On Mon, Jan 12, 2009 at 7:44 PM, Eldon Ulrich <[email protected]> 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 _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
