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Thank you Tom, I am trying it right now and it seems working!</div>
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Ibrahim</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Thursday, November 4, 2021 6:14 PM<br>
<b>To:</b> Moustafa, Ibrahim M. <ria2@psu.edu><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] alpha-fold error</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Ibrahim,
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<div class=""> ChimeraX AlphaFold prediction should be back to working now. Thanks for reporting the problem.<br class="">
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<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>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<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>
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Dear all,</div>
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I am trying to use alpha fold in ChimeraX but I get the following error during computing multiple sequence alignmenet step:</div>
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<span class="" style="font-weight:400; font-family:monospace; font-size:14px; orphans:2; widows:2; background-color:rgb(255,255,255)">TypeError</span><span class="" 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)"> </span></div>
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<span class=""><span class=""></span></span><span class="x_summary" style="font-weight:normal!important">2 frames</span>
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<pre class="" 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)"><a href="https://localhost:8080/#" class="" style=""><ipython-input-1-a242dc837c9a></a><span class="" style="font-weight:normal!important"> in </span><span class="" style="font-weight:normal!important">multiple_seq_align</span><span class="" style="font-weight:normal!important">(dbs)</span><span class="" style="font-weight:normal!important">
</span><span class="" style="font-weight:bold"> 247</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">for</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">i</span><span class="" style="font-weight:normal!important">,</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">result</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">in</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">enumerate</span><span class="" style="font-weight:normal!important">(</span><span class="" style="font-weight:normal!important">db_results</span><span class="" style="font-weight:normal!important">)</span><span class="" style="font-weight:normal!important">:</span><span class="" style="font-weight:normal!important">
</span><span class="" style="font-weight:bold"> 248</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">from</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">alphafold</span><span class="" style="font-weight:normal!important">.</span><span class="" style="font-weight:normal!important">data</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">import</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">parsers</span><span class="" style="font-weight:normal!important">
</span><span class="" style="font-weight:normal!important">--> 249</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">msa</span><span class="" style="font-weight:normal!important">,</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">deletion_matrix</span><span class="" style="font-weight:normal!important">,</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">target_names</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">=</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">parsers</span><span class="" style="font-weight:normal!important">.</span><span class="" style="font-weight:normal!important">parse_stockholm</span><span class="" style="font-weight:normal!important">(</span><span class="" style="font-weight:normal!important">result</span><span class="" style="font-weight:normal!important">[</span><span class="" style="font-weight:normal!important">'sto'</span><span class="" style="font-weight:normal!important">]</span><span class="" style="font-weight:normal!important">)</span><span class="" style="font-weight:normal!important">
</span><span class="" style="font-weight:bold"> 250</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">e_values_dict</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">=</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">parsers</span><span class="" style="font-weight:normal!important">.</span><span class="" style="font-weight:normal!important">parse_e_values_from_tblout</span><span class="" style="font-weight:normal!important">(</span><span class="" style="font-weight:normal!important">result</span><span class="" style="font-weight:normal!important">[</span><span class="" style="font-weight:normal!important">'tbl'</span><span class="" style="font-weight:normal!important">]</span><span class="" style="font-weight:normal!important">)</span><span class="" style="font-weight:normal!important">
</span><span class="" style="font-weight:bold"> 251</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">e_values</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">=</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">[</span><span class="" style="font-weight:normal!important">e_values_dict</span><span class="" style="font-weight:normal!important">[</span><span class="" style="font-weight:normal!important">t</span><span class="" style="font-weight:normal!important">.</span><span class="" style="font-weight:normal!important">split</span><span class="" style="font-weight:normal!important">(</span><span class="" style="font-weight:normal!important">'/'</span><span class="" style="font-weight:normal!important">)</span><span class="" style="font-weight:normal!important">[</span><span class="" style="font-weight:normal!important">0</span><span class="" style="font-weight:normal!important">]</span><span class="" style="font-weight:normal!important">]</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">for</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">t</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">in</span><span class="" style="font-weight:normal!important"> </span><span class="" style="font-weight:normal!important">target_names</span><span class="" style="font-weight:normal!important">]</span><span class="" style="font-weight:normal!important">
</span>
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<pre class="" 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)"><span class="" style="font-weight:normal!important">TypeError</span><span class="" style="font-weight:normal!important">: cannot unpack non-iterable Msa object</span></pre>
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<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
I followed the instructions of ChimeraX tutorial. <span class="" style="background-color:rgb(255,255,255); display:inline!important">I was able to use it successfully before, but not sure why I keep getting this error.</span></div>
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<span class="" style="background-color:rgb(255,255,255); display:inline!important"><span class="x_Apple-converted-space"> Any idea what could be wrong?</span></span></div>
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<span class="" style="background-color:rgb(255,255,255); display:inline!important"><span class="x_Apple-converted-space">I use ChimeraX version 1.3 (09-08-2021)</span></span></div>
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<span class="" style="background-color:rgb(255,255,255); display:inline!important"><span class="x_Apple-converted-space"> Thanks for help</span></span></div>
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<span class="" style="background-color:rgb(255,255,255); display:inline!important"><span class="x_Apple-converted-space"> Ibrahim</span></span></div>
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