11 LD

Example 11. LD


MacroName LD
# main macro for single particle data collection in Low Dose Mode
# update @ 2014-10-23 08:01:15

Echo ===> Running LD ...

Call Parameters

ResetClock

## position (X,Y)
RealignToNavItem 1
Copy A P
Call AlignToP

## Center Beam, assume AutoCenterBeam policy has been set up
AutoCenterBeam

## CycleTargetFocus, range is set in macro "Parameters".
Call CycleTargetFocus

## Autofocus, twice to be more accurate 
G
G

## Drift control
# drift control or not is set in Parameters 
# with skip set value, skip = 1 -> no drift control.
Loop 1
If $skip == 1
    continue 
Else
    Call Drift
Endif
EndLoop

# final shots, uncomment the next line for K2 camera
Loop 1
If $k2 == 1
    EarlyReturnNextShot $no_return
Else
    break
Endif
EndLoop

R

## save return image or not
Loop 1
if $save == 1
   S
Else 
   echo R image in SerialEM window is not saved ...
Endif
EndLoop

ReportClock
echo ----------------------------------------------------------------

This is the Main macro to run for single particle application. It usually runs from menu Navigator → Acquire at points... and as major action. Thus, all the navigator items with acquiring flag "A" will run this macro, one by one.

This macro should not be hard to understand. It does a few things as we normally do: go to a place, focus and take final image. The line


RealignToNavItem 1

is to get current nav item to the center position using Realign built-in routine, possibly with small mount of ImageShift left. The argument "1" means to return to the initial image state after the routine is done. In this case of being in Low Dose, this means to get out of Low Dose to do Realign and return to Low Dose again it finishes. We use our macro ZeroIS to clear out the ImageShift, as explained earlier.

We use use Autofocus twice here. This is because if it is little further away from target focus, only once might not get close enough. Two rounds are usually sufficient. And centering beam is needed to make sure beam stays centered all the time, because beam could wander away with time.

Needless to say here, all this is on the base that the Low Dose has been setup right.