Last updated 10/29/2020
7
c.
Click “play” to collect atlas
13.
Insert and center objective aperture
a.
Go to square of non-interest
b.
Send scope to EN mag
c.
Lower flu screen and send scope to “DIFFRACTION” mode (right knobset)
i.
Should see bright green small beam on the flu screen with diffuse carbon
diffraction ring around it
ii.
D = 460 - 680 mm
d.
Insert objective aperture and center
e.
Exit “DIFFRACTION” mode
14.
Set up Ice Thickness
a.
Go to vacuum area
b.
Send scope to EN preset (make sure beam is centered)
c.
Simulate target in exposure node (~3000)
d.
Record the mean value and input into Ice_Thickness node (under ALS)
e.
ALS coefficient with 100 um objective aperture = 392
f.
ALS coefficient with 70 um objective aperture = 302
15.
Acquire total dose of the EN preset (target = 30 - 60 e
-
/A
2
)
16.
You are now ready to collect some images!
17.
In “Square_Targeting” select 1 square of interest
a.
Using “acquisition” mouse, select the center of square of interest
b.
Click “Submit target”
c.
Click “Submit queued targets”
18.
In “Hole_Targeting” select 1 - 2 regions of holes of interest
a.
Using “acquisition” mouse, select holes of interests (on the carbon, every 2x2 holes
away from each other)
b.
Using “focus” mouse, select area of carbon towards the center of the hole areas you
selected in the step above (this is where leginon will acquire the eucentric height of the
square)
c.
Click “Submit target”
d.
Click “Submit queued targets” when you are done with every hole target
19.
In “Exposure_Targeting” select exposure targets
a.
Using “acquisition” mouse, select the center of the holes of interests, on the ice. Select
up to 4 holes that are closest to the optical axis (use “toggle center crosshair” tool to find
where center is). This ensures that you do not collect images with a lot of image shift.
b.
Using “focus” mouse, select area of carbon towards the center of the stage (use “toggle
center crosshair” tool to find where center is). This is where leginon will acquire auto-
focusing for the exposure targets selected in the step above.
c.
Click “Submit target”
d.
Click “Submit queued targets”
20.
Under “Hole” node, select “toggle queue timeout” so that column valves will close once exposure
queue is done collecting
21.
To collect a new square, repeat steps 17 - 19 until you are done collecting data.
22.
Once you are done for the day, read
Summary of Contents for TF20
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