<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 class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thank you all for your suggestions!</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
We adjusted the speed of the insertion based on your feedback.</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Excited to have this working properly.</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
best regards</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Richard</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div id="Signature">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: Helvetica; font-size: 12px;">Richard M. Walsh , Ph.D.</span><br>
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: Helvetica; font-size: 12px;">Managing Director</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: Helvetica; font-size: 12px;">The Harvard Cryo-EM </span><br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: Helvetica; font-size: 12px;">Center for Structural Biology </span><br>
<br>
<span style="font-family: Helvetica; font-size: 12px;">Harvard Medical School</span><br>
<span style="font-family: Helvetica; font-size: 12px;">250 Longwood Avenue</span><br>
<span style="font-family: Helvetica; font-size: 12px;">SGM 102</span><br>
<span style="font-family: Helvetica; font-size: 12px;">Boston MA 02115</span><br>
<br>
<span style="font-family: Helvetica; font-size: 12px;">Phone: (617) 432-9042</span><br>
<span style="font-family: Helvetica; font-size: 12px;"><a href="mailto:Richard_Walsh@hms.harvard.edu" style="text-align: left;">Email:Richard_Walsh@hms.harvard.edu</a></span><br>
<span style="font-family: Helvetica; font-size: 12px;">Web: <a href="https://urldefense.com/v3/__http://cryoem.hms.harvard.edu/__;!!Mih3wA!AYCPdIUV47upLd9H591kORHY2zgoY7pCVXZPLXc7XWeeoEdcdMugmcUmkE8ZuReYEC8xDOCywiiZ_oWOLvtEqV4IAxhAUKDHcA$" style="text-align: left;">
cryoem.hms.harvard.edu</a></span><br>
</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 sebastiantacke@freenet.de <sebastiantacke@freenet.de><br>
<b>Sent:</b> Tuesday, January 23, 2024 3:35 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> Re: [3dem] Calling Teamtomo: our CERES ICE-Shield isn't working properly</font>
<div> </div>
</div>
<style>
<!--
@font-face
{font-family:Helvetica}
@font-face
{font-family:"Cambria Math"}
@font-face
{font-family:Calibri}
p.x_MsoNormal, li.x_MsoNormal, div.x_MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif}
a:link, span.x_MsoHyperlink
{color:blue;
text-decoration:underline}
p.x_xelementtoproof, li.x_xelementtoproof, div.x_xelementtoproof
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif}
span.x_E-MailFormatvorlage21
{font-family:"Calibri",sans-serif;
color:windowtext}
span.x_E-MailFormatvorlage22
{font-family:"Calibri",sans-serif;
color:windowtext}
.x_MsoChpDefault
{font-size:10.0pt}
@page WordSection1
{margin:72.0pt 72.0pt 72.0pt 72.0pt}
div.x_WordSection1
{}
ol
{margin-bottom:0cm}
ul
{margin-bottom:0cm}
-->
</style>
<div lang="EN-US" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="x_WordSection1">
<p class="x_MsoNormal">Hello everyone,</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">Unfortunately, I accidentally sent my reply only to Richard but I agree with Sabrina, Honkit and Mark.</p>
<p class="x_MsoNormal">Attached my answer:</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">---</p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D">Dear all, Dear Richard,</span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D"> </span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D">I would suggest to increase (or decrease) the speed of shutter insertion.
<br>
You can do this on your own by opening one of the valve at the shutter a bit more.</span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D">But be gentle and test with small increments since you don’t want your shutter to fly in with warp 9 ;-)</span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D">If this doesn’t help, I would decrease the speed of shutter insertion by turning the valve the other way round.
</span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D">There might be a small shift between the reference image and the following images but typically AutoTEM can correct for this.<br>
If you need a picture of the valve or if you have any further questions, just let me know!
</span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D">Have a nice Sunday.</span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D"> </span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D">Best wishes,</span></p>
<p class="x_MsoNormal"><span lang="EN-GB" style="color:#1F497D"> </span></p>
<p class="x_MsoNormal"><span style="color:#1F497D">Sebastian</span></p>
<p class="x_MsoNormal"><span style="color:black">---</span></p>
<p class="x_MsoNormal"><span style="color:black"> </span></p>
<p class="x_MsoNormal"><span style="color:black">Happy milling and have a nice week.</span></p>
<p class="x_MsoNormal"><span style="color:black"> </span></p>
<p class="x_MsoNormal"><span style="color:black">Best wishes,</span></p>
<p class="x_MsoNormal"><span style="color:black"> </span></p>
<p class="x_MsoNormal"><span lang="DE" style="color:black">Sebastian</span></p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal"> </p>
<div>
<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">
<p class="x_MsoNormal"><b><span lang="DE">Von:</span></b><span lang="DE"> 3dem <3dem-bounces@ncmir.ucsd.edu>
<b>Im Auftrag von </b>Mark Ebrahim<br>
<b>Gesendet:</b> Montag, 22. Januar 2024 19:40<br>
<b>An:</b> Walsh, Richard Michael <Richard_Walsh@hms.harvard.edu>; 3dem@ncmir.ucsd.edu<br>
<b>Cc:</b> Honkit Ng <hng@rockefeller.edu><br>
<b>Betreff:</b> Re: [3dem] Calling Teamtomo: our CERES ICE-Shield isn't working properly</span></p>
</div>
</div>
<p class="x_MsoNormal"> </p>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">Hi Richard,</span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">Honkit (my research support specialist and Aquilos guru) and I were discussing this in the morning. We watched your video which was very helpful and noticed the following:</span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">At about 7 seconds into the video the Z unlinks, this is what causes the ice shield to retract. When the stage is done moving, the Z re-links and about 18 seconds into the video the ice shield
starts reinserting. The ice shield isn't fully inserted until the 22 second mark. However, the image acquisition takes place at the 20 second mark. i.e. the first half of the image is taken while the shield is still out of the field of view and the second
half (just noise) is somewhere in the middle of insertion. </span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">A few ideas on how to solve this or work around it:</span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
</div>
<ol start="1" type="1">
<li class="x_MsoNormal" style="color:black; list-style-type:"1) ""><span style="font-size:12.0pt">The simplest workaround is to retake the image immediately after the shield is fully inserted. This should work and you can carry on until someone from either
company is able to solve the issue </span>permanently<span style="font-size:12.0pt">.</span></li><li class="x_MsoNormal" style="color:black; list-style-type:"2) ""><span style="font-size:12.0pt">We would try to increase the rate of insertion such that the shield is fully inserted before the reference image is taken. By the looks of the video, the insertion
needs to be about 3 seconds faster or the imaging could be delayed by 3-4 seconds.</span></li><div>
<li class="x_MsoNormal" style="color:black; list-style-type:"3) ""><span style="font-size:12.0pt">Prevent unlinking/retraction.
<span style="background:white">Our system also unlinks but I am not sure if others face the same issue.
</span>It may be argued this is done as a safety feature but we don't really see a significant risk here. As long as the stage is not moved up, there is no risk and this would not be required at this point in the workflow. It would make more sense to only retract
if a Z stage movement is called. Additionally, it would make more sense to just get a pole touch instead of retracting the shield at all. Honkit noted that if the shield happened to crash into the stage, you would get no touch alarm but if the stage moves
into the shield you would get a touch alarm i.e. you only get touch alarms when the stage is being called to move. So, it makes sense to us to just leave the shield inserted and get a touch alarm if the stage ever came into contact with the shield. </span></li></div>
</ol>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">Best,</span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">Honkit and Mark</span></p>
</div>
<div>
<p class="x_MsoNormal"> </p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
</div>
<div id="x_Signature">
<div class="x_MsoNormal" align="center" style="text-align:center">
<hr size="2" width="100%" align="center">
</div>
<div>
<p class="x_MsoNormal"><b><span style="font-size:12.0pt; color:black">Mark Ebrahim</span></b><span style="font-size:12.0pt; color:black">
</span></p>
</div>
<p><span style="font-size:12.0pt; color:black">Senior Staff Scientist</span></p>
<p><span style="font-size:12.0pt; color:black">Cryo Electron Microscopy Resource Center (CEMRC)</span></p>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">The Rockefeller University</span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">1230 York Avenue</span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black">New York, NY 10065</span></p>
</div>
</div>
<div class="x_MsoNormal" align="center" style="text-align:center">
<hr size="2" width="98%" align="center">
</div>
<div id="x_divRplyFwdMsg">
<p class="x_MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> 3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu">3dem-bounces@ncmir.ucsd.edu</a>> on behalf of Walsh, Richard Michael <<a href="mailto:Richard_Walsh@hms.harvard.edu">Richard_Walsh@hms.harvard.edu</a>><br>
<b>Sent:</b> Saturday, January 20, 2024 7:56 AM<br>
<b>To:</b> <a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a> <<a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>><br>
<b>Subject:</b> [3dem] Calling Teamtomo: our CERES ICE-Shield isn't working properly</span>
</p>
<div>
<p class="x_MsoNormal"> </p>
</div>
</div>
<div>
<div>
<div align="center">
<table class="x_MsoNormalTable" border="0" cellspacing="4" cellpadding="0" style="background:white">
<tbody>
<tr>
<td style="padding:.75pt .75pt .75pt .75pt">
<p class="x_MsoNormal" align="center" style="text-align:center"><b><span style="font-size:13.5pt; color:#AF1F0A">Caution: External email</span></b></p>
</td>
</tr>
</tbody>
</table>
</div>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:"Arial",sans-serif; color:#1D1C1D; background:#F8F8F8">We have heard of several sites using the CERES Ice-Shield on their Aquilos with no issues, but we have a reoccurring problem, during the
thinning stage and its effecting our lamella quality.</span></p>
</div>
<div>
<p class="x_MsoNormal"> </p>
</div>
<div>
<p class="x_MsoNormal"> </p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; font-family:"Arial",sans-serif; color:#1D1C1D; background:#F8F8F8">When using the CERES Ice-Shield in tandem with AutoTEM, we notice that each time the stage moves, the ice shield retracts and re-inserts,
and thus during the thinning stage of the AutoTEM automation, the shield blocks reference image collection, thus resulting in a misplaced pattern and inconsistent lamella quality.</span></p>
</div>
<div>
<p class="x_MsoNormal"> </p>
</div>
<p class="x_xelementtoproof"><span style="font-size:12.0pt; font-family:"Arial",sans-serif; color:black">Link to Video For Reference:
</span><span style="font-size:12.0pt; font-family:"Arial",sans-serif; color:#242424"><a href="https://urldefense.com/v3/__https:/drive.google.com/file/d/1dyQR57ZPr6SQv_AypQvH-uOSCqPkD9jp/view__;!!Mih3wA!E4y-pfw8EsMkATaLFu-CyxAq6fvhvv2ObUTsGRwM7Zuf9I7SZj3gejlAO1pKmek9JdeXQL0L8NxOyAI8Sr8M5sPNdEuM68CYxg$" target="_blank">https://drive.google.com/file/d/1dyQR57ZPr6SQv_AypQvH-uOSCqPkD9jp/view</a></span></p>
<p class="x_xelementtoproof"> </p>
<p class="x_xelementtoproof"><span style="font-size:12.0pt; font-family:"Arial",sans-serif">So far neither Delmic nor ThermoFisher have any idea how to resolve this problem.</span></p>
<p class="x_xelementtoproof"> </p>
<p class="x_xelementtoproof">Any ideas would be greatly appreciated.</p>
<p class="x_xelementtoproof"> </p>
<p class="x_xelementtoproof">best regards,</p>
<p class="x_xelementtoproof"> </p>
<p class="x_xelementtoproof">Richard</p>
<p style="background:white"><span style="color:#242424"> </span></p>
<div>
<p class="x_MsoNormal"><span style="font-size:12.0pt; color:black"> </span></p>
</div>
<div id="x_x_Signature">
<div>
<p class="x_MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">Richard M. Walsh , Ph.D.</span><span style="font-size:12.0pt; color:black"></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">Managing Director</span><span style="font-size:12.0pt; color:black"></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">The Harvard Cryo-EM </span><span style="font-size:12.0pt; color:black"></span></p>
</div>
<div>
<p class="x_MsoNormal"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">Center for Structural Biology </span><span style="font-size:12.0pt; color:black"><br>
<br>
</span><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">Harvard Medical School</span><span style="font-size:12.0pt; color:black"><br>
</span><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">250 Longwood Avenue</span><span style="font-size:12.0pt; color:black"><br>
</span><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">SGM 102</span><span style="font-size:12.0pt; color:black"><br>
</span><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">Boston MA 02115</span><span style="font-size:12.0pt; color:black"><br>
<br>
</span><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">Phone: (617) 432-9042</span><span style="font-size:12.0pt; color:black"><br>
</span><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black"><a href="mailto:Richard_Walsh@hms.harvard.edu">Email:Richard_Walsh@hms.harvard.edu</a></span><span style="font-size:12.0pt; color:black"><br>
</span><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif; color:black">Web:
<a href="https://urldefense.com/v3/__http:/cryoem.hms.harvard.edu/__;!!Mih3wA!E4y-pfw8EsMkATaLFu-CyxAq6fvhvv2ObUTsGRwM7Zuf9I7SZj3gejlAO1pKmek9JdeXQL0L8NxOyAI8Sr8M5sPNdEuMOhc5rw$">
cryoem.hms.harvard.edu</a></span><span style="font-size:12.0pt; color:black"></span></p>
</div>
</div>
</div>
</div>
</div>
</body>
</html>