<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="">Using the command "alphafold predict #1,2" is handing the 3 monomer sequences (two from the #1 dimer, and one from the #2 monomer) to Alphafold and making a prediction for the interaction of those 3 monomers. It is not using the PDB models of the dimer and monomer. AlphaFold does not dock existing models, it makes predictions from sequences.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 5, 2022, at 6:44 AM, Tan, Wei Ren 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=""><span style="caret-color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14.666666984558105px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?</span></div></blockquote></div><br class=""></div></body></html>