Hi Stefano,
Please see below:
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.
In this setup, relax will only look at the first monomer.
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.
There is no need to send the files. Do you have someone there who
knows scripting? One option is to write a script (perl, Python, sed,
etc.) which adds 147 to the residue number for all parts of the Bruker
DC file. Or maybe using the script at
http://thread.gmane.org/gmane.science.nmr.relax.user/1661/focus=1677
to renumber the PDB file will be sufficient. Loading the two
molecules into relax and then loading the Bruker DC data might put the
data into the spin containers of both molecules, as the residue
numbers for both molecules will match. This would have to be very
carefully checked as this is completely untested behaviour for relax.
You would also need to carefully look at the log messages.
If you would like me to make this last option 100% functional for
relax, I would recommend creating a support request and attaching your
Bruker DC files there - but they must be truncated to 1 or 2 residues.
You can randomise the data slightly too for complete secrecy, if you
wish. I could then use this and the PDB file to create a relax system
test. Having a system test allows me to fix things in relax in ~5 to
10 minutes. The support request creation link is
http://gna.org/support/?func=additem&group=relax.
Regards,
Edward
Re: dimer