Dear Edward,
I have doubled the spins for the NOE, T1, T2 files to run the analysis for
the dimer. The analysis took more than a month, and it was not completed
(stopped at the 'prolate' step), I believe because we were running it on a
virtual machine (Xubuntu), and not on a Linux computer, which we are going
to do.
However, I wanted also to try running Relax on the separate protein parts.
The protein we are working with is composed of the domains arranged as
N-C-C-N. And I would like to run the first calculation for the C-C part,
for which I prepared the NOE, T1 and T2 files (output from DC) by doubling
the spins and cutting off the N-terminal parts (in the same way I have
prepared also the data for the N-terminal domain of the protein). However,
I can not load the data and therefore start the calculations. Whereas the
NOE files loading went well, for the T1 or T2 files upload Relax gives me
the following error message:
relax> bruker.read(ri_id='T1_700_N',
file='/home/olena/Desktop/BpUreE_domains/T1_UreE_700_Nterm.txt', dir=None)
Opening the file '/home/olena/Desktop/BpUreE_domains/T1_UreE_700_Nterm.txt'
for reading.
Traceback (most recent call last):
File "/usr/local/relax-3.2.1/gui/wizards/wiz_objects.py", line 670, in
_go_next
self._pages[self._current_page]._apply(event)
File "/usr/local/relax-3.2.1/gui/wizards/wiz_objects.py", line 164, in
_apply
self.exec_status = self.on_execute()
File "/usr/local/relax-3.2.1/gui/uf_objects.py", line 887, in on_execute
return_status = self.execute(self.name, **kargs)
File "/usr/local/relax-3.2.1/gui/uf_objects.py", line 809, in execute
return_status = interpreter.apply(uf, *args, **kwds)
File "/usr/local/relax-3.2.1/gui/interpreter.py", line 109, in apply
apply(fn, args, kwds)
File "/usr/local/relax-3.2.1/pipe_control/bruker.py", line 54, in read
values, errors, res_nums, int_type, frq, ri_type, spin_name, isotope,
version = parse_file(file=file, dir=dir)
File "/usr/local/relax-3.2.1/lib/software/bruker_dc.py", line 164, in
parse_file
rx = float(row[-2])
IndexError: list index out of range
Therefore, I couldn't even load the dataset for this protein part, or
precisely the T1 and T2 data. The files format is identical to those used
for the full protein. Why then it doesn't want to load? For me it is
unclear in this message where could be the problem. Could you please help?
If you want I can send you only the files I prepared and would appreciate
if you have a look.
Thank you.
Olena
________________________________________
From: Stefano Luciano Ciurli
Sent: 10 June 2014 13:39
To: Edward d'Auvergne
Cc: relax-users@xxxxxxx; Olena Dobrovolska
Subject: Re: dimer
Hi Edward,
thinking about it, and considering that we erroneously run Relax using the
full PDB for the homodimer but provided only the T1, T2 and NOE data for
one monomer, as output of Dynamics Center, could you tell us how to modify
the .txt files from Dynamics Center so that Relax "thinks" it has a full
set of data for the full homodimer? The PDB that we used has residues
already numbered consecutively from residue 1 to the last residue of the
dimer.
We really need to change the input files for T1, T2 and NOE in order to
decide which part of the protein we are looking at, but we would like to
know which parts of the output files from DC should be duplicated. If you
want and need it, I can send you the files in a private email to you only.
Looking forward to hearing from you
Stefano
On Jun 6, 2014, at 8:35 AM, Edward d'Auvergne wrote:
Hi Stefano,
It will be interesting to see the results in your final publication.
Especially considering that the relaxation data you observe is the
average of two states experiencing different global tumbling (the two
vectors intersect different parts of a single Brownian diffusion
tensor), but the assumption is made that they only sample one. Maybe
you should perform a full analysis on one monomer, and then another
full analysis on the second, and compare. Are you sure there are no
published theoretical treatments of such a situation?
As for the PyMOL or MOLMOL macros, I've had a look at the PDB file you
attached to http://gna.org/support/?3110, and this might be difficult.
Although both molecules are represented as different chains, the
residue numbers are not reset between the A to B transition:
"""
ATOM 2437 HE1 HIS A 147 14.544 -14.592 44.384 1.00142.09
H
ATOM 2438 C HIS A 147 15.448 -12.825 50.108 1.00142.09
C
ATOM 2439 O HIS A 147 16.622 -12.826 50.563 1.00142.09
O
ATOM 2440 OXT HIS A 147 14.601 -13.730 50.336 1.00142.09
O
TER 2441 HIS A 147
ATOM 2442 N MET B 148 34.965 4.924 102.588 1.00 83.68
N
ATOM 2443 H MET B 148 35.604 5.224 103.352 1.00 83.68
H
ATOM 2444 CA MET B 148 33.567 5.117 103.004 1.00 83.68
C
"""
Do you have the ability to renumber residues? This is rather simple
in relax, though not so obvious as it plays directly with the relax
data store object and uses Python programming:
"""
# Create a data pipe.
pipe.create('renumber', 'N-state')
# Load the original PDB as two molecules.
structure.read_pdb('BpUreE_apo_model_full.pdb')
# Renumber all residues of the second molecule directly in the
internal structural object.
for i in range(len(cdp.structure.structural_data[0].mol[1].res_num)):
cdp.structure.structural_data[0].mol[1].res_num[i] -= 147
# Write out the renumbered structure as a PDB file.
structure.write_pdb('BpUreE_apo_renumbered.pdb', force=True)
"""
If the residues are all the same, then the PyMOL or MOLMOL macros
should apply to both structures. I just had a look and the macros
from the model-free analysis apply to residue numbers:
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.pymol-pysrc.html#Pymol.classic_colour
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.molmol-pysrc.html#Molmol.classic_colour
Regards,
Edward
On 5 June 2014 23:32, Stefano Luciano Ciurli <stefano.ciurli@xxxxxxxx>
wrote:
Hi Edward,
I reached the end of the calculation of our protein dimer, and everything
went smooth. We used two fields, and tomorrow I am about to start
collecting the third field data. I wonder how to make it so that the
molmol or pymol macros used to visualize the various parameters along the
protein backbone can be twisted so that these are applied to both
monomers instead of just one.
Cheers,
Stefano
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Re: dimer