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<p>Hi Reza,<br>
</p>
<p><br>
</p>
<p>It's a great idea to have a tool in Phenix to visualize NCS. We don't have one yet but I'll see what it would take to make one... We do have methods to identify symmetry axes from NCS operators that could be use in such a tool.<br>
</p>
<p><br>
</p>
<p>All the best,<br>
</p>
<p>Tom T<br>
</p>
<p><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Reza Khayat <rkhayat@ccny.cuny.edu><br>
<b>Sent:</b> Tuesday, July 26, 2016 8:17 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] Visualizing phenix.autosol NCS axis</font>
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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>
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<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>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>
</div>
<br>
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