On 29 September 2016 at 00:23, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx>
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?
Hi,
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
easy.
Cheers,
Edward