<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="">Hi Yunsik,<div class=""><br class=""></div><div class=""> Inspired by your question and Tristan Croll's comment that the AlphaFold database has human proteins longer than 1400 amino acids computed as separate 1400 amino acid chunks I made a ChimeraX command "bigalpha" that loads and aligns these chunks.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://rbvi.github.io/chimerax-recipes/big_alphafold/bigalpha.html" class="">https://rbvi.github.io/chimerax-recipes/big_alphafold/bigalpha.html</a><br class=""><div><br class=""></div><div>I attach two images and a PDB model made by running that command in ChimeraX for 5005 amino acid transmembrane protein</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Q2LD37 | K1109_HUMAN Transmembrane protein KIAA1109 OS=Homo sapiens OX=9606 GN=KIAA1109 PE=1 SV=2</div><div><br class=""></div><div>and also here are a few other examples I looked at yesterday.</div><div><br class=""></div><div><a href="https://twitter.com/UCSFChimeraX/status/1435870388043411458" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>https://twitter.com/UCSFChimeraX/status/1435870388043411458</a></div><div><br class=""></div><div><a href="https://twitter.com/UCSFChimeraX/status/1435760774824169474" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>https://twitter.com/UCSFChimeraX/status/1435760774824169474</a></div><div><br class=""></div><div><a href="https://twitter.com/UCSFChimeraX/status/1435859111053193216" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>https://twitter.com/UCSFChimeraX/status/1435859111053193216</a></div><div><br class=""></div><div>Keep in mind that the pieces of these models are not aligned in a reliable way and probably clash badly with each other because AlphaFold did not compute them as part of one structure. So these structures should only give you a very rough idea about the protein.</div><div><br class=""></div><div> Tom</div><div><br class=""></div><div>This is the confidence coloring determined by AlphaFold, red low, blue high confidence. To reproduce this color using ChimeraX daily build open the PDB model and type command "color bfactor #1 palette alphafold". (The confidence value is saved as the bfactor in the PDB file).</div><div></div></div></body></html>