>", line 1, in <module></div><pre class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_41913" style="word-wrap:break-word;"> chimera --nogui --script get-pip.py</pre><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_36693">NameError: name 'nogui' is not defined</div><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_36694"><br clear="none" class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_36695"></div><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_36694">Thanks,</div><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_36694">SL</div><div class="yiv1366939342" dir="ltr" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_34919"><br clear="none" class="yiv1366939342"></div><div class="yiv1366939342" id="yiv1366939342yui_3_16_0_ym19_1_1491870728257_26173"><br clear="none" 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