<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Hi Sepideh,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
It sounds like something might be going wrong in the translation of the mask from Chimera to cryoSPARC and perhaps a volume outside the bounds of the object is being masked (though I would have thought this would have thrown an error before cryosparc progressed
to eigenvalue analysis). Did you use the Chimera command "vop resample #1 onGrid #2", where #1 is your off-grid mask and #2 is your original structure, before exporting the mask from Chimera? See the section on mask creation in "<a href="https://urldefense.com/v3/__https://cryosparc.com/blog/local-refinement__;!!Mih3wA!XwnmZGTMtwfpIVuTP1U02xvQVT-7vUZVWTYZkETrV5s8PiL7mq8B-r0hFuEtvF3AdQ$" id="LPlnk">https://cryosparc.com/blog/local-refinement</a>".
As a check you can download the mask and input volume from the 3D variability job and input them into chimera before applying any translation or rotation to see if they line up as intended.<br>
</div>
<div class="_Entity _EType_OWALinkPreview _EId_OWALinkPreview _EReadonly_1">
<div id="LPBorder_GTaHR0cHM6Ly9jcnlvc3BhcmMuY29tL2Jsb2cvbG9jYWwtcmVmaW5lbWVudA.." class="LPBorder933462" style="width: 100%; margin-top: 16px; margin-bottom: 16px; position: relative; max-width: 800px; min-width: 424px;">
<table id="LPContainer933462" role="presentation" style="padding: 12px 36px 12px 12px; width: 100%; border-width: 1px; border-style: solid; border-color: rgb(200, 200, 200); border-radius: 2px;">
<tbody>
<tr style="border-spacing: 0px;" valign="top">
<td style="width: 100%;">
<div id="LPTitle933462" style="font-size: 21px; font-weight: 300; margin-right: 8px; font-family: "wf_segoe-ui_light", "Segoe UI Light", "Segoe WP Light", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; margin-bottom: 12px;">
<a target="_blank" id="LPUrlAnchor933462" href="https://urldefense.com/v3/__https://cryosparc.com/blog/local-refinement__;!!Mih3wA!XwnmZGTMtwfpIVuTP1U02xvQVT-7vUZVWTYZkETrV5s8PiL7mq8B-r0hFuEtvF3AdQ$" style="text-decoration: none; color:var(--themePrimary);">cryoSPARC | Leading Cryo-EM Software Solutions</a></div>
<div id="LPDescription933462" style="font-size: 14px; max-height: 100px; color: rgb(102, 102, 102); font-family: "wf_segoe-ui_normal", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; margin-bottom: 12px; margin-right: 8px; overflow: hidden;">
cryoSPARC | Leading Cryo-EM Software Solutions. Local Refinement Beta in cryoSPARC v2 September 17, 2018 Ali Haydaroglu. With cryoSPARC v2.2, we are rolling out a beta version of a new set of tools to refine your dynamic and flexible structures down to atomic
resolutions!For now, the Local Refinement toolkit includes Particle Subtraction and Local Refinement jobs that can be implemented in ...</div>
<div id="LPMetadata933462" style="font-size: 14px; font-weight: 400; color: rgb(166, 166, 166); font-family: "wf_segoe-ui_normal", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif;">
cryosparc.com</div>
</td>
</tr>
</tbody>
</table>
</div>
</div>
Cheers,<br>
<div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div id="Signature">
<div>
<div></div>
<div></div>
<div><b><span style="font-size:10.0pt; color:#002060" lang="EN-AU">Dr Hamish G Brown | Electron Cryo Microscopy Fellow</span></b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<p style="text-autospace:none"><span style="font-size:10.0pt; color:#002060" lang="EN-AU"><font size="2"><span style="font-size:10pt; font-family:calibri,arial,helvetica,sans-serif; color:rgb(0,32,96); background-color:rgba(0,0,0,0)">Advanced Microscopy Facility</span></font></span><span style="font-size:10pt; color:rgb(0,32,96); font-family:calibri,arial,helvetica,sans-serif; background-color:rgba(0,0,0,0)" lang="EN-AU">
| Bio2</span><span style="font-size:10pt; color:rgb(0,32,96); font-family:calibri,arial,helvetica,sans-serif; background-color:rgba(0,0,0,0)" lang="EN-AU">1 Molecular Science & Biotechnology Institute</span><span style="font-size:10.0pt; color:#002060" lang="EN-AU"></span></p>
<p style="text-autospace:none"><span style="font-size:10.0pt; color:#002060" lang="EN-AU">30 Flemington Road, Parkville Victoria 3052<br>
</span></p>
<p style="text-autospace:none"><span style="font-size:10.0pt; color:#002060" lang="EN-AU"><b>E:
</b></span><a href="mailto:hgbrown@unimelb.edu.au"><span style="font-family:calibri,arial,helvetica,sans-serif; font-size:10pt; color:rgb(0,32,96); background-color:rgba(0,0,0,0)">hgbrown@unimelb.edu.au</span></a><span style="font-size:10.0pt; color:#002060" lang="EN-AU"><b><br>
</b></span></p>
<p style="text-autospace:none"><span style="font-size:10.0pt; color:#002060" lang="EN-AU"><b>T:
</b>+61383440959</span><a href="mailto:hgbrown@unimelb.edu.au"><span style="font-family:calibri,arial,helvetica,sans-serif; font-size:10pt; color:rgb(0,32,96); background-color:rgba(0,0,0,0)"></span></a><br>
</p>
<div style="margin-top:16px; margin-bottom:16px"><span style="font-size:10.0pt; color:#002060" lang="EN-AU"></span></div>
<p style="text-autospace:none"><span style="font-size:10.0pt; color:#002060" lang="EN-AU">bio21.unimelb.edu.au | facebook.com/Bio21Institute | twitter.com/bio21institute</span></p>
<i><span style="font-size:10.0pt; color:#002060" lang="EN-AU">I acknowledge the Traditional Owners of the land on which I work, and pay my respects to the Elders, past and present.</span></i>
<p style="text-autospace:none"><b><i><span style="font-size:10.0pt; font-family:"Arial",sans-serif; color:black" lang="EN-AU"><img class="EmojiInsert" style="width:234.75px" data-outlook-trace="F:1|T:1" src="cid:59d4b2b2-879e-4baa-8d6a-7402e379b7a8"><br>
</span></i></b></p>
<p><b><i><span style="font-size:10.0pt; font-family:"Arial",sans-serif; color:black" lang="EN-AU"></span></i></b><span style="font-size:7.5pt; font-family:"Arial",sans-serif; color:#919191" lang="EN-AU">This email and any attachments may contain personal information
or information that is otherwise confidential or the subject of copyright. Any use, disclosure or copying of any part of it is prohibited. The University does not warrant that this email or any attachments are free from viruses or defects. Please check any
attachments for viruses and defects before opening them. If this email is received in error, please delete it and notify us by return email.</span><span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#919191" lang="EN-AU"></span></p>
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
</div>
</div>
</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Sepideh Valimehr <svalimehr@student.unimelb.edu.au><br>
<b>Sent:</b> 21 October 2020 09:33<br>
<b>To:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> [EXT] [3dem] NaNs error in 3D variability job in cryoSPARC</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div class="x_mc-ip-hide">
<div style="color:#000000; font-size:12px; text-align:left; font-family:Helvetica,Arial,sans-serif">
<strong>
<table border="1" cellspacing="0" cellpadding="5" style="width:100%; float:left; background-color:lemonchiffon">
<tbody>
<tr>
<td><b>UoM notice: </b>External email. Be cautious of links, attachments, or impersonation attempts</td>
</tr>
</tbody>
</table>
</strong><br>
</div>
<hr>
</div>
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="x_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="x_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="x_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>
</div>
</body>
</html>