Tutorial for model-free analysis sam mahdi
Contents
Background
This follow the discussion with Sam Mahdi, at the mailing list: https://mail.gna.org/public/relax-users/2016-09/threads.html#00001
Files has been uploaded to: bug #25044: https://gna.org/bugs/?25044
- Model Free Analysis problems when attempting to run on multi-processors and using the script to run
Available data
- R1 600 MHz
- R2 600 MHz
- R1 800 MHz
- R2 800 MHz
- ssNOE 600 MHz
- ssNOE 800 MHz
Version of relax and computer
Version og relax is 4.0.2
Hardware information:
Machine: x86_64
Processor: x86_64
Processor name: Intel(R) Core(TM)2 Duo CPU E7500 @ 2.93GHz
Endianness: little
Total RAM size: 2756 Mb
Total swap size: 2815 Mb
Operating system information:
System: Linux
Release: 4.5.7-300.fc24.x86_64
Version: #1 SMP Wed Jun 8 18:12:45 UTC 2016
GNU/Linux version: Fedora 24 Twenty Four
Distribution: fedora 24 Twenty Four
Full platform string: Linux-4.5.7-300.fc24.x86_64-x86_64-with-fedora-24-Twenty_Four
Python information:
Architecture: 64bit
Python version: 2.7.12
Python branch:
Python build: default, Aug 9 2016 15:48:18
Python compiler: GCC 6.1.1 20160621 (Red Hat 6.1.1-3)
Libc version: glibc 2.2.5
Python implementation: CPython
Python revision:
Python executable: /usr/bin/python
Python flags: sys.flags(debug=0, py3k_warning=0, division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0, tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
Python float info: sys.float_info(max=1.7976931348623157e+308, max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021, min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16, radix=2, rounds=1)
Python module path: ['/home/student/relax-4.0.2', '/usr/lib/python27.zip', '/usr/lib64/python2.7', '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk', '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7/site-packages', '/usr/lib64/python2.7/site-packages/openmpi', '/usr/lib64/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages']
Python packages and modules (most are optional):
Name Installed Version Path
minfx True 1.0.12 /home/student/relax-4.0.2/minfx
bmrblib True 1.0.4 /home/student/relax-4.0.2/bmrblib
numpy True 1.11.0 /usr/lib64/python2.7/site-packages/numpy
scipy True 0.16.1 /usr/lib64/python2.7/site-packages/scipy
wxPython False
matplotlib True 1.5.2rc2 /usr/lib64/python2.7/site-packages/matplotlib
mpi4py True 2.0.0 /usr/lib64/python2.7/site-packages/openmpi/mpi4py
epydoc False
optparse True 1.5.3 /usr/lib64/python2.7/optparse.pyc
readline True /usr/lib64/python2.7/lib-dynload/readline.so
profile True /usr/lib64/python2.7/profile.pyc
bz2 True /usr/lib64/python2.7/lib-dynload/bz2.so
gzip True /usr/lib64/python2.7/gzip.pyc
io True /usr/lib64/python2.7/io.pyc
xml True 0.8.4 (internal) /usr/lib64/python2.7/xml/__init__.pyc
xml.dom.minidom True /usr/lib64/python2.7/xml/dom/minidom.pyc
relax information:
Version: 4.0.2
Processor fabric: Uni-processor.
Current script
Sam has provided this script.
It is not entirely clear how the "The dauvergne_protocol model-free auto-analysis" was initiated.
Maybe a combination of GUI and scripts?
relax> from time import asctime, localtime
relax> 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=11
relax> MIN_ALGOR='newton'
relax> MC_NUM=500
relax> CONV_LOOP=True
relax> pipe_bundle="mf(%s)"%asctime(localtime())
relax> name="origin-"+pipe_bundle
relax> 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*')
Make suggestion script
Copy sample script
To provide a suggestion script, the relax example script is copied to the folder with the data.
# Find where relax is called from. It's a symbolic link in the users bin folder.
tlinnet@linmac:Sam_25044$ which 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 data
tlinnet@linmac:Sam_25044$ pwd
/Users/tlinnet/Desktop/Sam_25044
# Copy sample script
cp /Users/tlinnet/software/relax_trunk_svn/sample_scripts/model_free/dauvergne_protocol.py sam_script.py
Now modify sample script
We are going to edit "sam_script.py".
Initial script
# 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)
Now we are just going to try this.
relax sam_script.py
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
# Get pdb
wget http://www.rcsb.org/pdb/files/2d9j.pdb.gz
# Extract
gzip -d 2d9j.pdb.gz
We open the .pdb file in PyMOL and see that it is a NMR file with 20 states.
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.
relax
# Relax start
help(structure.read_pdb)
exit
In the help menu, it says:
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.
Now add the following line to "sam_script.py".
structure.read_pdb('2d9j.pdb', set_mol_name='hRGS7', read_model=1)
exit
Now we are just going to try this.
relax sam_script.py
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.
relax
# Relax start
help(structure.load_spins)
exit
There is a lengthy description. But what relax need to do internal inside python, is to create data-containers where it can add data.
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.
After this, we alter the nitrogens to be isotope N15, and the same for hydrogen.
Now add the following line to "sam_script.py".
# 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*')
Now we are just going to try this.
relax sam_script.py
Check the spin containers via GUI
Right now, we want to check the spin containers.
First we do in the the GUI.
Now add the following line to "sam_script.py".
state.save('ini_setup', force=True)
Now we are just going to try this. Run relax to save the state, and then start in GUI.
relax sam_script.py
# Start relax in GUI
relax -g
Now do in the GUI
- File -> Open relax state
- Point to "ini_setup.bz2"
- Go to: View -> Spin Viewer
And inspect the spins!
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".
# 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
Now we are just going to try this.
relax sam_script.py
That gives some output in the command as this.
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
This looks good.
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.
relax
# Relax start
help(relax_data.read)
exit
