Hi, Another set of issues are with the entries:
bmr15097.str bmr15445.str bmr15536.str bmr15562.str These seem to only have order parameters - the correlation times and all other model-free parameters are absent. One of the programs used was Loria's FastModelfree, so correlations times should be present. Do you know if the authors forgot to submit this data, or if the entry is missing some of the submitted data? Cheers, Edward On 2 February 2011 14:35, Edward d'Auvergne <[email protected]> wrote: > Hi Eldon, > > I don't know if this is the best channel for this information. Is > there a BMRB mailing list where it would be better for this > information? > > Ok, this is how I have found these inconsistencies. I have used relax > to read in the BMRB NMR-STAR formatted files. This uses bmrblib which > I wrote (http://gna.org/projects/bmrblib/). This library is pretty > close to complete for relaxation data and model-free data, and would > be very easy to extend to handle the entirety of the NMR-STAR > dictionary. It can both read and write valid NMR-STAR formatted files > in versions 2.1, 3.0, and 3.1 (a little debugging might be still > required, and expansion to different revisions such as 2.1.1 is also > possible). This Python library is an abstraction of the underlying > file format. The very low level reading and writing of the STAR > format is handled by Jurgen F. Doreleijers' pystarlib (jurgenfd att > gmail dott com, http://code.google.com/p/pystarlib/). > > For reading the entire BMRB model-free data content, I have performed > the following. I have downloaded all of the files from > http://www.bmrb.wisc.edu/search/query_grid/query_1_46.html using the > link http://www.bmrb.wisc.edu/ftp/pub/bmrb/compress/query_1_46.tar.gz. > These are all in the version 2.1 or 2.1.1 format. Then using the > file names, I have downloaded all of the corresponding v3.1 files from > http://www.bmrb.wisc.edu/ftp/pub/bmrb/entry_lists/nmr-star3.1/. It > looks like maybe 30% of the old formatted files have been converted to > the newer format so far. I will write 2 subsequent emails with > explanations of the problems with the version 2.1 files and the 3.1 > files separately. > > In this mail, I would like to describe general problems. The first is > that pystarlib cannot handle the semi-colon notation in non-free > looping tag categories, e.g.: > > loop_ > _Vendor.Name > _Vendor.Address > _Vendor.Electronic_address > _Vendor.Entry_ID > > _Vendor.Software_ID > > 'J. Patrick Loria' . > ; > http://xbeams.chem.yale.edu/~loria/ > [email protected] > ; 15097 1 > > This is in the v3.1 file bmr15097.str. The basic pystarlib > functionality probably needs to be fixed, assuming this construct is a > valid STAR format. The second is that the bmr4970.str entry is not > parsable. This file has multiple 15N S2_parameters saveframes: > > save_S2_parameters_15N_22C > save_S2_parameters_15N_35C > save_S2_parameters_15N_47C > save_S2_parameters_15N_60C > save_S2_parameters_15N_73C > > > But these all have: > > loop_ > _Sample_label > > $sample_one > > stop_ > > _Sample_conditions_label $sample_conditions_one > > They might be the same sample, but the sample conditions are different > as the temperature is changing. By eye, this is obvious, but for the > automatic parsing of this data, the file has to be blacklisted and > skipped. > > 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
