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<p>Dear all,</p>
<p><br>
</p>
<p>we have also seen very often these disagreeing measurements of
resolution depending on the mask being used. In our experience,
MonoRes tends to provide a number that is less biased than other
measures. To use MonoRes you need either two half maps (the
preferred option) or a map and a mask (outside this mask there
should be noise that is supposed to be of the same nature as the
noise inside the mask).</p>
<p><br>
</p>
<p>Kind regards, Carlos Oscar<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">El 14/06/2019 a las 11:09, Mohamed A
Sayed escribió:<br>
</div>
<blockquote type="cite" cite="mid:1560503382032.81832@kaust.edu.sa">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<style type="text/css" style="display:none"><!-- p { margin-top: 0px; margin-bottom: 0px; } @font-face { font-family: "Cambria Math"; } @font-face { font-family: Calibri; } p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; } a:link, span.MsoHyperlink { color: blue; text-decoration: underline; } a:visited, span.MsoHyperlinkFollowed { color: purple; text-decoration: underline; } p.msonormal0, li.msonormal0, div.msonormal0 { margin-right: 0in; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; } span.EmailStyle18 { font-family: Calibri, sans-serif; color: windowtext; } .MsoChpDefault { font-size: 10pt; } @page WordSection1 { margin: 1in; } div.WordSection1 { }--></style>
<p>Hello<br>
</p>
<p> Sorry just for clarification "<span style="color: rgb(33, 33,
33); font-family: Calibri, sans-serif; font-size: 14.6667px;
background-color: rgb(255, 255, 255);">get 0.x Ang lower
resolution compared to Resmap"</span>. I really meant that I
got two numbers for the same map. I realize that the map quality
itself did not change. Thank you<br>
</p>
<p>Best regards<br>
</p>
<p><br>
</p>
<div style="color: rgb(33, 33, 33);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
Collaborative Computational Project in Electron
cryo-Microscopy <a class="moz-txt-link-rfc2396E" href="mailto:CCPEM@JISCMAIL.AC.UK"><CCPEM@JISCMAIL.AC.UK></a> on behalf of
Egelman, Edward H (ehe2n) <a class="moz-txt-link-rfc2396E" href="mailto:egelman@VIRGINIA.EDU"><egelman@VIRGINIA.EDU></a><br>
<b>Sent:</b> Friday, June 14, 2019 1:44 AM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:CCPEM@JISCMAIL.AC.UK">CCPEM@JISCMAIL.AC.UK</a><br>
<b>Subject:</b> Re: [ccpem] Resolution estimation</font>
<div> </div>
</div>
<div>
<div class="WordSection1">
<p class="MsoNormal">Hi,</p>
<p class="MsoNormal"> I feel compelled to make a comment.
When people say that the map has improved (or worsened) by
0.x Å after doing something, do they ever actually look at
the map? Or even the FSC curve? Or are they simply looking
at the value where FSC=0.143? I think that the most
important thing is actually the appearance of the map, and
many experienced people have realized that many things can
be done to improve or degrade the FSC without changing the
overall appearance of the map.</p>
<p class="MsoNormal">Regards,</p>
<p class="MsoNormal">Ed</p>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black"> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black">Edward Egelman</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black">Harrison Distinguished Professor</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black">Department of Biochemistry and
Molecular Genetics</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black">University of Virginia</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black">phone: 434-924-8210</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black">fax: 434-924-5069</span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black"><a class="moz-txt-link-abbreviated" href="mailto:egelman@virginia.edu">egelman@virginia.edu</a></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;
color:black"><a
href="http://www.people.virginia.edu/~ehe2n"
moz-do-not-send="true">www.people.virginia.edu/~ehe2n</a></span></p>
<p class="MsoNormal"> </p>
<div style="border:none; border-top:solid #B5C4DF 1.0pt;
padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;
color:black">From: </span>
</b><span style="font-size:12.0pt; color:black">Collaborative
Computational Project in Electron cryo-Microscopy
<a class="moz-txt-link-rfc2396E" href="mailto:CCPEM@JISCMAIL.AC.UK"><CCPEM@JISCMAIL.AC.UK></a> on behalf of Takanori
Nakane <a class="moz-txt-link-rfc2396E" href="mailto:tnakane@MRC-LMB.CAM.AC.UK"><tnakane@MRC-LMB.CAM.AC.UK></a><br>
<b>Reply-To: </b>Takanori Nakane
<a class="moz-txt-link-rfc2396E" href="mailto:tnakane@MRC-LMB.CAM.AC.UK"><tnakane@MRC-LMB.CAM.AC.UK></a><br>
<b>Date: </b>Friday, June 14, 2019 at 6:32 AM<br>
<b>To: </b><a class="moz-txt-link-rfc2396E" href="mailto:CCPEM@JISCMAIL.AC.UK">"CCPEM@JISCMAIL.AC.UK"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:CCPEM@JISCMAIL.AC.UK"><CCPEM@JISCMAIL.AC.UK></a><br>
<b>Subject: </b>Re: [ccpem] Resolution estimation</span></p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Hi,</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">ResMap and RELION use different
algorithms to estimate local resolution.</p>
</div>
<div>
<p class="MsoNormal">They are not necessarily comparable.</p>
</div>
<div>
<p class="MsoNormal">(ResMap tends to be more optimistic
in my experience)</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">> Sorry is there any short anwer
for how to make the mask less tight.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Please apply low pass filtering at 15
A and add more soft</p>
</div>
<div>
<p class="MsoNormal">edges in MaskCreate.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Best regards,</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Takanori Nakane</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">On 2019/06/13 23:25, Mohamed A Sayed
wrote:</p>
</div>
<blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE"
style="border:none; border-left:solid #B5C4DF 4.5pt;
padding:0in 0in 0in 4.0pt; margin-left:3.75pt;
margin-right:0in">
<div>
<p class="MsoNormal">Hi Takanori,</p>
</div>
<div>
<p class="MsoNormal">Thank you for your help. This may
answer the FSC curve but even when I use Relion to
determine the local resolution on the unfiltered
refined 3D model I get 0.4 Ang lower resolution
compared to Resmap.</p>
</div>
<div>
<p class="MsoNormal">I used b-factor from post
processing and k2 correction curve.</p>
</div>
<div>
<p class="MsoNormal">Sorry is there any short anwer for
how to make the mask less tight. Thank you</p>
</div>
<div>
<p class="MsoNormal">________________________________________</p>
</div>
<div>
<p class="MsoNormal">From: Takanori Nakane <<a
href="mailto:tnakane@mrc-lmb.cam.ac.uk"
moz-do-not-send="true">tnakane@mrc-lmb.cam.ac.uk</a>></p>
</div>
<div>
<p class="MsoNormal">Sent: Thursday, June 13, 2019 9:44
PM</p>
</div>
<div>
<p class="MsoNormal">To: Mohamed A Sayed;</p>
</div>
<div>
<p class="MsoNormal">Subject: Re: [ccpem] Resolution
estimation</p>
</div>
<div>
<p class="MsoNormal">Hi,</p>
</div>
<div>
<p class="MsoNormal">Probably your mask is too tight
and/or sharp.</p>
</div>
<div>
<p class="MsoNormal">Please look at Note 4.16 of</p>
</div>
<div>
<p class="MsoNormal"><a
href="ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/multibody_protocol.pdf"
moz-do-not-send="true">ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/multibody_protocol.pdf</a>.</p>
</div>
<div>
<p class="MsoNormal">Best regards,</p>
</div>
<div>
<p class="MsoNormal">Takanori Nakane</p>
</div>
<div>
<p class="MsoNormal">On 2019/06/13 19:27, Mohamed A
Sayed wrote:</p>
</div>
<blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE"
style="border:none; border-left:solid #B5C4DF 4.5pt;
padding:0in 0in 0in 4.0pt; margin-left:3.75pt;
margin-right:0in">
<div>
<p class="MsoNormal">Hello,</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">I hope you would please advise on
the following:</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">When I apply post processing in
Relion on a refined 3D map, the FSC</p>
</div>
<div>
<p class="MsoNormal">curve gives 0.3 Angstrom worse
resolution than that before post processing.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">If I use Resmap v 1.95 to
estimate the resolution from the</p>
</div>
<div>
<p class="MsoNormal">unfiltered half maps of the
refined model, the resolution is 0.4 A</p>
</div>
<div>
<p class="MsoNormal">better than when I use the
resolution estimation from Relion on the same</p>
</div>
<div>
<p class="MsoNormal">unfiltered half map.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">- Which value to believe?</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">- How to calculate FSC without
post processing ?</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">- What caused the post processing
to give lower resolution and</p>
</div>
<div>
<p class="MsoNormal">resolution estimation to be
lower?</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Can you please point out for a
source on how to reliably fit a pdb into</p>
</div>
<div>
<p class="MsoNormal">an cryo map?</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Thank you very much for your help
and time.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">------------------------------------------------------------------------</p>
</div>
<div>
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</blockquote>
<div>
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<pre class="moz-signature" cols="72">--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano e-mail: <a class="moz-txt-link-abbreviated" href="mailto:coss@cnb.csic.es">coss@cnb.csic.es</a>
Biocomputing unit <a class="moz-txt-link-freetext" href="http://i2pc.es/coss">http://i2pc.es/coss</a>
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510
28049 MADRID (SPAIN) Fax: 34-91-585 4506
------------------------------------------------------------------------
</pre>
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