<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sanjeev,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Take a look at this chimera-users message: <a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009904.html">[Chimera-users] easy way to make alignments in chimera</a> . I think it answers most of your questions. The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA".</div><div><br></div><div>--Eric</div><div><div><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br><br></div><div><div>On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya <<a href="mailto:s.sariya_work@ymail.com">s.sariya_work@ymail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="background-color: rgb(255, 255, 255); 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="background-color: rgb(255, 255, 255); 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="background-color: rgb(255, 255, 255); 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></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div><br><br></body></html>