On 29 September 2016 at 00:23, Mahdi, Sam <sam.mahdi....@my.csun.edu> wrote:
> Hi Troels,
> Update on both proteins: So for protein 1, I can upload all the spins (H
> and N), but then I recieve an error. This is the error I recieved for
> protein 2 as well. These are both dimer pdb files. Meaning they have 2 sets
> (set A) and set (B) (e.g.
> http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb
> protein has 4 sets, A,B,C, and D ours only have A and B). For both these
> proteins I recieve this error
>  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
>     self.callback.init_master(self)
>   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
> default_init_master
>     self.master.run()
>   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
>     self.interpreter.run(self.script_file)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in run
>     return run_script(intro=self.__intro_string, local=locals(),
> script_file=script_file, show_script=self.__show_script,
> raise_relax_error=self.__raise_relax_error)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
> run_script
>     return console.interact(intro, local, script_file,
> show_script=show_script, raise_relax_error=raise_relax_error)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
> interact_script
>     exec_script(script_file, local)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
> exec_script
>     runpy.run_module(module, globals)
>   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
>     fname, loader, pkg_name)
>   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
>     exec code in run_globals
>   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line
> 31, in <module>
> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 246, in __init__
>     self.execute()
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 600, in execute
>     self.multi_model(local_tm=True)
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 888, in multi_model
>     self.interpreter.minimise.grid_search(inc=self.grid_inc)
>   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
> __call__
>     self._backend(*new_args, **uf_kargs)
>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172, in
> grid_search
>     model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
> verbosity=verbosity, skip_preset=skip_preset)
>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341, in
> grid_setup
>     elif values[i] in [None, {}, []]:
> IndexError: index out of bounds
> Which from my understanding basically means, the co-ordinates of the spins
> are out of the acceptable range for relax. I've checked all the
> co-ordinates for both, nothing is extreme or outlandish (all within a range
> of -20 to 20).
> Is relax unable to process pdb files that are dimers (with 2 sets A and
> B).? Furthermore, is it unable to process trimers and tetramers?


For the model-free analysis in relax, as well as all other analyses,
we have designed the program to try to catch all user input errors and
to produce a specific RelaxError prior to minimisation explaining
exactly what went wrong.  An IndexError here simply shows that not all
erroneous data input has been caught.  Let me go back to your PDB
file.  You should not edit this file unless you know exactly what you
are doing, but relax will handle all PDB files.  There is no need to
rename protons.  You just specify the correct proton name in the input
script.  I may have missed it as there is a lot of correspondence I
have to catch up on, but did you upload your script and a truncated
set of data to the relax bug or support trackers?  Do you have a
mini-data set (1 or 2 residues) and script that triggers this error?
If we can reproduce the IndexError, then finding the error would be



relax (http://www.nmr-relax.com)

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