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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Pavel,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks, it’s as I anticipated.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best wishes,<br>
Reza<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Reza Khayat, PhD</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Assistant Professor</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Department of Chemistry</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">City College of New York<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">85 Saint Nicholas Terrace, CDI 2.318</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">New York, NY 10031</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><a href="http://www.khayatlab.org/"><span style="color:#0563C1">http://www.khayatlab.org/</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">212-650-6070</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"> Pavel Afonine [mailto:pafonine@lbl.gov]
<br>
<b>Sent:</b> Monday, February 08, 2016 11:08 AM<br>
<b>To:</b> Reza Khayat <rkhayat@ccny.cuny.edu>; Oliver Clarke <olibclarke@gmail.com>; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Refine pixel size of map (for EM data)?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">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>
<o:p></o:p></p>
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<p class="MsoNormal">On 2/8/16 02:38, Reza Khayat wrote:<o:p></o:p></p>
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<p>Hi Oliver,<o:p></o:p></p>
<p><o:p> </o:p></p>
<p>Out of curiosity:<o:p></o:p></p>
<p> 1. what kind of R-factors and CC-values do you get when refining against the two different pixel size? <o:p></o:p></p>
<p> 2. how different are your refined pixel sizes from one reconstruction to another?<o:p></o:p></p>
<p> 3. how much of an affect does the wrong pixel size have on your downstream structure analysis (e.g. BDA, ASA, electrostatic...)? <o:p></o:p></p>
<p><o:p> </o:p></p>
<p style="margin-bottom:12.0pt">Best wishes,<br>
Reza<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif">Reza Khayat, PhD
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif">Assistant Professor <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif">City College of New York<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif">Department of Chemistry<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif">New York, NY 10031<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
<a href="mailto:phenixbb-bounces@phenix-online.org"><phenixbb-bounces@phenix-online.org></a> on behalf of Oliver Clarke
<a 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 href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] Refine pixel size of map (for EM data)?</span><span style="color:#212121">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#212121">Hello,<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#212121">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 Å, but the pixel size calibrated based on a crystal structure
of a fragment of the protein is 1.25 Å. 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?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#212121">Cheers,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#212121">Oli<o:p></o:p></span></p>
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<o:p></o:p></p>
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