See bug
18dd6d0a-3c45-4aba-80da-
fa32ffaaf5db for example banded data.
(plot deflection without lines to see why I call it "banded"). Reducing
the stepsize reduces the jolt on the cantilever, and reducing the
points-per-step accordingly means we don't have to change the
card-clock rate. It might be worth adding "target-clock-rate" option,
and letting the stepsize be determined automatically (as an
alternative to setting the stepsize explicitly) but we'll
put that off for now...
--- /dev/null
+For some pulling speeds and step sizes, the deflection jumps around
+after each piezo step. This is obviously not something we want
+happening during our purportedly smooth unfolding.
+
+I've attached raw ADC data from a pull showing this effect in the next
+comment. View (e.g. with gnuplot) by
+
+ $ be show --only-raw-body 18dd6d0a-3c45-4aba-80da-fa32ffaaf5db:2 > data
+ $ echo "plot 'data' using 1, 'data' using 2 with linespoints axis x1y2" | gnuplot -persist
+
+The parameters for that particular pull (20090523132533_unfold) are:
+ Environment
+ Time: 20090523132533
+
+ Piezo parameters
+ Z piezo sensitivity (nm/Vp): 6.79
+ Z piezo gain (Vp/Vo): 20
+ X piezo sensitivity (nm/Vp): 34.0
+ X piezo gain (Vp/Vo): 20
+ X piezo position (nm): 134.57846952
+
+ Approach parameters
+ Setpoint (V): 0.777676050965
+ Bind pos (nm): -159
+
+ Binding parameters
+ Bind time (s): 3
+
+ Unfolding parameters
+ Distance (nm): 800
+ Step size (nm): 0.5
+ Points per step: 10
+ Unfold rate (nm/s): 718.762732761
+ Sample rate (Hz): 14375.2546552
+
+ Data fields: Z_piezo_out Deflection_in Z_piezo_in
+
+I thought I'd avoided this before by setting the default
+points-per-step to 1, but I must have overwritten unfold.py with
+another version. This is why version control systems are good ;).
+
--- /dev/null
+Content-type: text/plain
+
+
+Date: Mon, 06 Jul 2009 20:16:45 +0000
+
+
+From: W. Trevor King <wking@drexel.edu>
+
--- /dev/null
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--- /dev/null
+Content-type: text/plain
+
+
+Date: Mon, 06 Jul 2009 20:19:40 +0000
+
+
+From: W. Trevor King <wking@drexel.edu>
+
+
+In-reply-to: 3447dbc0-2357-4510-805e-3e843f9c31da
+
--- /dev/null
+creator: W. Trevor King <wking@drexel.edu>
+
+
+reporter: W. Trevor King <wking@drexel.edu>
+
+
+severity: minor
+
+
+status: closed
+
+
+summary: Banded deflection in unfolded regime
+
+
+time: Mon, 06 Jul 2009 19:17:27 +0000
+
else: self.T = None
self.log = unfold_data_log(dataDirectory, log_name="unfold")
def unfold(self, setpoint=None, rel_setpoint=1.0, sBindTime = 10.0,
- nmDist=600, nmStep=0.5, ppStep=10, nmPsRate=1000,
+ nmDist=600, nmStep=0.05, ppStep=1, nmPsRate=1000,
dataDirectory=LOG_DIR, fileID=None) :
while True :
try :
projects / unfold-protein.git / commitdiff