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albertogomcas / hooke

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problem with distance curves #42

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. create a playlist with genlist
2.
3.

What is the expected output? What do you see instead?
I want to have a playlist and from this the plotted curves

What version of the product are you using? On what operating system?
hooke 0.8.3 on Windows xp professional Service pack 3

Please provide any additional information below.
the data was made with a veeco multimode. I downloaded a sample file from on e 
of the issues here and had no problem to plot it. So I guess I've a problem 
with my data.

Original issue reported on code.google.com by ssala...@gmx.de on 8 Apr 2011 at 1:34

GoogleCodeExporter commented 8 years ago 
Sorry I forgot to recomment that the problem i have is after creating a 
playlist i get the message: "indexerror: list index out of range" in the cmd

Original comment by ssala...@gmx.de on 8 Apr 2011 at 1:57

GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
With which instrument and software did you obtain the curves? And, how many 
curves you have?

To create a list in your current directory use " genlist * " with the "*" to 
select all the files (like in a normal shell or command line).

Let me know if it worked.

Original comment by fabrizio...@gmail.com on 11 Apr 2011 at 10:02

GoogleCodeExporter commented 8 years ago 
The AFM i used was a Bioscope from VEeco with the software from them. The 
instrumwnt was about 8 years old. The amount of curves depend in the first try 
I only want to open three. But in the end i want to investigate over thousand 
curves.

Original comment by ssala...@gmx.de on 12 Apr 2011 at 2:28

GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
Have you tried " genlist * "?  If so, could you put the output from the shell?

I mean the entire input output after these lines:
"This is Hooke, version 0.8.3_devel Seinei

(c) Massimo Sandal & others, 2006-2008. Released under the GNU Lesser General 
Public License Version 3
Hooke is Free software.
"

I may need also one of the curve to see if there is a problem.

Original comment by fabrizio...@gmail.com on 13 Apr 2011 at 6:13

GoogleCodeExporter commented 8 years ago 
Ok I added two pictures of the cmd with the problem i had before and the 
problem i've know when i tried genlist *.

Original comment by ssala...@gmx.de on 21 Apr 2011 at 7:24

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GoogleCodeExporter commented 8 years ago 
Your file format (0x05120005) was too old for Hooke to understand.  I've just 
added support for it to my branch:

  http://www.physics.drexel.edu/~wking/code/hg/hgweb.cgi/hooke/rev/670432bcb913

but I may have made some assumptions based on your single example that don't 
end up holding for *all* your data files.  Does the following interpretation 
look like what you expected for mica_030311.001?  It is a screenshot of

    ./bin/hk.py -u gui -c 'new_playlist' -c 'glob_curves_to_playlist test/data/vclamp_picoforce/0x05120005' -p

Original comment by tvrkng@gmail.com on 21 Apr 2011 at 12:18

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GoogleCodeExporter commented 8 years ago 
Hey thanks for your help. the force curve shoot look the other way around like 
the picture i attached. Im really a beginner with these code stuff so can you 
explain me how i've to use your code to plot my curve ???

Original comment by ssala...@gmx.de on 26 Apr 2011 at 8:11

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GoogleCodeExporter commented 8 years ago 
Don't worry about the orientation.  The convention with globular protein 
unfolding is to display the contact region in the lower left, so attractive 
surface-tip connections rise into the upper right.  Hooke displays your curve 
in the same manner.  If you want to replot your data using some other 
convention after analyzing it with Hooke, there's an `export_block` command 
which will export selected data from your (analyzed) curve as TAB-delimited 
ASCII text.

I've been talking with Fabrizio about incorporating the changes that allow 
Hooke to read your data into the Hooke trunk, but at the moment they only work 
in my GUI branch.  You can get descriptions of the installation and usage 
procedure for my branch here:
  http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/Hooke/html/

If you're already running the trunk Hooke on a Windows computer (judging by 
your terminal screenshots above), will probably only need to install PyYAML and 
wxPython.  If you used the Enthought Python Distribution version 7.0 
(recommended by the SciPy folks as the easiest way to get a working Python 
setup), both of these packages will already be installed.

Anyhow, try following the installation instructions and let me know if you have 
any problems!

Original comment by tvrkng@gmail.com on 26 Apr 2011 at 11:03