URL:
<http://gna.org/bugs/?25054>
Summary: Running scripts for model free
Project: relax
Submitted by: sam
Submitted on: Mon 12 Sep 2016 03:35:12 PM UTC
Category: None
Specific analysis category: Model-free analysis
Priority: 5 - Normal
Severity: 3 - Normal
Status: None
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Release: 4.0.2
Discussion Lock: Any
Operating System: 64-bit GNU/Linux
_______________________________________________________
Details:
Hi, this is a response to Troels. I have simply copied and pasted the email I
sent earlier.
Additional question that I had, if you could also look into this as well on
Tuesday please. I have decided to try to write a script to automate this whole
process (since I won't be using the gui to do model free), and I've come
across a problem. I can successfully open up relax using openmpi, and can load
the pdb file, and assign all the spins and isotopes; however, it appears it
will only load one data file (the very first one I'll have inputed in the
script). I don't know if there is a problem with how I wrote my script. Not
only will it not load the rest of my data sets, it won't actually run
dAuvergne's protocol either, it'll just load the data set and exit out of the
program. Attached is the script I wrote for relax.
This is the output once relax has loaded
script = 'model_free_sample_script.py'
----------------------------------------------------------------------------------------------------
from time import asctime, localtime
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoid','final']
MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9']
LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6','tm7','tm7','tm8','tm9']
GRID_INC=11
MIN_ALGOR='newton'
MC_NUM=500
CONV_LOOP=True
pipe_bundle="mf(%s)"%asctime(localtime())
name="origin-"+pipe_bundle
pipe.create(name,'mf',bundle=pipe_bundle)
structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7')
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*')
relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
file='R2_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
file='ssNOE_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R1_NMRFAM',ri_type='R1',frq=799.642*1e6,
file='R1_NMRFAM',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R2_NMRFAM',ri_type='R2',frq=799.642*1e6,
file='R2_NMRFAM',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='ssNOE_NMRFAM',ri_type='NOE',frq=799.642*1e6,
file='ssNOE_NMRFAM',res_num_col=1,data_col=2,error_col=3)
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()
value.set(-172*1e-6,'csa',spin_id='@N*')
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)
So it indicates that my script has loaded. However, after it loads the spins
from the pdb file, this is what happens after my first data set has been
loaded:
relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1', frq=599642000.0,
file='R1_Agnes', 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=None, data_col=2,
error_col=3, sep=None, spin_id=None)
Opening the file 'R1_Agnes' for reading.
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 ['16'] 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 ['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 ['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 ['31'] 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 ['46'] 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 ['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 ['73'] 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 ['79'] 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 ['85'] 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 ['97'] 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 ['106'] 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 ['121'] 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 ['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'.
crowlab: [~/relax-4.0.2]>
As you can see, I have all 6 data sets set to load, but only the very first
one appears to do so, and after it loads, it just exits out of relax. Again, I
don't know if this is a problem with how I wrote the script. The Relax_script1
is the one that I load up to run the whole thing. The model free script.py is
just the script it reads once relax has opened up. Again, I can see all the
spins are properly loaded, and the isotopes are set. It just everything after
the first data set that doesn't load. Thanks again in advance.
Sincerely,
Sam
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Mon 12 Sep 2016 03:35:13 PM UTC Name: model_free_sample_script.py
Size: 2kB By: sam
<http://gna.org/bugs/download.php?file_id=28602>
-------------------------------------------------------
Date: Mon 12 Sep 2016 03:35:13 PM UTC Name: Relax_script1 Size: 103B By:
sam
<http://gna.org/bugs/download.php?file_id=28603>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?25054>
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