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?