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
Now add the following line to "sam_script.py".
from pipe_control.mol_res_spin import spin_loop
for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
print("%20s %20s" % (repr(spin_id), spin.model))
Now we are just going to try this.
relax sam_script.py
