Difference between revisions of "Clustering"
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(Created page with " == Example == === File with clustering === Flat text file with info <source lang="text"> # Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispers...") |
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=== File with clustering === | === File with clustering === | ||
Flat text file with info | Flat text file with info | ||
| − | < | + | <syntaxhighlight lang="text"> |
# Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. | # Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. | ||
# Residues used for global fitting, in Figure 2. | # Residues used for global fitting, in Figure 2. | ||
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V52N-HN | V52N-HN | ||
A53N-HN | A53N-HN | ||
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=== Cluster these residues === | === Cluster these residues === | ||
Script file: '''relax_global.py''' | Script file: '''relax_global.py''' | ||
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import os | import os | ||
from auto_analyses.relax_disp import Relax_disp | from auto_analyses.relax_disp import Relax_disp | ||
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for curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=False): | for curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=False): | ||
print curspin.select, curspin.name, curspin.isotope, mol_name, res_num, res_name, spin_id | print curspin.select, curspin.name, curspin.isotope, mol_name, res_num, res_name, spin_id | ||
| − | </ | + | </syntaxhighlight> |
Execute with: | Execute with: | ||
relax -p relax_global.py | relax -p relax_global.py | ||
Latest revision as of 19:00, 19 September 2020
Example
File with clustering
Flat text file with info
# Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.
# Residues used for global fitting, in Figure 2.
# This uses the data from Kjaergaard's paper at http://dx.doi.org/10.1021/bi4001062
L13N-HN
R15N-HN
T16N-HN
Q25N-HN
Q26N-HN
Q28N-HN
L39N-HN
M40N-HN
A41N-HN
F43N-HN
I44N-HN
K45N-HN
A49N-HN
V52N-HN
A53N-HN
Cluster these residues
Script file: relax_global.py
import os
from auto_analyses.relax_disp import Relax_disp
from pipe_control.mol_res_spin import spin_loop
# Set settings for run.
pre_run_directory = os.path.join(os.getcwd(),"results")
results_directory = os.path.join(os.getcwd(),"results_clustering")
cluster_file = "global_fit_residues.txt"
# Load set
state.load(state='bug_21344.bz2', force=True)
# Open file for writing
f = open(cluster_file, 'r')
cluster_spins = []
for line in f:
if line[0] == "#":
continue
else:
resnspin = line.split()[0]
resn = resnspin[0]
resi = resnspin[1:].split("N-HN")[0]
spinid = ":%s@N"%(resi)
print spinid
relax_disp.cluster('model_cluster', spinid)
# Close file
f.close()
# De-select for analysis those spins who have not been clustered
for free_spin in cdp.clustering['free spins']:
deselect.spin(spin_id=free_spin, change_all=False)
# Print info
for curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=False):
print curspin.select, curspin.name, curspin.isotope, mol_name, res_num, res_name, spin_id
Execute with:
relax -p relax_global.py
