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cd relax> from time import asctime, localtimerelax> from auto_analyses.dauvergne_protocol import dAuvergne_protocol relax> DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoid','final']relax> MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9']relax> LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6','tm7','tm7','tm8','tm9']relax> GRID_INC=11relax> MIN_ALGOR='newton'relax> MC_NUM=500relax> CONV_LOOP=Truerelax> pipe_bundle="mf(%s)"%asctime(localtime())relax> name="origin-"+pipe_bundlerelax> pipe.create(name,'mf',bundle=pipe_bundle)relax> structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7')relax> structure.load_spins('@N',ave_pos=True)relax> structure.load_spins('@NE1',ave_pos=True)relax> structure.load_spins('@H',ave_pos=True)relax> structure.load_spins('@HE1',ave_pos=True)relax> spin.isotope('15N',spin_id='@N*')relax> spin.isotope('1H',spin_id='@H*')relax> interatom.define(spin_id1='@N',spin_id2='@H', direct_bond=True)relax> interatom.define(spin_id1='@NE1',spin_id2='@HE1', direct_bond=True)relax> interatom.set_dist(spin_id1='@N*',spin_id2='@H*',ave_dist=1.02*1e-10)relax> interatom.unit_vectors()relax> value.set(-172*1e-6,'csa',spin_id='@N*')</source> == Make suggestion script ===== Copy sample script ===To provide a suggestion script, the relax example script is copied to the folder with the data. <source lang="bash"># Find where relax is called from. It's a symbolic link in the users bin folder.tlinnet@linmac:Sam_25044$CWDwhich relax/Users/tlinnet/bin/relax # Read the link to the folder where relax is installed.tlinnet@linmac:Sam_25044$ readlink `which relax`/Users/tlinnet/software/relax_trunk_svn/relax # The current working folder with datatlinnet@linmac:Sam_25044$ pwd/Users/tlinnet/Desktop/Sam_25044 # Copy sample scriptcp /Users/tlinnet/software/relax_trunk_svn/sample_scripts/model_free/dauvergne_protocol.py sam_script.py</source> === Now modify sample script ===We are going to edit "sam_script.py". ==== Initial script ====<source lang="python"># Python module imports.from time import asctime, localtime# relax module imports.from auto_analyses.dauvergne_protocol import dAuvergne_protocol # Analysis variables.###################### The diffusion model.DIFF_MODEL = 'local_tm' # The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed.MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9'] # The grid search size (the number of increments per dimension).GRID_INC = 11 # The optimisation technique.MIN_ALGOR = 'newton' # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.MC_NUM = 10 # Automatic looping over all rounds until convergence (must be a boolean value of True or False).CONV_LOOP = True # Set up the data pipe.####################### # The following sequence of user function calls can be changed as needed. # Create the data pipe.pipe_bundle = "mf (%s)" % asctime(localtime())name = "origin - " + pipe_bundlepipe.create(name, 'mf', bundle=pipe_bundle)</source>
set FIDS=`cat fid_filesNow we are just going to try this.ls`set DIRN1=`dirname $PWD/${FIDS[1]}` foreach I (`seq 2 ${#FIDS}`)set FID<source lang=${FIDS[$I]}; set DIRN=`dirname $FID`cd $DIRNecho $DIRNcp -f $DIRN1/fid.com .cp -f $DIRN1/nmrproc.com ."bash">relax sam_script./fid.com./nmrproc.comcd ..endpy
→Background: Link fixes and use of a. New template.
== 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">
== Current script ==
Sam has provided this script. <br> It is not entirely clear how the "The dauvergne_protocol model-free auto-analysis" was initiated. Maybe a combination of GUI and scripts?
<source lang="python">
</source>
This works fine. Lets add the next line.
==== Loading model from pdb file ====
From Sams script, we see that he uses the PDB ID: 2d9j
<source lang="bash">
# Get pdb
wget http://www.rcsb.org/pdb/files/2d9j.pdb.gz
# Extract
gzip -d 2d9j.pdb.gz
</source>
We open the .pdb file in PyMOL and see that it is a NMR file with 20 states. <br>
We need to figure out how to use the command '''structure.read_pdb'''
So we open relax in the prompt, and use the help command.
<source lang="bash">
relax
# Relax start
help(structure.read_pdb)
exit
</source>
In the help menu, it says:
<source lang="text">
read_model: If set, only the given model number(s) from the PDB file will be read. Otherwise
all models will be read. This can be a single number or list of numbers.
</source>
Now add the following line to "sam_script.py".
<source lang="python">
structure.read_pdb('2d9j.pdb', set_mol_name='hRGS7', read_model=1)
</source>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
This works fine. Lets add the next line.
==== Create data containers ====
In the sample script, we see that we should use the command "structure.load_spins".
Since we do not know what that is, we use the help command.
So we open relax in the prompt, and use the help command.
<source lang="bash">
relax
# Relax start
help(structure.load_spins)
exit
</source>
There is a lengthy description. But what relax need to do internal inside python, is to create data-containers where it can add data. <br>
It is as simple as that. We need some place to store relax data, and relax generate some "variables" on a naming scheme from the pdb file. <br>
After this, we alter the nitrogens to be isotope N15, and the same for hydrogen.
Now add the following line to "sam_script.py".
<source lang="python">
# 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*')
</source>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
==== Check the spin containers via GUI====
Right now, we want to check the spin containers.<br>
First we do in the the GUI.<br>
Now add the following line to "sam_script.py".
<source lang="python">
state.save('ini_setup', force=True)
</source>
Now we are just going to try this. Run relax to save the state, and then start in GUI.
<source lang="bash">
relax sam_script.py
# Start relax in GUI
relax -g
</source>
Now do in the GUI
# File -> Open relax state
# Point to "ini_setup.bz2"
# Go to: View -> Spin Viewer
And inspect the spins! <br>
Close relax
==== Check the spin containers via script ====
Instead of using the GUI to inspect the spins, we can use the command
Add the following line to "sam_script.py".
<source lang="python">
# Import
from pipe_control.mol_res_spin import spin_loop
# Loop and print
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
print spin, mol_name, res_num, res_name, spin_id
</source>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
That gives some output in the command as this.
<source lang="text">
Objects:
element: 'H'
isotope: '1H'
name: 'H'
num: 2204
pos: array([-26.478999999999999, -4.86 , 6.999 ])
select: True
hRGS7 139 GLY #hRGS7:139@H
</source>
This looks good.
==== Try to load the relaxation data ====
Now comes the time to load the relaxation data.
In the sample script, we see that we should use the command "relax_data.read".
Since we do not know what that is, we use the help command.
So we open relax in the prompt, and use the help command.
<source lang="bash">
relax
# Relax start
help(relax_data.read)
exit
</source>
Let us inspect just one file date. Open in a text browser "R1_600".
It says
<source lang="text">
Residue R1 Error
1
2
3
4
5
6
7
8
9
10
11
12 1.58 0.06
13 1.23 0.05
14 1.48 0.1
15 2.06 0.04
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
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104
105
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112
113
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119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
139
</source>
This will probably not work. The file does not contain the same separators in the file. <br>
But let us try!
Add the following line to "sam_script.py".
<source lang="python">
relax_data.read(ri_id='R1_600', ri_type='R1', frq=599.719*1e6, file='R1_600', res_num_col=1, data_col=2, error_col=3)
</source>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
That gives some output in the command as this.
<source lang="text">
RelaxWarning: The sequence data in the line ['Residue', 'R1', 'Error'] is invalid, the residue number data 'Residue' is invalid.
RelaxWarning: The sequence data in the line ['1'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['2'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['3'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['4'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['5'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['6'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['7'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['8'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['9'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['10'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['11'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['17'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['18'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['19'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['20'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['21'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['22'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['23'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['24'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['25'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['26'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['27'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['28'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['29'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['30'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['31'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['32'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['33'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['34'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['35'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['36'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['37'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['38'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['39'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['40'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['41'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['42'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['43'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['44'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['45'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['46'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['47'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['48'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['49'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['50'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['51'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['52'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['53'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['54'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['55'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['56'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['57'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['58'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['59'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['60'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['61'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['62'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['63'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['64'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['65'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['66'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['67'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['68'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['69'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['70'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['71'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['72'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['73'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['74'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['75'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['76'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['77'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['78'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['79'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['80'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['81'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['82'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['83'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['84'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['85'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['86'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['87'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['88'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['89'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['90'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['91'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['92'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['93'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['94'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['95'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['96'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['97'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['98'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['99'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['100'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['101'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['102'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['103'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['104'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['105'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['106'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['107'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['108'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['109'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['110'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['111'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['112'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['113'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['114'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['115'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['116'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['117'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['118'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['119'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['120'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['121'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['122'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['123'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['124'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['125'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['126'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['127'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['128'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['129'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['130'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['131'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['132'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['133'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['134'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['135'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['136'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['137'] is invalid, the data is missing.
RelaxWarning: The sequence data in the line ['139'] is invalid, the data is missing.
RelaxError: The spin ID '#hRGS7:12' corresponds to multiple spins, including '#hRGS7:12@N' and '#hRGS7:12@H'.
</source>
A lot of problems! <br>
We modify the data file to look like this. Note the hashtag "#".
<source lang="text">
#Residue R1 Error
12 1.58 0.06
13 1.23 0.05
14 1.48 0.1
15 2.06 0.04
</source>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
That gives some output in the command as this.
<source lang="text">
RelaxError: The spin ID '#hRGS7:12' corresponds to multiple spins, including '#hRGS7:12@N' and '#hRGS7:12@H'.
</source>
NOTE: Instead of a "Warning", this is an "Error". <br>
This will not work.
And why? Relax does not know if the associated data is the R1 for the nitrogen or proton of spin 12. And then relax STOPS. <br>
'''Errors make relax STOP.'''
The data is insufficient or not labelled correct.
How could it look like? <br>
Have a look in: "relax_installation/test_suite/shared_data/model_free/sphere"
'''r1.500.out'''
<source lang="text">
# mol_name res_num res_name spin_num spin_name value error
sphere_mol1 1 GLY 1 N 1.4639691658223886 0.029279383316447773
sphere_mol1 1 GLY 2 H None None
sphere_mol1 2 GLY 3 N 1.4639691658223886 0.029279383316447773
sphere_mol1 2 GLY 4 H None None
</source>
Let us then alter '''R1_600''' file.
<source lang="bash">
#res_num spin_name R1 Error
12 N 1.58 0.06
13 N 1.23 0.05
14 N 1.48 0.1
15 N 2.06 0.04
</source>
Now MODIFY the following line in "sam_script.py".
<source lang="python">
# From
relax_data.read(ri_id='R1_600', ri_type='R1', frq=599.719*1e6, file='R1_600', res_num_col=1, data_col=2, error_col=3)
# To
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)
</source>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
Now it works.
<source lang="text">
Opening the file 'R1_600' for reading.
The following 599.719 MHz R1 relaxation data with the ID 'R1_600' has been loaded into the relax data store:
# Spin_ID Value Error
#hRGS7:12@N 1.58 0.06
#hRGS7:13@N 1.23 0.05
#hRGS7:14@N 1.48 0.1
#hRGS7:15@N 2.06 0.04
</source>
==== Alter rest of the data ====
Let us then alter '''R1_800''' file.
<source lang="bash">
#res_num spin_name R1 Error
12 N 1.15 0.03
13 N 0.832 0.011
14 N 1.07 0.05
15 N 0.78 0.17
</source>
Let us then alter '''R2_600''' file.
<source lang="bash">
#res_num spin_name R2 Error
12 N 18.6 0.6
13 N 14.58 0.39
</source>
Let us then alter '''ssNOE_600''' file.
<source lang="bash">
#res_num spin_name Noe Error
13 N 0.663870952 0.0386263336
14 N 0.8132898597 0.1578765885
</source>
Let us then alter '''ssNOE_800''' file.
<source lang="bash">
#res_num spin_name Noe Error
12 N 0.4833302155 0.1078027894
13 N 0.8142253659 0.0290794774
14 N 0.7922308188 0.0801096067
</source>
Now add the following lines in "sam_script.py", so there is 6 in total..
<source lang="python">
# From before
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)
# Add this
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)
</source>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
This looks fine
<source lang="text">
relax> relax_data.read(ri_id='R1_600', ri_type='R1', frq=599719000.0, file='R1_600', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=2, data_col=3, error_col=4, sep=None, spin_id=None)
Opening the file 'R1_600' for reading.
The following 599.719 MHz R1 relaxation data with the ID 'R1_600' has been loaded into the relax data store:
# Spin_ID Value Error
#hRGS7:12@N 1.58 0.06
#hRGS7:13@N 1.23 0.05
#hRGS7:14@N 1.48 0.1
#hRGS7:15@N 2.06 0.04
relax> relax_data.read(ri_id='R2_600', ri_type='R2', frq=599719000.0, file='R2_600', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=2, data_col=3, error_col=4, sep=None, spin_id=None)
Opening the file 'R2_600' for reading.
The following 599.719 MHz R2 relaxation data with the ID 'R2_600' has been loaded into the relax data store:
# Spin_ID Value Error
#hRGS7:12@N 18.6 0.6
#hRGS7:13@N 14.58 0.39
relax> relax_data.read(ri_id='ssNOE_600', ri_type='NOE', frq=599719000.0, file='ssNOE_600', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=2, data_col=3, error_col=4, sep=None, spin_id=None)
Opening the file 'ssNOE_600' for reading.
The following 599.719 MHz NOE relaxation data with the ID 'ssNOE_600' has been loaded into the relax data store:
# Spin_ID Value Error
#hRGS7:13@N 0.663870952 0.0386263336
#hRGS7:14@N 0.8132898597 0.1578765885
relax> relax_data.read(ri_id='R1_800', ri_type='R1', frq=799719000.0, file='R1_800', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=2, data_col=3, error_col=4, sep=None, spin_id=None)
Opening the file 'R1_800' for reading.
The following 799.719 MHz R1 relaxation data with the ID 'R1_800' has been loaded into the relax data store:
# Spin_ID Value Error
#hRGS7:12@N 1.15 0.03
#hRGS7:13@N 0.832 0.011
#hRGS7:14@N 1.07 0.05
#hRGS7:15@N 0.78 0.17
relax> relax_data.read(ri_id='R2_800', ri_type='R2', frq=799719000.0, file='R2_800', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=2, data_col=3, error_col=4, sep=None, spin_id=None)
Opening the file 'R2_800' for reading.
The following 799.719 MHz R2 relaxation data with the ID 'R2_800' has been loaded into the relax data store:
# Spin_ID Value Error
#hRGS7:12@N 24.9 0.9
#hRGS7:13@N 16.1 0.3
#hRGS7:14@N 27.0 3.0
#hRGS7:15@N 22.96 0.19
relax> relax_data.read(ri_id='ssNOE_800', ri_type='NOE', frq=799719000.0, file='ssNOE_800', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=2, data_col=3, error_col=4, sep=None, spin_id=None)
Opening the file 'ssNOE_800' for reading.
The following 799.719 MHz NOE relaxation data with the ID 'ssNOE_800' has been loaded into the relax data store:
# Spin_ID Value Error
#hRGS7:12@N 0.4833302155 0.1078027894
#hRGS7:13@N 0.8142253659 0.0290794774
#hRGS7:14@N 0.7922308188 0.0801096067
</source>
==== Define the magnetic dipole-dipole relaxation interaction ====
In the sample script, we see that we should use the command "interatom.define".
'''Use the help command to find out more.'''
Add this
<source lang="python">
# 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>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
We see that relax calculates a lot of stuff, for spins we have no data for.
'''Let us practice to select and deselect spins.'''
So instead we do this:
<source lang="python">
# 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')
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
print spin, mol_name, res_num, res_name, spin_id
# 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>
==== Let us try to execute ====
Now add the following lines in "sam_script.py"
<source lang="python">
# Execution.
############
# Change some opt params.
# COMMENT THESE OUT FOR REAL CALCULATION. THIS IS ONLY TO SPEED UP THE PROCESS IN ERROR SEARCHING.
dAuvergne_protocol.opt_func_tol = 1e-5
dAuvergne_protocol.opt_max_iterations = 1000
# Do not change!
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>
Now we are just going to try this AND using a log file
<source lang="bash">
relax sam_script.py -t log.txt
</source>
==== The whole script file looked like this ====
<source lang="python">
# Python module imports.
from time import asctime, localtime
# relax module imports.
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
# Analysis variables.
#####################
# The diffusion model.
DIFF_MODEL = 'local_tm'
# The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed.
MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
# The grid search size (the number of increments per dimension).
GRID_INC = 11
# The optimisation technique.
MIN_ALGOR = 'newton'
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 10
# Automatic looping over all rounds until convergence (must be a boolean value of True or False).
CONV_LOOP = True
# Set up the data pipe.
#######################
# The following sequence of user function calls can be changed as needed.
# Create the data pipe.
pipe_bundle = "mf (%s)" % asctime(localtime())
name = "origin - " + pipe_bundle
pipe.create(name, 'mf', bundle=pipe_bundle)
# 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*')
state.save('ini_setup', force=True)
# Import
from pipe_control.mol_res_spin import spin_loop
# Loop and print
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
print spin, mol_name, res_num, res_name, spin_id
# From before
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)
# Add this
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')
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
print spin, mol_name, res_num, res_name, spin_id
# 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*')
# Execution.
############
# Change some opt params.
# COMMENT THESE OUT FOR REAL CALCULATION. THIS IS ONLY TO SPEED UP THE PROCESS IN ERROR SEARCHING.
dAuvergne_protocol.opt_func_tol = 1e-5
dAuvergne_protocol.opt_max_iterations = 1000
# Do not change!
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 ==
The data was insufficient or not labelled correct.
That made relax make an ERROR and make a STOP.
Please use the help function.
== See also ==
[[Category:Tutorials]]
[[Category:Relaxation dispersion analysisModel-free_analysis]]