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I was NOT suggesting to run an FSC between one of the constituent maps and its counterpart in the model. I was suggesting to simply report the resolutions of the constituent maps and be done with it. J<span id="ms-outlook-android-cursor"></span><br>
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<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 Basil Greber <basilgreber@gmx.net><br>
<b>Sent:</b> Friday, May 21, 2021 5:12:26 AM<br>
<b>To:</b> Jay Rai <jrai@fsu.edu><br>
<b>Cc:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> [EXTERNAL] Re: [3dem] About over-estimation</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi,
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<div class="">That model vs. map FSC does not look normal. You should be rather skeptical of this outcome.</div>
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<div class="">Basil</div>
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<div class="">Am 20.05.2021 um 19:33 schrieb Jay Rai <<a href="mailto:jrai@fsu.edu" class="">jrai@fsu.edu</a>>:</div>
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Thank you for your suggestion.<br class="">
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Yes, I did same. out of curiosity -i can still use chimeric maps for model refinement, right?</div>
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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="x_Apple-converted-space"> </span><br class="">
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Thank you once again.<br class="">
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<span class="" style="font-family:"Times New Roman",Times,serif; font-size:14pt">With kind regards,</span><br class="">
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<span class="" style="font-family:"Courier New",monospace; font-size:10pt; color:rgb(81,167,249)">Email:<span class="x_Apple-converted-space"> </span><a href="mailto:jrai@fsu.edu" class="" style="color:purple; text-decoration:underline">jrai@fsu.edu</a></span></div>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Frank, Joachim <<a href="mailto:jf2192@cumc.columbia.edu" class="" style="color:purple; text-decoration:underline">jf2192@cumc.columbia.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Thursday, May 20, 2021 2:03 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Jay Rai <<a href="mailto:jrai@fsu.edu" class="" style="color:purple; text-decoration:underline">jrai@fsu.edu</a>>;<span class="x_Apple-converted-space"> </span><a href="mailto:3dem@ncmir.ucsd.edu" class="" style="color:purple; text-decoration:underline">3dem@ncmir.ucsd.edu</a><span class="x_Apple-converted-space"> </span><<a href="mailto:3dem@ncmir.ucsd.edu" class="" style="color:purple; text-decoration:underline">3dem@ncmir.ucsd.edu</a>>;
3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" class="" style="color:purple; text-decoration:underline">3dem-bounces@ncmir.ucsd.edu</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>RE: About over-estimation</font>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">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>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">--Joachim</span></div>
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<b class=""><span class="" style="font-size:10pt; font-family:Tahoma,sans-serif">From:</span></b><span class="" style="font-size:10pt; font-family:Tahoma,sans-serif"><span class="x_Apple-converted-space"> </span>3dem [<a href="mailto:3dem-bounces@ncmir.ucsd.edu" class="" style="color:purple; text-decoration:underline">mailto:3dem-bounces@ncmir.ucsd.edu</a>]<span class="x_Apple-converted-space"> </span><b class="">On
Behalf Of<span class="x_Apple-converted-space"> </span></b>Jay Rai<br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Thursday, May 20, 2021 1:59 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span><a href="mailto:3dem@ncmir.ucsd.edu" class="" style="color:purple; text-decoration:underline">3dem@ncmir.ucsd.edu</a>; 3dem<br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>[EXTERNAL] [3dem] About over-estimation</span></div>
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Dear Cryo EM folks,</div>
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<span class="" style="font-size:14pt">I am just curious..</span></div>
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<span class="" style="font-size:14pt">I focus refine each subunit of maps seperately. Then I used chimera's vop maximum to stich the map.</span></div>
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<span class="" style="font-size:14pt">But when I refine that map to model, it is showing my resolution 2 angstrom.</span></div>
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<span class="" style="font-size:14pt">I even take the unfiltered map from each subunits and stich and so the relion_preprocess and again same resolution.</span></div>
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<span class="" style="font-size:14pt">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>
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<span class="" style="font-size:14pt">Is there any way to calculate the resolution? Or in other words, is there any way to create the composite map?</span></div>
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<span class="" style="font-size:14pt">Any help is greatly appreciated.</span></div>
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<span class="" style="font-size:14pt">With kind regards,</span><span class="" style="font-family:Calibri,sans-serif"></span></div>
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<span class="" style="font-size:14pt">Jay Rai</span><span class="" style="font-family:Calibri,sans-serif"></span></div>
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<span id="x_cid:B1A009E9-25BF-4435-A543-534E92F906F3@Home"><model_map_fsc1.pdf></span><span class="" style="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; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="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; text-decoration:none">
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