Hello everyone,
I've been attempting to run model free models (due to only have data at one
field strength), but I've come across a problem. I have set up both the
model free models script and the model free model selection, both models
run fine, and I do end up receiving data that does make sense and is good;
however, the script doesn't seem to actually select any models. I.e. if I
put in the m0-m9 in the script, it'll select m9 for every single reside and
only give me Rex data and no S^2. If I run m0-m4 same thing, it'll run
every residue at m4, instead of running through all the models and
selecting the data that fits that model. I know it states that the model is
supposed to loop through every model, then you run the model selection to
select what model fits which data set, but I don't know if my script is set
up incorrectly or what. Here is my script for model-free models:
pipes = ['m0','m1','m2','m3','m4']
for name in pipes:
pipe.create(name,'mf')
sequence.read('ssNOE_RGS4Agnes',res_num_col=1)
spin.name('N')
spin.element(element='N',spin_id='@N')
spin.isotope('15N',spin_id='@N')
structure.read_pdb('cluster1_12.pdb',read_mol=1)
relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
file='R1_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
file='R2_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
file='ssNOE_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
diffusion_tensor.init(1e-8,fixed=True)
sequence.attach_protons()
interatom.define(spin_id1='@N',spin_id2='@H',direct_bond=True)
interatom.set_dist(spin_id1='@N',spin_id2='@H',ave_dist=1.02*1e-10)
structure.get_pos('@N')
structure.get_pos('@H')
interatom.unit_vectors()
value.set(-172*1e-6,'csa',spin_id='@N')
model_free.select_model(model=name)
minimise.grid_search(inc=11)
minimise.execute('newton')
results.write(file='results',force=True)
state.save('save',force=True)
Again I only have it at m0-m4 because I wanted to obtain the m4 data, but
even if it is to m9, it'll only run the m9 model (i.e. I will only receive
Rex data because that's whats attributed to m9). Here is my model
selection script:
pipes = ['m0','m1','m2','m3','m4']
for name in pipes:
print("\n\n#"+name+"#")
pipe.create(name,'mf')
results.read(file='results.bz2',dir=name)
eliminate()
model_selection(method='AIC',modsel_pipe='aic')
state.save('save',force=True)
results.write(file='results',force=True)
Again, this is only set up to m4 for the same reasons as before. I don't
know whether or not I have something in my script set up, but my final
results file just shows the model that was selected for every residue, is
the last model I have in my pipes (i.e. if m4 is the last model, it'll run
model 4, if m9 is the last one, it'll run m9). In this sence it appears to
be a single model scenario even though I've set up to be for multiple
models. Thank you again in advance.
Sincerely,
Sam
Using Model-free models