Dear Boaz,
I'm afraid to tell you, but you will need to study and understand the
area of model-free analysis prior to applying it (at least a little
anyway, you cannot bypass the scientific knowledge ;) A good
introduction is chapter 1 of my PhD thesis downloadable at
http://www.nmr-relax.com/refs.html#dAuvergne06 or available in paper
form from Amazon
(http://www.amazon.com/Protein-Dynamics-Model-free-Analysis-Relaxation/dp/3639057627/ref=sr_1_1?ie=UTF8&s=books&qid=1254732645&sr=8-1).
Note that model-free analysis is quite a complex modelling issue.
For example see http://www.nmr-relax.com/refs.html#dAuvergneGooley07
for how I have encompased the entire problem and defined the universal
solution (the solution in the universal set of model-free and
diffusion models).
If you would like to perform a full analysis, I would suggest you look
at the 'sample_scripts/full_analysis.py' script. I have written this
one so you can perform model-free analysis as a black box. You must
nevertheless know of a few of the 'issues' associated with model-free.
Again, these issues are all detailed in my review at
http://www.nmr-relax.com/refs.html#dAuvergneGooley07.
For the problem you saw, it would be useful to know the relax version
you used, how you modified the script, what input data you used, etc.
Oh, I think I just worked out what happened. Did you run relax and
then simply type 'model-free.py' at the prompt? I tried this and it
gave the error message you mentioned. If so, this is not how you use
relax. If you have a script file, you need to type:
$ relax script_file
at the prompt. It would be useful if you read at least the
introductory part manual, specifically section "1.2 How to use relax"
and the subsection "1.2.7 Scripting". You may not want to learn
Python, but all programs require you to become familiar with their
basic operation, be that a powerful scripting interface such as
Python, a self written scripting interface such as in Dasha, or the
creation of a collection of intricately formatted input files such as
in Art Palmer's Modelfree4. I hope this helps.
Cheers,
Edward
2009/9/16 Boaz Shapira <bshapira@xxxxxxxxxxxx>:
Hi,
I just installed relax and tried to figure out how it works (couldn't).
I have no idea about python and I don't mind to keep it that way unless i
have no other choice.
Still, I tried to play with the examples and couldn't make it work (the
relax --text-suite didn't give me error)
I tried to run model-free.py from the relax prompt but it gives me error.
" Traceback (most recent call last):
File "<console>", line 1, in <module>
NameError: name 'model' is not defined "
Then I copied line by line and it did work.
It save it in a .bz2 format.
Now If I want to read the data what format should I use?
It looks like a source html file.
In general I collected data on two fields and want to analyze the data with
a black box (the full_analysis.py ?)
I have the input files in the right format as in the examples
I have the pdb file
Is it possible to simply run a black-box that will give me an output:
List of the residues with the best model for each, the values for this model
(S2, tau ...), the goodness of the fitting, and
the overall diffusion tensor?
This black box will also reject "bad" relaxation data.
and all of that will be given in a text file?
It is too much to ask?
Thank you,
Boaz
------------------------------------------------
Boaz Shapira PhD
Complex Carbohydrate Research Center
University of Georgia
315 Riverbend Rd
Athens, GA 30602-4712
706-542-6286
bshapira@xxxxxxxxxxxx
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
Re: a black box is needed