SerialEM Note: Flexible Timer


Chen Xu








Note about the flexible timer available for scripting and an example how to use it.

Background information

In SerialEM scripting, there are a few commands with timer built in. For example, command LongOperation can take a few specific actions with timer defined. Here is one of the example:

LongOperation Da 3

This will perform dark reference for K2/K3 camera every 3 hours. This is very handy indeed. Another example is RefineZLP.

RefineZLP 30

This will perform refining ZLP every 30 minutes.

However, if we want to set a timer and to do a multiple and general actions when time is up, a more flexible timer is needed. In the case shown in picture below, which is Au-foil grid, we use multiple hole mechanism to collected images in these 4 holes using beam-image shift while the stage is centered at the middle of the 4 hole pattern. When the procedure is finished, the shift is reset and Record beam would be hitting on the black Au crystals.

Fig.1 4-hole black Au crystals


It is known that this kind of black crystal film is bad for refineZLP routine to work properly. It needs to use a hole area to make it work. As you can see, a simple timer built in for a specific function is not sufficient here. Two actions are needed: 1) move to one of the four holes and 2) perform RefineZLP. It requires a more flexible timer to do this.

Flexible Timer

A typical timer which could handle multiple actions would be like this:

If time is up
   do task1
   do task2

One of the script commands related to timer is SetCustomTime. Below is example code to perform two actions mentioned above.

### move to a hole and refineZLP every 30 minutes
ReportCustomTime ZLP
if $elapsed >= 30
    RefineZLP              # refine now
    SetCustomTime ZLP      # reset it