<div dir="ltr">Dear all,<div><br></div><div><span style="font-family:Helvetica,Arial,sans-serif">I have NaNs error in 3D variability in cryoSPARC . I am trying to repeat the 3D variability analysis based on the recent paper of Key Lewis “Probing cooperativity of N-terminal domain orientations in the p97 molecular machine: synergy between NMR and cryo-EM. Rui Huang, Zev A Ripstein, John L Rubinstein, and Lewis E.Kay 2020”  but I got this error: </span></div><div><span style="font-family:Helvetica,Arial,sans-serif">Traceback (most recent call last):</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif">File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif">File “cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.py”, line 533, in cryosparc2_compute.jobs.var3D.run.run</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif">File “cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.py”, line 445, in cryosparc2_compute.jobs.var3D.run.run.M_step</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif">File “/home/sepideh/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/linalg/linalg.py”, line 903, in eigvals</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif">_assertFinite(a)</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif">File “/home/sepideh/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/linalg/linalg.py”, line 217, in _assertFinite</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif">raise LinAlgError(“Array must not contain infs or NaNs”)</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif">LinAlgError: Array must not contain infs or NaNs</span>  </div><div><span style="font-family:Helvetica,Arial,sans-serif"> I checked the version of the cryoSPARC they used and I am using the same version. According to the paper, I made volume out of the PDB files, and then using a simulated data job I got the particle images and did the refinement. First I tried the 3D variability using the particles and mask from refinement and it seems fine but when I put a mask on N domain as it is described in the paper  I got the error.</span></div><div>I posted the error in cryoSPARC forum but I didn't receive any answer.</div><div>Could you please help me to solve the problem?<br style=""><span style="font-family:Helvetica,Arial,sans-serif"></span></div><div><br></div><div>Thank you in advance for your help,</div><div><span style="font-family:Helvetica,Arial,sans-serif">Sepideh</span>  <br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><p><b><span style="font-size:12pt;background:rgb(255,255,255)"><font color="#3d85c6">Sepideh Valimehr</font></span></b><span style="font-size:12.0pt;color:black"></span></p>

<p><b><span style="color:rgb(12,100,192);background-image:initial;background-position:initial;background-repeat:initial">Graduate Researcher </span></b><span style="color:rgb(12,100,192);background-image:initial;background-position:initial;background-repeat:initial">I</span><b><span style="color:rgb(12,100,192);background-image:initial;background-position:initial;background-repeat:initial">
Rouiller Lab</span></b></p>

<p><font color="#000000">Department of Biochemistry and Molecular
Biology</font></p><p><font color="#000000">Bio21 Molecular Science & Biotechnology
Institute </font></p><p class="MsoNormal"><span style="background-image:initial;background-position:initial;background-repeat:initial"><font color="#000000">The University of Melbourne</font></span><span style="color:rgb(12,100,192);background-image:initial;background-position:initial;background-repeat:initial"> </span></p>

<p class="MsoNormal"><b><span style="color:rgb(12,100,192);background-image:initial;background-position:initial;background-repeat:initial">T:</span></b><span style="color:rgb(12,100,192);background-image:initial;background-position:initial;background-repeat:initial"> </span><span style="background-image:initial;background-position:initial;background-repeat:initial"><font color="#000000">+61 3 83440285 |</font></span><span style="color:rgb(12,100,192);background-image:initial;background-position:initial;background-repeat:initial"> <b>E:</b> <a href="mailto:ashish.sethi@unimelb.edu.au" target="_blank">sepideh.valimehr@student.unimelb.edu.au</a>
</span><span style="font-size:12pt;color:rgb(0,111,201);background-image:initial;background-position:initial;background-repeat:initial"><br>
<span style="font-family:Calibri,Helvetica,sans-serif,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;font-size:16px;font-style:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);color:rgb(12,100,192)"></span>
<span style="font-size:12.0pt;color:black"></span></span></p><div dir="auto" style="font-size:12px;font-family:Helvetica,serif,EmojiFont"><div dir="auto"><div dir="auto"><div style="font-size:16px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;margin-top:0px;margin-bottom:0px"><i><i style="font-size:13.32px;font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"><span style="font-size:9pt"><font color="#666666">I acknowledge the Traditional Owners of the land on which I work, and pay my respects to the Elders, past and present.</font></span></i></i></div></div><span style="color:rgb(12,100,192)"></span></div></div></div></div></div></div>