[3dem] [ccpem] on increasing EM map resolution by modifying the b-factor level

[De Carlo, Sacha]

Hi Marin,

maybe a paper along the explanations would help to illustrate the situation, especially for "visual" people like me :)
I found one for X-ray crystallography, and here is a link for cryo-EM:
http://www.sciencedirect.com/science/article/pii/S1047847708001445


Cheers,

Sacha De Carlo, PhD | Applications Manager

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From: 3dem [3dem-bounces at ncmir.ucsd.edu] on behalf of Marin van Heel [marin.vanheel at googlemail.com]
Sent: Sunday, May 24, 2015 10:31 AM
To: Smith Liu; CCPEM at JISCMAIL.AC.UK; 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] [ccpem] on increasing EM map resolution by modifying the b-factor level


Dear Smith Liu

Solving a 3D reconstruction problem is an optimization problem over a relevant resolution range ('RRR' :) ): finding the best possible 3D reconstruction, given a set of noisy molecular images. The very low frequency information in the cryo-EM images are not relevant to the 3D structure and can be removed by a high-pass filter. Similarly, the very high frequency information may be associated with noise only and may interfere with the structure determination; this can be suppressed by a low-pass filter. One can thus concentrate the analysis on the RRR by band-pass filtering the input data.  However, even within the RRR, the power distribution associated with the structural information we are after is not distributed homogeneously. Typically the low-frequency side of the structural information is over-represented compared to the high-frequency side of things due to all kinds of experimental reasons. This effect is described by an ad-hoc Gaussian low-pass filter called "the B-factor". Compensating for an estimated B-factor implies boosting the high frequency data components with respect to the low-frequency data components within the RRR. In any refinement/optimization of the structure, after this inverse B-factor filter, the relative influence of the high frequency components increases, which, in turn, results in a 3D reconstruction solution that is more focused on the fine structural details.

How to make use of this knowledge? That depends on the software being used and above all on the level of understanding that the user has over what is going on in the processing.

Hope this helps,

Marin van Heel


On 24/05/2015 07:15, Smith Liu wrote:
Dear All,

It was said the resolution of the EM map can be improved by modifying the b-factor level. Will you please tell me the reason behind it and how to process it?

Smith





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