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
Re: dimer