<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Yao-Chi,</div><div class=""><br class=""></div>AlphaFold by default predicts 5 models using 5 neural nets that were trained with different protocols. There is no way to know which of the 5 will give the highest scoring model without computing all of them. ChimeraX and the web browser ColabFold notebook<div class=""><br class=""></div><div class=""><a href="https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb</a><br class=""><div><br class=""></div><div>don't offer the ability to choose one of the 5 neural networks. But you can make your own ColabFold or AlphaFold installation on your own computer and edit the code to do that. That is a lot of work to set up, needs Linux and ideally a nice GPU.</div><div><br class=""></div><div>Energy minimization removes atom clashes between neighboring residues. Whether you need it depends on how you intend to use the predicted model. The default in ChimeraX daily builds is to not energy minimize, but the default in ChimeraX 1.4 is to energy minimize. You can set that option using the Options button in the ChimeraX AlphaFold panel.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><br class=""></div><div> <br class=""><blockquote type="cite" class=""><div class="">On Sep 21, 2022, at 7:09 PM, Yao-Chi Chen via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi: <div class="">By ChimeraX, I am using AlphaFold to predict several protein-protein complexes. These complexes totally comprised about 600-800 amino acids.</div><div class=""><br class=""></div><div class="">To have the predicted results as soon as possible, I would like to ask: </div><div class="">1: Is there a way to predict only one model(the best one)?</div><div class="">2: what's the advantage of using the Energy-minimized structures?</div><div class=""> Could I just not use it?</div><div class=""><br class=""></div><div class=""> Thanks for your help.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">backy</div></div>
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