<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">That model vs. map FSC does not look normal. You should be rather skeptical of this outcome.</div><div class=""><br class=""></div><div class="">Basil</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">Am 20.05.2021 um 19:33 schrieb Jay Rai <<a href="mailto:jrai@fsu.edu" class="">jrai@fsu.edu</a>>:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 14pt;" class="">Thank you for your suggestion.<br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 14pt;" class="">Yes, I did same. out of curiosity -i can still use chimeric maps for model refinement, right?</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 14pt;" class="">In my case, I use it for phenix real space refinement. Since, I need to provide the resolution, I provide the resolution from the largest maps. I found out that map to model resolution is somewhat acceptable (0.5). I have attached the map to model fsc too.<span class="Apple-converted-space"> </span><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 14pt;" class="">Thank you once again.<br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div style="font-family: "Times New Roman", Times, serif; font-size: 14pt;" class=""><br class=""></div><div id="Signature" class=""><div class=""><div class=""></div><div class=""></div><div class=""></div><div id="divtagdefaultwrapper" dir="ltr" style="background-color: rgb(255, 255, 255);" class=""><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-family: "Times New Roman", Times, serif; font-size: 14pt;" class="">With kind regards,</span><br class=""></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-family: "Times New Roman", Times, serif; font-size: 14pt;" class=""></span><span style="font-family: inherit; font-size: inherit; font-style: inherit; font-variant-ligatures: inherit; font-variant-caps: inherit;" class=""><span style="font-size: 14pt; font-family: "Times New Roman", Times, serif;" class="">Jay Ra</span><span style="font-size: 14pt; font-family: "Times New Roman", Times, serif;" class="">i</span><span style="font-size: 14pt; font-family: "Times New Roman", Times, serif;" class=""></span></span></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><br class=""></div><div style="margin: 0px 0in; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><font face="Times New Roman, Times, serif" class=""><span style="font-size: 10pt; font-family: "Courier New", monospace; color: rgb(81, 167, 249);" class="">Jay Rai, Ph.D.</span></font></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-family: inherit; font-size: inherit; font-style: inherit; font-variant-ligatures: inherit; font-variant-caps: inherit;" class=""><span style="font-size: 10pt; color: rgb(81, 167, 249); font-family: "Courier New", monospace;" class="">Assistant in Research</span></span></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-family: "Courier New", monospace; font-size: 10pt; color: rgb(81, 167, 249);" class="">Florida State Universit</span></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-family: "Courier New", monospace; font-size: 10pt; color: rgb(81, 167, 249);" class="">Institute Of Molecular Biophysics</span></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-family: "Courier New", monospace; font-size: 10pt; color: rgb(81, 167, 249);" class="">Email:<span class="Apple-converted-space"> </span><a href="mailto:jrai@fsu.edu" style="color: purple; text-decoration: underline;" class="">jrai@fsu.edu</a></span></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-family: "Courier New", monospace; font-size: 10pt; color: rgb(81, 167, 249);" class="">Twitter: @nepalijamesbond</span></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><br class=""></div><div style="margin: 0px 0in; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><br class=""></div></div></div></div></div><div id="appendonsend" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline-block; width: 899.625px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Frank, Joachim <<a href="mailto:jf2192@cumc.columbia.edu" style="color: purple; text-decoration: underline;" class="">jf2192@cumc.columbia.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, May 20, 2021 2:03 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Jay Rai <<a href="mailto:jrai@fsu.edu" style="color: purple; text-decoration: underline;" class="">jrai@fsu.edu</a>>;<span class="Apple-converted-space"> </span><a href="mailto:3dem@ncmir.ucsd.edu" style="color: purple; text-decoration: underline;" class="">3dem@ncmir.ucsd.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:3dem@ncmir.ucsd.edu" style="color: purple; text-decoration: underline;" class="">3dem@ncmir.ucsd.edu</a>>; 3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" style="color: purple; text-decoration: underline;" class="">3dem-bounces@ncmir.ucsd.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>RE: About over-estimation</font><div class=""> </div></div><div lang="EN-US" link="blue" vlink="purple" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div class="x_WordSection1"><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">After stitching there is no way to determine the resolution – you have introduced sharp boundaries that will lead to incorrect estimation of resolution. Why not simply report the resolutions of the individual maps that you have used to produce the chimeric structure?</span></div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></p><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">--Joachim</span></div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></p><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><b class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""><span class="Apple-converted-space"> </span>3dem [<a href="mailto:3dem-bounces@ncmir.ucsd.edu" style="color: purple; text-decoration: underline;" class="">mailto:3dem-bounces@ncmir.ucsd.edu</a>]<span class="Apple-converted-space"> </span><b class="">On Behalf Of<span class="Apple-converted-space"> </span></b>Jay Rai<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, May 20, 2021 1:59 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:3dem@ncmir.ucsd.edu" style="color: purple; text-decoration: underline;" class="">3dem@ncmir.ucsd.edu</a>; 3dem<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] [3dem] About over-estimation</span></div></div></div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;"> </p><div class=""><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;"><span style="font-size: 14pt;" class=""> </span></p></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Dear Cryo EM folks,</div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 14pt;" class="">I am just curious..</span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 14pt;" class="">I focus refine each subunit of maps seperately. Then I used chimera's vop maximum to stich the map.</span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 14pt;" class="">But when I refine that map to model, it is showing my resolution 2 angstrom.</span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 14pt;" class="">I even take the unfiltered map from each subunits and stich and so the relion_preprocess and again same resolution.</span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 14pt;" class="">I know it is because of the noise from each maps (which are outside the mask). I stick the maps from multi body refinement and it is ok so it must be the noise that makes the resolution higher.</span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 14pt;" class="">Is there any way to calculate the resolution? Or in other words, is there any way to create the composite map?</span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 14pt;" class="">Any help is greatly appreciated.</span></div></div><div class=""><div class=""><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;"><span style="font-size: 14pt;" class=""> </span></p></div><div id="x_x_Signature" class=""><div class=""><div id="x_x_divtagdefaultwrapper" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span style="font-size: 14pt;" class="">With kind regards,</span><span style="font-family: Calibri, sans-serif;" class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span style="font-size: 14pt;" class="">Jay Rai</span><span style="font-family: Calibri, sans-serif;" class=""></span></div><p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-family: Calibri, sans-serif;" class=""> </span></p><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white; background-position: initial initial; background-repeat: initial initial;"> </p><p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-family: Calibri, sans-serif;" class=""> </span></p><p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-family: Calibri, sans-serif;" class=""> </span></p></div></div></div></div></div></div></div></div><span id="cid:B1A009E9-25BF-4435-A543-534E92F906F3@Home"><model_map_fsc1.pdf></span><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">3dem mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:3dem@ncmir.ucsd.edu" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">3dem@ncmir.ucsd.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""></div></blockquote></div><br class=""></div></body></html>