Re: latex script on final resultsRe: latex script on final resultsHi,
Tyler, would you know what fixed the first traceback issue? I'd like
to try to fix that in relax as any traceback message in relax is
considered a bug. The only errors that don't count as bugs are the
RelaxError messages. This one seems like a directory issue within the
structure section of the results file. Could you possibly cut and
paste the results files lines corresponding to the loaded structure?
I would suggest submitting a bug report as well - and I think I might
be able to reproduce it with all the mol, res, and spin entries
deleted. If I can get the test suite to reproduce this, I should be
able to easily fix this.
As for the .tex file, this is a LaTeX formatted table. You can simply
use an \input{} command in your LaTeX document and the table will be
included. You'll need the 2 packages as described in the script in
the preamble of your document. If you haven't used LaTeX before, you
can create a very simple PDF document from this file by adding the
lines:
\documentclass[a4paper, 11pt, twoside, openright]{book}
\usepackage{longtable}
\usepackage{booktabs}
\begin{document}
to the start of the file, and the line:
\end{document}
to the end. Then compile using latex by typing something like:
$ latex results.tex
$ latex results.tex
$ latex results.tex
$ dvips -o results.ps results.dvi
$ ps2pdf results.ps
You'll then have the results.pdf file to play with.
Regards,
Edward
On Mon, Nov 10, 2008 at 3:47 AM, Tyler Reddy <TREDDY@xxxxxx> wrote:
Right, it's opening the file now and procuding a .tex file as well, but there is still this output: RelaxWarning: The structure file 'PDB_file.pdb' cannot be found in the current directory or the directory of the results file. Which seems odd because I have a copy of this PDB file in the same directory as the script and in the directory with the results.bz2 file, just in case. Also, what is the normal way to view a .tex file like this one? Tyler Quoting Douglas Kojetin <douglas.kojetin@xxxxxxxxx>:Are you certain your RESULTS variable points towards 'final/ results.bz2'? The output from your job below differs vs. mine, in particular these lines in the output: relax> results.read(file='final/results.bz2', dir=None) Opening the file 'final/results.bz2' for reading. Perhaps you should attach the input script text as well as the output text? Doug On Nov 9, 2008, at 5:45 PM, Tyler Reddy wrote:It looks like both problems were already fixed in my script, so it must be something else? Quoting Douglas Kojetin <douglas.kojetin@xxxxxxxxx>:I made the following changes to the distributed latex_mf_table.py file, and it seemed to work OK. % diff updated_latex_mf_table.py old_latex_mf_table.py 42c42 < RESULTS_FILE = 'final/results.bz2' ---RESULTS_FILE = 'final'171c171 < for spin, spin_id in spin_loop(return_id=True): ---for spin, spin_id in spin_loop(return_id=True)I think your error might be caused by the change on line 42, but an error will popup for the change on line 171 (the for statement is missing a semi-colon ). Doug On Nov 9, 2008, at 7:55 AM, Tyler Reddy wrote:Hi, My model-free results from the full analysis python script have converged and the 'final' run is complete. I moved the latex table script into the 'final' directory, but when I execute the script I get the output below. I think Edward mentioned this script might need some work. Has anyone used it successfully? Tyler Output: Latex() ---------------------------------------------------------------------------------------------------- relax> pipe.create(pipe_name='results', pipe_type='mf') relax> results.read(file='results', dir=None) Opening the file 'results' for reading. Traceback (most recent call last): File "/Applications/relax-1.3.1/relax-1.3/relax", line 422, in <module> Relax() File "/Applications/relax-1.3.1/relax-1.3/relax", line 131, in __init__ self.interpreter.run(self.script_file) File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", line 270, in run return run_script(intro=self.__intro_string, local=self.local, script_file=script_file, quit=self.__quit_flag, show_script=self.__show_script, raise_relax_error=self.__raise_relax_error) File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", line 531, in run_script return console.interact(intro, local, script_file, quit, show_script=show_script, raise_relax_error=raise_relax_error) File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", line 427, in interact_script execfile(script_file, local) File "latex_mf_table.py", line 220, in <module> Latex() File "latex_mf_table.py", line 53, in __init__ results.read(RESULTS_FILE, dir=None) File "/Applications/relax-1.3.1/relax-1.3/prompt/results.py", line 99, in read results.read(file=file, directory=dir) File "/Applications/relax-1.3.1/relax-1.3/generic_fns/ results.py", line 98, in read read_function = ds.from_xml(file, dir=directory) File "/Applications/relax-1.3.1/relax-1.3/data/__init__.py", line 185, in from_xml self[self.instance.current_pipe].from_xml(relax_node, dir=dir) File "/Applications/relax-1.3.1/relax-1.3/data/ pipe_container.py", line 164, in from_xml self.structure.from_xml(str_nodes[0], dir=dir) File "/Applications/relax-1.3.1/relax-1.3/generic_fns/structure/ api_base.py", line 276, in from_xml loaded = self.load_pdb(file_path=dir + sep + self.file[i], model=None, struct_index=i) TypeError: unsupported operand type(s) for +: 'NoneType' and 'str' _______________________________________________ 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_______________________________________________ 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