<html><head></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div><span>OK, thank you, Eric!</span></div> <div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font size="2" face="Arial"> On Thursday, April 13, 2017 2:03 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:<br></font></div>  <br><br> <div class="y_msg_container"><div id="yiv9103323430"><div>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="yiv9103323430"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430">—Eric</div><div class="yiv9103323430"><br clear="none" class="yiv9103323430"><div><blockquote class="yiv9103323430" type="cite"><div class="yiv9103323430yqt3312961438" id="yiv9103323430yqt09653"><div class="yiv9103323430">On Apr 12, 2017, at 2:30 PM, hy liao <<a rel="nofollow" shape="rect" class="yiv9103323430" 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="yiv9103323430Apple-interchange-newline"><div class="yiv9103323430"><div class="yiv9103323430"><div class="yiv9103323430" style="background-color:rgb(255, 255, 255);font-family:'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;font-size:16px;"><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_6492">Thank you, Eric! but I get this error, will it cause later malfunctions?</div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_6492"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_6492">> chimera/bin/chimera --nogui --script "chimera/bin/pip install scipy"<br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7610">Starting extension 'IDLE' failed </div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7610">(and then blah...)</div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7610"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7610">Thanks again,</div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7610">SL</div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7611"><br clear="none" class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7612"></div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7611"><br clear="none" class="yiv9103323430"></div> <div class="yiv9103323430qtdSeparateBR" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7737"><br clear="none" class="yiv9103323430"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430yahoo_quoted" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7219" style="display:block;"> <div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7218" style="font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7217" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div class="yiv9103323430" dir="ltr"><font class="yiv9103323430" size="2" face="Arial"> On Tuesday, April 11, 2017 1:28 PM, Eric Pettersen <<a rel="nofollow" shape="rect" class="yiv9103323430" ymailto="mailto:pett@cgl.ucsf.edu" target="_blank" href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:<br clear="none" class="yiv9103323430"></font></div>  <br clear="none" class="yiv9103323430"><br clear="none" class="yiv9103323430"> <div class="yiv9103323430y_msg_container" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7216"><div class="yiv9103323430" id="yiv9103323430"><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7215">You type that to the Unix shell, the same way you started Chimera.  So:<div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7285"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7287"><span class="yiv9103323430Apple-tab-span" style="white-space:pre;">   </span><whatever command you use to start Chimera>  --nogui --script get-pip.py</div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7283"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7281">—Eric</div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7214"><br clear="none" class="yiv9103323430"><div class="yiv9103323430">
<div class="yiv9103323430" style="letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word;"><div class="yiv9103323430"><span class="yiv9103323430Apple-tab-span" style="white-space:pre;">       </span>Eric Pettersen</div><div class="yiv9103323430"><span class="yiv9103323430Apple-tab-span" style="white-space:pre;"> </span>UCSF Computer Graphics Lab</div></div><br clear="none" class="yiv9103323430Apple-interchange-newline">

</div>
<br clear="none" class="yiv9103323430"><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7298"><blockquote class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7297" type="cite"><div class="yiv9103323430yqt5056269139" id="yiv9103323430yqt21607"><div class="yiv9103323430">On Apr 10, 2017, at 6:23 PM, hy liao <<a rel="nofollow" shape="rect" class="yiv9103323430" 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="yiv9103323430Apple-interchange-newline"><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7296"><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7295"><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1492028541676_7294" style="background-color:rgb(255, 255, 255);font-family:'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;font-size:16px;"><div class="yiv9103323430" id="yiv9103323430yui_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="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_26173"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34913">Python 2.7.10 (default, May  4 2016, 01:09:35) </div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34914">[GCC 4.6.2] on linux2</div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34915">Type "copyright", "credits" or "license()" for more information.</div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34916">==== No Subprocess ====</div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34917">>>> </div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34918">>>> import chimera</div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34919">>>></div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34919"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34919">I tried what the posting said, but got an error</div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_36689">>>> <span class="yiv9103323430" style="font-family:'Courier New';white-space:pre-wrap;">chimera --nogui --script get-pip.py</span></div><pre class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_40156" style="word-wrap:break-word;"><span class="yiv9103323430" style="font-family:'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;">Traceback (most recent call last):</span><br clear="none" class="yiv9103323430"></pre><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_36691">  File "<pyshell#3>", line 1, in <module></div><pre class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_41913" style="word-wrap:break-word;">   chimera --nogui --script get-pip.py</pre><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_36693">NameError: name 'nogui' is not defined</div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_36694"><br clear="none" class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_36695"></div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_36694">Thanks,</div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_36694">SL</div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_34919"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_26173"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_26173"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_26173"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" dir="ltr" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_26173"><a rel="nofollow" shape="rect" class="yiv9103323430enhancr2_efd3df9f-8b89-4c4a-d978-10218e102912" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_29656" target="_blank" href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-November/012851.html">[Chimera-users] How to install package in chimera python?</a><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430" id="yiv9103323430yui_3_16_0_ym19_1_1491870728257_31371"><br clear="none" class="yiv9103323430"></div><div class="yiv9103323430ymail-preserve-class yiv9103323430yahoo-link-enhancr-not-al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