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

Pavel Afonine pafonine at lbl.gov
Mon Feb 8 08:07:33 PST 2016

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 
Journal of Structural Biology 192 (2015) 204–208

Electron cryomicroscopy observation of rotational states in a eukaryotic 
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
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
> ------------------------------------------------------------------------
> *From:* phenixbb-bounces at phenix-online.org 
> <phenixbb-bounces at phenix-online.org> on behalf of Oliver Clarke 
> <olibclarke at gmail.com>
> *Sent:* Monday, February 8, 2016 4:28 AM
> *To:* phenixbb at phenix-online.org
> *Subject:* [phenixbb] Refine pixel size of map (for EM data)?
> Hello,
> 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?
> Cheers,
> Oli
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