From: W. Trevor King <wking@drexel.edu>
Date: Mon, 6 Jul 2009 20:23:26 +0000 (-0400)
Subject: Avoid banded non-contact region by reducing default stepsize.
X-Git-Tag: v0.2~28
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=a0866d61816d73459ba43904f44f3547a9665af1;p=unfold-protein.git

Avoid banded non-contact region by reducing default stepsize.

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...
---

diff --git a/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/3447dbc0-2357-4510-805e-3e843f9c31da/body b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/3447dbc0-2357-4510-805e-3e843f9c31da/body
new file mode 100644
index 0000000..bc0f514
--- /dev/null
+++ b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/3447dbc0-2357-4510-805e-3e843f9c31da/body
@@ -0,0 +1,41 @@
+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 ;).
+
diff --git a/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/3447dbc0-2357-4510-805e-3e843f9c31da/values b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/3447dbc0-2357-4510-805e-3e843f9c31da/values
new file mode 100644
index 0000000..2315bfe
--- /dev/null
+++ b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/3447dbc0-2357-4510-805e-3e843f9c31da/values
@@ -0,0 +1,8 @@
+Content-type: text/plain
+
+
+Date: Mon, 06 Jul 2009 20:16:45 +0000
+
+
+From: W. Trevor King <wking@drexel.edu>
+
diff --git a/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/a00ae6c4-0c0a-49ee-9026-c294f830ace4/body b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/a00ae6c4-0c0a-49ee-9026-c294f830ace4/body
new file mode 100644
index 0000000..4874df8
--- /dev/null
+++ b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/a00ae6c4-0c0a-49ee-9026-c294f830ace4/body
@@ -0,0 +1,600 @@
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diff --git a/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/a00ae6c4-0c0a-49ee-9026-c294f830ace4/values b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/a00ae6c4-0c0a-49ee-9026-c294f830ace4/values
new file mode 100644
index 0000000..cc2cbeb
--- /dev/null
+++ b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/comments/a00ae6c4-0c0a-49ee-9026-c294f830ace4/values
@@ -0,0 +1,11 @@
+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
+
diff --git a/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/values b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/values
new file mode 100644
index 0000000..a54f63d
--- /dev/null
+++ b/.be/bugs/18dd6d0a-3c45-4aba-80da-fa32ffaaf5db/values
@@ -0,0 +1,17 @@
+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
+
diff --git a/unfold.py b/unfold.py
index 05fe4bd..570c9fd 100644
--- a/unfold.py
+++ b/unfold.py
@@ -107,7 +107,7 @@ class unfold :
         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 :