SerialEM HowTo: Vary Defocus Value in Fly

Chen Xu

$BrandeisEM: ~emdoc-xml/en_US.ISO8859-1/articles/SerialEM-howto:change-target-defocus, 1 2013-02-11 02:31:56 xuchen Exp$

SerialEM is a powerful program for EM data collection. Although it is maybe originally designed for tomography data collection, it is equally powerful and flexible for single particle EM tasks.

One task that single particle user would like to do is to take images with slightly different defocus values, but within certain range. It would be better if this can be done without manually set for each image by user. In this document, I want to show you how to do this, automatically with SerialEM.

You can also get pdf version of this document here.

Table of Contents
1 The Task Description
2 Change Target Defocus using Macro

1 The Task Description

In single particle application, we take many images for the same sample. We wish to take them with defocus values in a certain range, but we like to have slightly different defocus values for CTF flattening purpose.

We can do it manually by setting to a different value to each shot. However, if we take images in automatic fashion, we would want to change the defocus value in fly.