Changes

Make a '''06_check_intermediate_convert.py ''' file, with this content. {| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="python"># Python module imports.import os # relax module imports. # Read the state with the setupvar = 'result_06_check_intermediate'results_dir = os.getcwd() + os.sep + var + os.sep + 'final'# Load the state with setup data.state.load(state='results.bz2', dir=results_dir, force=True) #######Create the Modelfree4 input files.##### #Defaults# dir: The directory to place the files.# force: A flag which if set to True will cause the results file to be overwritten if it already exists.# binary: The name of the executable Modelfree program file.# diff_search: See the Modelfree4 manual for 'diffusion_search'.# sims: The number of Monte Carlo simulations.# sim_type: See the Modelfree4 manual.# trim[https: See the Modelfree4 manual.# steps: See the Modelfree4 manual//github.# constraints: A flag specifying whether the parameters should be constrained. The default is to turn constraints on (constraints=True).# heteronuc_type: A three letter string describing the heteronucleus type, ie '15N', '13C', etc.# atom1: The symbol of the X heteronucleus in the PDB file.# atom2: The symbol of the H nucleus in the PDB file.# spin_id: The spin identification string. # The following files are created# - 'dircom/mfin'# - 'dirtlinnet/mfdata'# - 'dirrelax_modelfree_scripts/mfpar'# - 'dirblob/mfmodel'# - 'dirmaster/run06_check_intermediate_convert.sh' # The file 'dir/runpy 06_check_intermediate_convert.sh' contains the single command,# 'modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out', # which can be used to execute modelfree4.# If you would like to use a different Modelfree executable file, change the binary name to the# appropriate file name. If the file is not located within the environment's path, include the full# path in front of the binary file name. #palmer.create(dir=None, force=False, # binary='modelfree4', diff_search='none', sims=0,# sim_type='pred', trim=0, steps=20, # constraints=True, heteronuc_type='15N', atom1='N', atom2='H',# spin_id=None) # Define write outwrite_modelfree = os.getcwd() + os.sep + var + os.sep + "Modelfree4"# Fix bugcdp.structure.structural_data[0].mol[0py].file_path = '.' outdir = os.getcwd() palmer.create(dir=write_modelfree, force=True, binary='modelfree4', diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=True, heteronuc_type='15N', atom1='N', atom2='H', spin_id=None) #######Create the Dasha script ##### #Defaults# algor: The minimisation algorithm.# dir: The directory to place the files.# force: A flag which if set to True will cause the results file to be overwritten if it already exists. # Optimisation algorithms#The two minimisation algorithms within Dasha are accessible through the algorithm which can be set to:# 'LM': The Levenberg-Marquardt algorithm,# 'NR': Newton-Raphson algorithm.# For Levenberg-Marquardt minimisation, the function 'lmin' will be called, while for Newton-Raphson, # the function 'min' will be executed. # dasha.create(algor='LM', dir=None, force=False) # Define write outout = 'result_06_check_intermediate'write_dasha = os.getcwd() + os.sep + out + os.sep + "Dasha"#dasha.create(algor='LM', dir=write_dasha, force=True)</source>|}