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@xxxxxxxxxxxxxx>:
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