Hi Stefano,
To test your Bruker DC files, please follow these steps:
- Start a new model-free analysis in the GUI.
- Load the spins from your PDB file.
- Click on the 'Add' button in the relaxation data list box which has
the Bruker logo. This is for reading these files.
- Check the relax controller window for any warning or errors.
relax has has support for reading Bruker DC files for a long time now
via the bruker.read user function. This was via a direct
collaboration with the Bruker people (specifically Peter Neidig).
These are tested continuously with the Bruker.test_bruker_read_noe and
Bruker.test_bruker_read_r1 system tests, so the code will always be
functional. I can see a slight format change. The Bruker DC versions
supported by relax are for example "ProteinCenter 1.1.5 (2011
Feb/24)". The data for the spins looks like:
SECTION: integrals
Spectrum [ ]: 0 1
Peak name I0 I1
Gln [2] 237314720.00000000 166446723.00000000
Ile [3] 239803653.00000000 173288612.00000000
Phe [4] 196080508.00000000 153754736.00000000
See the test_suite/shared_data/bruker_files/testNOE.txt for example.
The file you have attached has the version "Dynamics Center daily
(2013 Jan/25)" which I cannot recognise (and relax will also not be
able to identify). Are you using a special DC version? I can see
that the format looks different:
SECTION: integrals
Spectrum [ ]: 0 1
Peak name I0 I1
L2 534647.12500000 214904.12500000
I3 660662.37500000 401012.56250000
T4 237175.62500000 171186.81250000
Would you know why this could be? This does not matter however as the
residue number will nevertheless be correctly extracted, as relax will
accept any number in the first column (these are tab separated files
so for the first example "Gln [2]" is all in the first column.
Cheers,
Edward
On 8 February 2014 20:05, Stefano Luciano Ciurli
<stefano.ciurli@xxxxxxxx> wrote:
Dear Troels,
another question (I was able to load the spins from the PDB file): I have
previously run the Bruker Dynamics Center software, and the manual of that
software indicates how to export the results of its analysis to Relax. In
particular, it produces text files of the kind attached for NOE. Could you
please check that Relax reads those files smothlessly?
Stefano
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Re: [sr #3112] unable to upload PDB