From: W. Trevor King <wking@drexel.edu>
Date: Fri, 26 Jun 2009 18:55:20 +0000 (-0400)
Subject: Added README file.
X-Git-Tag: v0.2~29
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=3b3c945457b98745c1de9c5feb6e274d8500c31e;p=unfold-protein.git

Added README file.

Also a bug/thoughts on packaging trouble (blocked by temperature).
---

diff --git a/.be/bugs/a2b804be-9892-452c-8c82-4b2cd245c5f3/comments/ebbf4721-8e0b-4d9f-a1e3-bbf1f26fbff9/body b/.be/bugs/a2b804be-9892-452c-8c82-4b2cd245c5f3/comments/ebbf4721-8e0b-4d9f-a1e3-bbf1f26fbff9/body
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+This is waiting while I figure out how to bundle temperature
+appropriately.  Currently my SWIG MelcorTempControl depends on my C
+serial_io code, but there's no setup/distutils method of automatically
+including this dependency information.  Maybe I should just write an
+ebuild?
+
diff --git a/.be/bugs/a2b804be-9892-452c-8c82-4b2cd245c5f3/comments/ebbf4721-8e0b-4d9f-a1e3-bbf1f26fbff9/values b/.be/bugs/a2b804be-9892-452c-8c82-4b2cd245c5f3/comments/ebbf4721-8e0b-4d9f-a1e3-bbf1f26fbff9/values
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+Content-type: text/plain
+
+
+Date: Fri, 26 Jun 2009 18:53:22 +0000
+
+
+From: W. Trevor King <wking@drexel.edu>
+
diff --git a/.be/bugs/a2b804be-9892-452c-8c82-4b2cd245c5f3/values b/.be/bugs/a2b804be-9892-452c-8c82-4b2cd245c5f3/values
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+creator: W. Trevor King <wking@drexel.edu>
+
+
+reporter: W. Trevor King <wking@drexel.edu>
+
+
+severity: minor
+
+
+status: open
+
+
+summary: unfold.py not packaged
+
+
+time: Fri, 26 Jun 2009 18:12:32 +0000
+
diff --git a/.be/settings b/.be/settings
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+++ b/.be/settings
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+rcs_name: git
+
diff --git a/.be/version b/.be/version
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+Bugs Everywhere Tree 1 0
diff --git a/README b/README
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+Unfolding experiment procedure:
+
+At the ipython command line (use -pylab option for easy plotting)
+>>> import unfold
+>>> u = unfold.unfold(controlTemp=False)
+
+Approach the surface
+>>> u.stepApproach(setpoint=1.0)
+Hold down during approach to keep O-ring from lifting the
+head. Diagnose by watching under video-microscope: head movement
+shifts picture.  Alternatively, use the flexible S-crossectioned
+"o-rings" or scrunchies to clamp head on tighter ;).
+
+Wiggle for interference just off the surface
+>>> u.stepAway(); u.stepAway(); u.stepAway()
+>>> import z_piezo_utils
+>>> z_piezo_utils.wiggleForInterferenceMin(u.zp, wig_freq=1.0)
+
+Calibrate
+>>> import calibcant.calibrate
+>>> calibcant.config.DEFAULT_TEMP = 25 # degrees C
+>>> calibcant.calibrate.calib(stepper=u.step, zpiezo=u.zp, push_depth=90)
+push_depth is in nm.  There are a host of other keyword arguments to
+calib.  See them all with
+>>> calibcant.calibrate.calib._kwargs(calibcant.calibrate.calib)
+
+Tweak coarse surface position (these are stepper-backlash protected functions)
+>>> u.stepCloser()
+>>> u.stepAway()
+
+Unfold a protein
+>>> u.unfold(rel_setpoint=2, nmDist=1400,...)
+
+There's also a convenience function `loop_rates`
+>>> rates = [250, 500, 750, 1000]
+>>> unfold.loop_rates(u, rates=rates, num_loops=10, die_file="~/die",
+                      rel_setpoint=1, nmDist=800, sBindTime=2, ...)
+which unfolds at each rate 10 times, unless ~/die exist, in which case
+it stops nicely.  rel_setpoint, nmDist, sBindTime, and other additional
+options are just passed on to unfold.unfold().
+
+Modules :
+see unfold.png
+
+
+Remember,
+>>> help(whatever)
+is your friend in Python, and
+$ man whatever
+and
+$ whatever --help
+are your friends in a shell.