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== Background ==
This follow the discussion with Sam Mahdi, at the mailing list: https://mail.{{gna.org/public/mailing list url|relax-users/2016-09/threads.html#00001}}
Files has been uploaded to: {{gna bug #25044: https://gna.org/bugs/?link|25044}}
* Model Free Analysis problems when attempting to run on multi-processors and using the script to run
== Version of relax and computer ==
Version og of relax is 4.0.2
<source lang="text">
<source lang="python">
structure.read_pdb('2d9j.pdb', set_mol_name='hRGS7', read_model=1)
</source>
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)
</source>
== Make suggestion script for GUI ==
Let us try to analyse it in the GUI.
First copy the script over
<source lang="bash">
cp sam_script.py sam_script_GUI.py
</source>
Modify it, so it look like this
<source lang="bash">
# Load the PDB file.
structure.read_pdb('2d9j.pdb', set_mol_name='hRGS7', read_model=1)
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
structure.load_spins('@N', ave_pos=True)
structure.load_spins('@NE1', ave_pos=True)
structure.load_spins('@H', ave_pos=True)
structure.load_spins('@HE1', ave_pos=True)
spin.isotope('15N', spin_id='@N*')
spin.isotope('1H', spin_id='@H*')
# read data
relax_data.read(ri_id='R1_600', ri_type='R1', frq=599.719*1e6, file='R1_600', res_num_col=1, spin_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='R2_600', ri_type='R2', frq=599.719*1e6, file='R2_600', res_num_col=1, spin_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='ssNOE_600', ri_type='NOE', frq=599.719*1e6, file='ssNOE_600', res_num_col=1, spin_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='R1_800', ri_type='R1', frq=799.719*1e6, file='R1_800', res_num_col=1, spin_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='R2_800', ri_type='R2', frq=799.719*1e6, file='R2_800', res_num_col=1, spin_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='ssNOE_800', ri_type='NOE', frq=799.719*1e6, file='ssNOE_800', res_num_col=1, spin_name_col=2, data_col=3, error_col=4)
# Deselect
deselect.all()
# Select
#select.spin(':12@N|:12@H|:13@N|:13@H|:14@N|:14@H|:15@N|:15@H')
select.spin(':12|:13|:14|:15')
# Define the magnetic dipole-dipole relaxation interaction.
interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True)
interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)
interatom.unit_vectors()
# Define the chemical shift relaxation interaction.
value.set(-172 * 1e-6, 'csa', spin_id='@N*')
</source>
=== Start relax in GUI ===
<source lang="bash">
relax -g -t log_gui.txt
</source>
Now do
# File -> New analysis
# Select "Model-free" -> Next
# Just hit Start in the box for pipe name
# Goto "User functions (n-z)" -> Script
# Find and open the script file "sam_script_GUI.py"
This should now fill out the data. Inspect the data
# View -> Spin Viewer
Save the state before execution. This state is easy to load in the GUI afterward
# File -> Save relax state -> as "test.bz2"
Exit relax. And start relax again
<source lang="bash">
relax -g -t log_gui_2.txt
</source>
Now do
# File -> Open relax state
# Select "test.bz2"
It should now show all the data.
Hit "Execute"
Consider
# Setting the number of Monte-Carlo simulations to 10, for initial faster calculation
== Conclusion ==
== See also ==
[[Category:Tutorials]]
[[Category:Relaxation dispersion analysisModel-free_analysis]]