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List:       relax-users
Subject:    Re: Now Member of list: Fwd: Displaying output from Model free  analysis
From:       "Edward d'Auvergne" <edward () domain ! hid>
Date:       2009-12-14 15:33:50
Message-ID: 7f080ed10912140733h5bee6a52jf4c9765f57f34eec () domain ! hid
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Dear Ed,

Welcome to the relax mailing lists!  Thank you for your questions, I
will try to answer them below.  Note that I'll be on holidays soon
until the 4th of Jan, so I may not be able to respond for a while.
Also, it would be appreciated if attachments were not sent to mailing
lists.  As the mailing list is broadcast out to many people and the
messages are archived across the web, this causes a massive strain on
the internet.  Attachments are best attached to the trackers, the bug
tracker (https://gna.org/bugs/?group=relax), the task tracker
(https://gna.org/task/?group=relax), and the support request tracker
(https://gna.org/support/?group=relax).

Edward



2009/12/13 Ed Olejniczak <edward.t.olejniczak@domain.hid>:
> I am using relax/1.3.3
>
> (1) I ran through the protocol and generated in the aic directory a xml
> file.
> How do I view it?

I hope Tiago's answer was enough.  The XML file is for data storage
and not really for reading.  If you can write scripts and read XML,
then this data is more accessible.  Otherwise there are the
value.display() and value.write() user functions.  There are also the
grace, pymol, and molmol user functions for displaying the data as
well.  How to use these is written out in full detail in the relax
manual.


> (2) I ran latex_mf_table.py and gnerated a tex file input=aic/results
>   output= results.tex
>
> How do I view this latex file?
>
> I have tried:       latex results.tex
>
> latex  find errors in the file.

This you need to include in your LaTeX document - it is not a LaTeX
document by itself.  If you don't have a LaTeX document, then this
won't work.  You will need something like \input{} or \include{} (I
can't remember the exact command) or copy and paste the entire thing.
Or you could convert it into a LaTeX document by adding:

\documentclass[a4paper, 12pt, twoside]{article}
\begin{document}

to the top and:

\end{document}

to the bottom.



> (3)   When I run the "relax_fit"protocols all of the "grace" view operations
> show a graph with the wrong limits, and thus no data.

In Grace there are AY and AX buttons.  You might have to repetitively
click on the two, one after the other.  This should bring the data in
range.  Otherwise double click on the axes to modify their ranges and
properties.


> (4) When I tried to use the output files from relax_fit protocols it was not
> the right format for model_free.
> I tried playing around to get it to read from the correct columns.  I gave
> up and just reformated the data to look like what you have in your
> sample data.  Why is my output in a different format?

Could you cut and paste a few lines of the output files?  Maybe also
the scripts used (copy and pasted)?  If this is the case, then the
scripts need to be modified to output what you need.  To track this
issue down and answer your question, I need a little bit more
information.

Cheers,

Edward


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