On Mon, Jan 12, 2009 at 7:44 PM, Eldon Ulrich <elu@xxxxxxxxxxxxx> wrote:
Hi Edward,
Glad to hear you are making progress with the NMR-STAR output. In general, a
BMRB entry in NMR-STAR format is a valid file to upload into the ADIT-NMR
deposition system as the starting point for a deposition. Partial files can
be used also (i.e., a saveframe with chemical shift or relaxation data), but
the system may not be able to extract as much information like the protein
sequence as the sequence may be incomplete.
Hi Eldon,
Progress has been slow, but hopefully relax will soon be creating
NMR-STAR files. The aim is to have one single 100% complete v3.1 file
output by relax containing the entire contents of a full model-free
analysis, such as:
http://svn.gna.org/svn/relax/branches/bmrb/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
as well as all additional data required by the BMRB (and possibly
other non-mandatory records which are useful for dynamics). Is there
a way that I could validate the output from relax? One test for the
completeness of the data is by using the above relax results file,
creating the NMR-STAR file, reading this file back into relax, and
then creating the relax results file a second time. If the data is
not complete, the 2 relax results files will not be the same. But
this will not be sufficient for checking if all mandatory records are
present or if the BMRB records are correct. Is there a way of
submitting test data into ADIT-NMR?
Additionally, I think I remember that in a previous mail you sent me a
link where I could find v3.1 formatted files containing relaxation
data. Is this correct? And if so, do you remember what this link is
as I cannot find this message? I would like to add one of these files
(truncated for speed) into the relax test suite for checking the BMRB
NMR_STAR v3.1 reading and writing abilities of relax.
We are revisiting the values to be used for the 'coherence_type' tag. The
current enumerations are not really correct it seems. Also, in discussion
here, it appears that double quantum, single quantum antiphase, longitudinal
spin order, and other forms of coherences are not truly R1, R2, or R1rho
relaxation. It may be useful to create another saveframe to capture these
kinds of data. I will document our current thinking and send it in another
e-mail. I would be very pleased to have your input on this.
Do the cross-correlated relaxation rates eta_z and eta_xy fit into
these categories / saveframes? Although these are not yet handled by
relax, they will be in the future. Would it be better to have one
saveframe type for all the numerous types of relaxation data instead
and then use a number of tags to identify the type?
Cheers,
Edward
Re: relaxing the BMRB.