Hi Edward, I have uploaded a bug with the pdb file, the relax data, and the script as well. I can upload the original pdb file I recieved from HADDOCK (without changing the HN to H). I will attempt to re-run my data again then on both computer. Most of the data was the same, but there were some data in from one computer, that was virtually non-existent in the other. Also to the relax -x error, I believe that was on the relax 2.5 version. I am re-running it on the 4.0.2. version.
Sincerely, Sam On Fri, Sep 30, 2016 at 12:04 AM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > 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? > > 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 > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
