<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear ChimeraX community,<div class=""><br class=""></div><div class="">I am a graduate student from Harvard Medical School who recently became interested in using AlphaFold-Multimer to predict protein complex structures of my interest. I have been tried a few times of predicting one protein complex and I was able to finish all MSA. However, when AlphaFold starts predicting the structure, all five models were reported as “error”. It is surprising to me because it is known that these two proteins should form a complex. I noticed in the script on the line is: “<span style="font-family: monospace, Menlo, Monaco, "Courier New", monospace; font-size: 14px; white-space: pre; background-color: rgb(255, 255, 254);" class="">print (</span><span style="font-family: monospace, Menlo, Monaco, "Courier New", monospace; font-size: 14px; white-space: pre; color: rgb(163, 21, 21);" class="">'\nAlphaFold generated an error computing %s, error logged to %s\n'</span><span style="font-family: monospace, Menlo, Monaco, "Courier New", monospace; font-size: 14px; white-space: pre; background-color: rgb(255, 255, 254);" class="">% (model_name, error_log_path))</span>”. The results printed exactly what this line says. </div><div class=""><br class=""></div><div class="">I am wondering whether it means the Multimer is not able to predict this complex structure? Is there any tutorial that I can find to change parameters in order to try to improve and get a structure?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Juntao</div><div class=""><br class=""></div><div class="">------------------------------------------</div><div class=""><b style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Juntao Yu | Ph.D. candidate</b><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Moazed Lab<br class="">Department of Cell Biology<br class="">Harvard Medical School</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Arial; font-size: 13px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">240 Longwood Avenue<br class="">Boston, MA 02115</div>
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