SerialEM Macros

• Following macros can be added by cut-and-paste into SerialEM Macro Editor

Auto Collection of many tomograms

• Need to have mid-mag montage (1700x or higher) of area of interest
• best to do whole grid montage, mark points, do small polygon montage centered around each point
• add points to mid-mag montages, and mark as Acquire
• Filename for each point must be put in Navigator Note
• script will fail if it tries to overwrite pre-existing files
• Need to have already set up tiltSeries Autostart
• Autostart Policies also need to be checked -- in general, choose to fail and go on to next in case of problems
• Roll buffers should be M or lower (image stored in O should be at least 2 from last rolled buffer)

ReportNavItem   #get info from Navigator
RealignToNavitem
Eucentricity 6  #Fine eucentric and realign
# now do the tilt series:
WalkupTo 70 #may not need this
OpenNewFile $NavNote   #filename stored in Note
Tiltseries   #Need to have already set up all params!
CloseFile
TiltTo 0

Random Conical Tilt

• following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
• All images saved into a single stack

# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less
# Uses buffers N,O,P

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
R
S

Center Hole

• Following macro will center based on an image stored in the "N" buffer

# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
# Roll Buffers set to M or less
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S

Quantifoil Macro

# need to have an image of a hole in buffer N
# this image should be taken with half-area of View
# (otherwise may align with other holes)
# need to Roll Buffers A-M (or less) to preserve N
# need to have 2 files open for writing:
# file1 = Record images
# file 2 = View images
# after imaging, it burns the area. This helps verify that all areas are "virgin"


SetCameraArea 0 H #center half for View
V
ResetImageShift
V
AlignTo B
V
AlignTo N  #N should have saved hole
V
ResetImageShift
AlignTo B
G
G
V
AlignTo N
Delay 20
R
SwitchToFile 1
S
SetCameraArea 0 F
V
SwitchToFile 2
S
ScreenDown #burn after imaging 
Delay 20 #seconds
ScreenUp

• Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010