<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 dir="ltr" id="yui_3_16_0_1_1414451692045_8862">*Sorry, I missed reply to all. <br></div><div id="yui_3_16_0_1_1414451692045_8883" dir="ltr"><br></div><div id="yui_3_16_0_1_1414451692045_8882" dir="ltr">Thank you Eric for the URL.</div><div id="yui_3_16_0_1_1414451692045_8881" dir="ltr"><br style="" class="" clear="none"></div><div style="" class="" dir="ltr" id="yiv6145691919yui_3_16_0_1_1414450966767_2627"><span style="" class="" id="yiv6145691919yui_3_16_0_1_1414450966767_2622"></span>Could you please help me understand what is going on here?<br style="" class="" clear="none"></div><pre class="" id="yiv6145691919yui_3_16_0_1_1414450966767_2626" style="">from chimera import openModels, Molecule # import
<br style="" class="" clear="none">models = openModels.list(modelTypes=[Molecule]) # array for model- different PDBs
<br style="" class="" clear="none">if models[0].id == 0: # what does this do?
m0, m1 = models
<br style="" class="" clear="none">else: #
m1, m0 = models # why interchanged the m1, mo?
chains = [m0.sequence('A'), m1.sequence('B')] # how do I know how many chains are present in PDB file?<br style="" class="" clear="none"><br></pre><div id="yui_3_16_0_1_1414451692045_8887">Thank you.</div><div id="yui_3_16_0_1_1414451692045_8888"><br> </div><div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: HelveticaNeue-Light, Helvetica Neue Light, 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 face="Arial" size="2"> On Monday, October 27, 2014 6:35 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:<br> </font> </div> <br><br> <div class="y_msg_container"><div id="yiv0743572947"><div>Hi Sanjeev,<div><span class="yiv0743572947Apple-tab-span" style="white-space:pre;"> </span>Take a look at this chimera-users message: <a rel="nofollow" shape="rect" target="_blank" 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 clear="none"></div><div>--Eric</div><div><div><br clear="none"> Eric Pettersen<br clear="none"> UCSF Computer Graphics Lab<br clear="none"> <a rel="nofollow" shape="rect" target="_blank" href="http://www.cgl.ucsf.edu/">http://www.cgl.ucsf.edu</a><br clear="none"><br clear="none"></div><div><div class="yiv0743572947yqt8864421039" id="yiv0743572947yqt54889"><div>On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya <<a rel="nofollow" shape="rect" ymailto="mailto:s.sariya_work@ymail.com" target="_blank" href="mailto:s.sariya_work@ymail.com">s.sariya_work@ymail.com</a>> wrote:</div><br class="yiv0743572947Apple-interchange-newline" clear="none"><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="yiv0743572947"><div id="yiv0743572947yui_3_16_0_1_1414444909641_2572"><div id="yiv0743572947yui_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="yiv0743572947"><div id="yiv0743572947yui_3_16_0_1_1414437427591_23567"><div id="yiv0743572947yui_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 clear="none"><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414437427591_7563"><span id="yiv0743572947yui_3_16_0_1_1414437427591_16595"><br clear="none"></span></div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414437427591_16594"><span id="yiv0743572947yui_3_16_0_1_1414437427591_16593">I've used chimera mostly by GUI inerface [click]. <br clear="none"></span></div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414437427591_23627"><div id="yiv0743572947yui_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="yiv0743572947yui_3_16_0_1_1414444909641_2671">I read a good description at:<br clear="none"></div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2643"><a rel="nofollow" shape="rect" id="yiv0743572947yui_3_16_0_1_1414444909641_2642" target="_blank" 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 dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2680"><br clear="none"></div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2681">work flow of the script is:</div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2682">take in 2 pdb files and match->align them.</div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2690"><br clear="none"></div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2687">I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ?<br clear="none"></div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2688"><br clear="none"></div><div dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2689">How do I get the output saved in a FASTA file without MAV interface?<br clear="none"></div><div class="yiv0743572947" dir="ltr" id="yiv0743572947yui_3_16_0_1_1414444909641_2670" style=""><br class="yiv0743572947" style="" clear="none"></div></div><span></span><div id="yiv0743572947yui_3_16_0_1_1414437427591_7564"> </div><br clear="none"></div></div></div></div></div></div></div></div>_______________________________________________<br clear="none">Chimera-users mailing list<br clear="none"><a rel="nofollow" shape="rect" ymailto="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br clear="none">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br clear="none"></blockquote></div></div><br clear="none"></div><br clear="none"><br clear="none"></div></div><br><br></div> </div> </div> </div> </div></body></html>