<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 Ibrahim,<div class=""><br class=""></div><div class=""> ChimeraX AlphaFold prediction should be back to working now. Thanks for reporting the problem.<br class=""><div class=""><br class=""></div><div class=""> The DeepMind developers released a new AlphaFold version 2.1.0 at GitHub on November 2 which broke the ChimeraX capability to predict AlphaFold structures. ChimeraX was using the most recent AlphaFold code but I have changed it now to use the specific AlphaFold version 2.0.1 which is the previous working version. You do not need a new ChimeraX (this configuration change was to the ChimeraX AlphaFold Python code which is loaded from the web each time it is run).</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 4, 2021, at 1:07 PM, Moustafa, Ibrahim M. 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=""><meta charset="UTF-8" class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Dear all,</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> I am trying to use alpha fold in ChimeraX but I get the following error during computing multiple sequence alignmenet step:</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">--------------------------------------------------------</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> <span style="caret-color: rgb(0, 0, 0); color: var(--ansi-red); font-weight: 400; font-family: monospace; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class="">TypeError</span><span style="font-weight: 400; color: rgb(33, 33, 33); font-family: monospace; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class=""> </span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><div class="error-expander" style="font-weight: 400; align-items: center; cursor: pointer; display: flex; color: rgb(33, 33, 33); font-family: Roboto, Noto, sans-serif; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><hr style="border-top: 1px solid var(--colab-bold-border-color); flex-grow: 1; height: 1px; margin: 0px 10px; max-width: 240px;" class=""><span class=""><span class=""></span></span><span class="summary" style="font-weight: normal !important;">2 frames</span><hr style="border-top: 1px solid var(--colab-bold-border-color); flex-grow: 1; height: 1px; margin: 0px 10px;" class=""></div><pre style="font-weight: 400; margin-bottom: 0px; margin-top: 0px; display: inline; color: rgb(33, 33, 33); font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class=""><a href="https://localhost:8080/#" data-href="<ipython-input-1-a242dc837c9a>" style="color: var(--colab-anchor-color);" class=""><ipython-input-1-a242dc837c9a></a><span style="font-weight: normal !important;" class=""> in </span><span style="color: var(--ansi-cyan); font-weight: normal !important;" class="">multiple_seq_align</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">(dbs)</span><span style="font-weight: normal !important;" class="">
</span><span style="font-weight: bold; color: var(--ansi-green);" class=""> 247</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-green); font-weight: normal !important;" class="">for</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">i</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">,</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">result</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-green); font-weight: normal !important;" class="">in</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">enumerate</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">(</span><span style="font-weight: normal !important;" class="">db_results</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">)</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">:</span><span style="font-weight: normal !important;" class="">
</span><span style="font-weight: bold; color: var(--ansi-green);" class=""> 248</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-green); font-weight: normal !important;" class="">from</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">alphafold</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">.</span><span style="font-weight: normal !important;" class="">data</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-green); font-weight: normal !important;" class="">import</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">parsers</span><span style="font-weight: normal !important;" class="">
</span><span style="color: var(--ansi-green); font-weight: normal !important;" class="">--> 249</span><span style="color: var(--ansi-red); font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">msa</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">,</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">deletion_matrix</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">,</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">target_names</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">=</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">parsers</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">.</span><span style="font-weight: normal !important;" class="">parse_stockholm</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">(</span><span style="font-weight: normal !important;" class="">result</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">[</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">'sto'</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">]</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">)</span><span style="font-weight: normal !important;" class="">
</span><span style="font-weight: bold; color: var(--ansi-green);" class=""> 250</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">e_values_dict</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">=</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">parsers</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">.</span><span style="font-weight: normal !important;" class="">parse_e_values_from_tblout</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">(</span><span style="font-weight: normal !important;" class="">result</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">[</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">'tbl'</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">]</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">)</span><span style="font-weight: normal !important;" class="">
</span><span style="font-weight: bold; color: var(--ansi-green);" class=""> 251</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">e_values</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">=</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">[</span><span style="font-weight: normal !important;" class="">e_values_dict</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">[</span><span style="font-weight: normal !important;" class="">t</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">.</span><span style="font-weight: normal !important;" class="">split</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">(</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">'/'</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">)</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">[</span><span style="color: var(--ansi-cyan); font-weight: normal !important;" class="">0</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">]</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">]</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-green); font-weight: normal !important;" class="">for</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">t</span><span style="font-weight: normal !important;" class=""> </span><span style="color: var(--ansi-green); font-weight: normal !important;" class="">in</span><span style="font-weight: normal !important;" class=""> </span><span style="font-weight: normal !important;" class="">target_names</span><span style="color: var(--ansi-blue); font-weight: normal !important;" class="">]</span><span style="font-weight: normal !important;" class="">
</span>
</pre><pre style="font-weight: 400; margin-bottom: 0px; margin-top: 0px; display: inline; color: rgb(33, 33, 33); font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class=""><span style="color: var(--ansi-red); font-weight: normal !important;" class="">TypeError</span><span style="font-weight: normal !important;" class="">: cannot unpack non-iterable Msa object</span></pre><span class="Apple-converted-space"> </span> </div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">---------------------------------------------------------</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> I followed the instructions of ChimeraX tutorial. <span style="caret-color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;" class="">I was able to use it successfully before, but not sure why I keep getting this error.</span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="caret-color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;" class=""><span class="Apple-converted-space"><br class=""></span></span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="caret-color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;" class=""><span class="Apple-converted-space"> Any idea what could be wrong?</span></span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="caret-color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;" class=""><span class="Apple-converted-space"><br class=""></span></span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="caret-color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;" class=""><span class="Apple-converted-space">I use ChimeraX version 1.3 (09-08-2021)</span></span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="caret-color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;" class=""><span class="Apple-converted-space"><br class=""></span></span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="caret-color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;" class=""><span class="Apple-converted-space"> Thanks for help</span></span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="caret-color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;" class=""><span class="Apple-converted-space"> Ibrahim</span></span></div><div id="Signature" class=""><div class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><div style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small; text-align: start; background-color: rgb(255, 255, 255);" class=""><br class=""></div></div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; 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;" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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="">Manage subscription:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; 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;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></div></body></html>