Clustering - Revision history

Bugman: Switch from the depreciated tags to .

2020-09-19T19:00:23Z

Switch from the depreciated <source> tags to <syntaxhighlight>.

Tlinnet: /* File with clustering */

2014-02-28T13:01:08Z

File with clustering

Tlinnet: Created page with " == Example == === File with clustering === Flat text file with info # Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispers..."

2014-02-28T13:00:47Z

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..."

New page

== Example ==

=== File with clustering ===
Flat text file with info
<source lang="text">
# 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
</souce>

=== Cluster these residues ===
Script file: '''relax_global.py'''
<source lang="python">
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
</source>

Execute with:
relax -p relax_global.py

@@ Line 4: / Line 4: @@
 === File with clustering ===
 Flat text file with info
-<source lang="text">
+<syntaxhighlight lang="text">
 # 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.
@@ Line 23: / Line 23: @@
 V52N-HN
 A53N-HN
-</source>
+</syntaxhighlight>
 === Cluster these residues ===
 Script file: '''relax_global.py'''
-<source lang="python">
+<syntaxhighlight lang="python">
 import os
 from auto_analyses.relax_disp import Relax_disp
@@ Line 66: / Line 66: @@
 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
-</source>
+</syntaxhighlight>
 Execute with:
   relax -p relax_global.py