[phenixbb] Refine pixel size of map (for EM data)?

Reza Khayat rkhayat at ccny.cuny.edu
Mon Feb 8 08:14:03 PST 2016

Hi Pavel,

Thanks, it’s as I anticipated.

Best wishes,

Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace, CDI 2.318
New York, NY 10031

From: Pavel Afonine [mailto:pafonine at lbl.gov]
Sent: Monday, February 08, 2016 11:08 AM
To: Reza Khayat <rkhayat at ccny.cuny.edu>; Oliver Clarke <olibclarke at gmail.com>; phenixbb at phenix-online.org
Subject: Re: [phenixbb] Refine pixel size of map (for EM data)?

Hi Reza,

geometry of refined model may be severely distorted if your target map on a wrong scale (magnification).

Some relevant reading:

Automatic estimation and correction of anisotropic magnification,distortion in electron microscopes,Timothy Grant, Nikolaus Grigorieff
Journal of Structural Biology 192 (2015) 204–208

Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase,
Jianhua Zhao, Samir Benlekbir & John L. Rubinstein
Nature 521, 241–245 (14 May 2015)

Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images.
Jianhua Zhao, Marcus A. Brubaker, Samir Benlekbir, John L. Rubinstein


On 2/8/16 02:38, Reza Khayat wrote:

Hi Oliver,

Out of curiosity:

    1. what kind of R-factors and CC-values do you get when refining against the two different pixel size?

    2. how different are your refined pixel sizes from one reconstruction to another?

    ​3. how much of an affect does the wrong pixel size have on your downstream structure analysis (e.g. BDA, ASA, electrostatic...)?

Best wishes,
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
From: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> <phenixbb-bounces at phenix-online.org><mailto:phenixbb-bounces at phenix-online.org> on behalf of Oliver Clarke <olibclarke at gmail.com><mailto:olibclarke at gmail.com>
Sent: Monday, February 8, 2016 4:28 AM
To: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Subject: [phenixbb] Refine pixel size of map (for EM data)?

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.

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.

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?


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