<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yiv9979908702"><div id="yui_3_16_0_1_1414444909641_2572"><div id="yui_3_16_0_1_1414444909641_2571" style="color:#000;background-color:#fff;font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div id="yiv9979908702"><div id="yiv9979908702yui_3_16_0_1_1414437427591_23567"><div id="yiv9979908702yui_3_16_0_1_1414437427591_23566" style="color:#000;background-color:#fff;font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;">Hi Chimera Developers,<br><div dir="ltr" id="yiv9979908702yui_3_16_0_1_1414437427591_7563"><span id="yiv9979908702yui_3_16_0_1_1414437427591_16595"><br></span></div><div id="yiv9979908702yui_3_16_0_1_1414437427591_16594" dir="ltr"><span id="yiv9979908702yui_3_16_0_1_1414437427591_16593">I've used chimera mostly by GUI inerface [click]. <br></span></div><div id="yiv9979908702yui_3_16_0_1_1414437427591_23627" dir="ltr"><div id="yui_3_16_0_1_1414444909641_2639">How do I get the match-align work from command line in a python script?</div><div dir="ltr" id="yui_3_16_0_1_1414444909641_2671">I read a good description at:<br></div><div id="yui_3_16_0_1_1414444909641_2643" dir="ltr"><a id="yui_3_16_0_1_1414444909641_2642" href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html</a></div><div id="yui_3_16_0_1_1414444909641_2680" dir="ltr"><br></div><div id="yui_3_16_0_1_1414444909641_2681" dir="ltr">work flow of the script is:</div><div id="yui_3_16_0_1_1414444909641_2682" dir="ltr">take in 2 pdb files and match->align them.</div><div id="yui_3_16_0_1_1414444909641_2690" dir="ltr"><br></div><div id="yui_3_16_0_1_1414444909641_2687" dir="ltr">I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ?<br></div><div id="yui_3_16_0_1_1414444909641_2688" dir="ltr"><br></div><div id="yui_3_16_0_1_1414444909641_2689" dir="ltr">How do I get the output saved in a FASTA file without MAV interface?<br></div><div id="yui_3_16_0_1_1414444909641_2670" style="" class="" dir="ltr"><br style="" class=""></div></div><span></span><div id="yiv9979908702yui_3_16_0_1_1414437427591_7564"> </div><br></div></div></div></div></div></div></div></body></html>