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<p>Hi,</p>
<p><br>
</p>
<p>Is it possible to visualize the NCS axis identified with phenix.autosol? Thanks.<br>
</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
<div id="Signature">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
<div style="color: rgb(33, 33, 33);">
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Pavel Afonine <pafonine@lbl.gov><br>
<b>Sent:</b> Monday, February 8, 2016 11:07 AM<br>
<b>To:</b> Reza Khayat; Oliver Clarke; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Refine pixel size of map (for EM data)?</font>
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<div>Hi Reza,<br>
<br>
geometry of refined model may be severely distorted if your target map on a wrong scale (magnification).<br>
<br>
Some relevant reading:<br>
<br>
1) <br>
Automatic estimation and correction of anisotropic magnification,distortion in electron microscopes,Timothy Grant, Nikolaus Grigorieff
<br>
Journal of Structural Biology 192 (2015) 204–208 <br>
<br>
2) <br>
Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase,
<br>
Jianhua Zhao, Samir Benlekbir & John L. Rubinstein <br>
Nature 521, 241–245 (14 May 2015) <br>
<br>
3) <br>
Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images.
<br>
Jianhua Zhao, Marcus A. Brubaker, Samir Benlekbir, John L. Rubinstein <br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 2/8/16 02:38, Reza Khayat wrote:<br>
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<p>Hi Oliver,<br>
</p>
<p><br>
</p>
<p>Out of curiosity:</p>
<p> 1. what kind of R-factors and CC-values do you get when refining against the two different pixel size? <br>
</p>
<p> 2. how different are your refined pixel sizes from one reconstruction to another?<br>
</p>
<p> ​3. how much of an affect does the wrong pixel size have on your downstream structure analysis (e.g. BDA, ASA, electrostatic...)? </p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
<br>
</p>
<div id="Signature">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
<div style="color:rgb(33,33,33)">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">
phenixbb-bounces@phenix-online.org</a> <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb-bounces@phenix-online.org">
<phenixbb-bounces@phenix-online.org></a> on behalf of Oliver Clarke <a class="moz-txt-link-rfc2396E" href="mailto:olibclarke@gmail.com">
<olibclarke@gmail.com></a><br>
<b>Sent:</b> Monday, February 8, 2016 4:28 AM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">
phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] Refine pixel size of map (for EM data)?</font>
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<div>
<div>Hello,<br>
<br>
</div>
I wonder whether it would be possible to add an option for phenix.real_space_refine to allow refinement of the pixel size of the map (or the unit cell dimensions - just an overall size scale factor), and write out the altered map at the end of refinement.<br>
<br>
Although we try to calibrate this as best as we are able at the time of data collection, it is never perfect - for example, in one case I have dealt with, our nominal pixel size out of the scope is 1.19 �, but the pixel size calibrated based on a crystal structure
of a fragment of the protein is 1.25 �. This is not a huge difference, but it is sufficient I think to have a substantial impact on refinement, particularly as regards clash assessment and H-bond/sec struc restraints.
<br>
<br>
In cases where one does not have a solved crystal structure to use for calibration, perhaps refining the pixel size in conjunction with the geometry might be of some use?<br>
<br>
</div>
<div>Cheers,<br>
</div>
<div>Oli<br>
</div>
</div>
</div>
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<br>
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