Hi Edward, Nice to hear from you again. It has been a while indeed. I joined an NMR lab in the Netherlands since but am still collaborating with BMRB too.
The best thing to start off with would be to look at the python unit tests such as the one in: http://code.google.com/p/pystarlib/source/browse/trunk/src/STAR/SaveFrameTest.py It shows you how to fill in a python data structure that can then be rendered to STAR text. All the best, Jurgen On Sun, Jan 11, 2009 at 7:29 PM, Edward d'Auvergne <[email protected]> wrote: > Dear Eldon and Jurgen, > > I have finally made some progress in interfacing relax with the BMRB > using the pystarlib library. Getting relax to produce perfectly > formatted and complete NMR_STAR v3.1 files for submission to the BMRB > is still a way off though. For this, I have a few questions regarding > both getting pystarlib to produce the v3.1 format and what the final > result should look like. For reference, the relax formatted XML file > which I would like to convert to NMR-STAR v3.1 format is located at: > > http://svn.gna.org/svn/relax/branches/bmrb/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2 > > This file is part of the relax test suite and is distributed with > relax. For submission, I would like to convert 100% of the data in > this file but I'm not exactly sure how this would look yet. Eldon, is > there a complete v3.1 formatted file containing model-free results > that I can use for a reference? It would be extremely useful if we > could find or create a complete reference file for relaxation data > using currently deposited data. This would be better if it was the > file for submission rather than for storage in the BMRB. Or, as I > will get relax to force the user into inputting all required fields > before relax creates the file, would the submitted file be identical > to the stored file? I have been using Steven van Doren's deposited > data at http://www.bmrb.wisc.edu/cgi-bin/explore.cgi?format=raw&bmrbId=5841, > but this is obviously quite different from the v3.1 format. > > For the formatting using pystarlib, I am using as reference > ftp://ftp.bmrb.wisc.edu/pub/data/nmr-star_dict/dictionary_files/nmrstar3_fake.txt. > I am currently trying to get relax to produce a file with just > relaxation data. The relevant section for R1 relaxation in this file > is: > > save_<heteronucl_T1_relaxation> > _Heteronucl_T1_list.Sf_category heteronucl_T1_relaxation > _Heteronucl_T1_list.Sf_framecode <heteronucl_T1_relaxation> > _Heteronucl_T1_list.Entry_ID 1 > _Heteronucl_T1_list.Sf_ID 2 > _Heteronucl_T1_list.ID 2 > _Heteronucl_T1_list.Data_file_name "Long string value" > _Heteronucl_T1_list.Sample_condition_list_ID 2 > _Heteronucl_T1_list.Sample_condition_list_label "Long string value" > _Heteronucl_T1_list.Spectrometer_frequency_1H 110.234 > _Heteronucl_T1_list.T1_coherence_type "String value" > _Heteronucl_T1_list.T1_val_units "Short string value" > _Heteronucl_T1_list.Details "Possible > multiline text" > _Heteronucl_T1_list.Text_data_format "String value" > _Heteronucl_T1_list.Text_data "Possible > multiline text" > > loop_ > _Heteronucl_T1_experiment.Experiment_ID > _Heteronucl_T1_experiment.Experiment_name > _Heteronucl_T1_experiment.Sample_ID > _Heteronucl_T1_experiment.Sample_label > _Heteronucl_T1_experiment.Sample_state > _Heteronucl_T1_experiment.Sf_ID > _Heteronucl_T1_experiment.Entry_ID > _Heteronucl_T1_experiment.Heteronucl_T1_list_ID > > 2 "Long string value" 2 "Long string value" "String value" 2 1 2 > > stop_ > > loop_ > _Heteronucl_T1_software.Software_ID > _Heteronucl_T1_software.Software_label > _Heteronucl_T1_software.Method_ID > _Heteronucl_T1_software.Method_label > _Heteronucl_T1_software.Sf_ID > _Heteronucl_T1_software.Entry_ID > _Heteronucl_T1_software.Heteronucl_T1_list_ID > > 2 "Long string value" 2 "Long string value" 2 1 2 > > stop_ > > loop_ > _T1.ID > _T1.Assembly_atom_ID > _T1.Entity_assembly_ID > _T1.Entity_ID > _T1.Comp_index_ID > _T1.Seq_ID > _T1.Comp_ID > _T1.Atom_ID > _T1.Atom_type > _T1.Atom_isotope_number > _T1.Val > _T1.Val_err > _T1.Resonance_ID > _T1.Auth_entity_assembly_ID > _T1.Auth_seq_ID > _T1.Auth_comp_ID > _T1.Auth_atom_ID > _T1.Sf_ID > _T1.Entry_ID > _T1.Heteronucl_T1_list_ID > > 2 2 2 2 2 2 1 1 "Short string value" 2 110.234 > 110.234 2 "Short string value" "Short string value" "Short > string value" "Short string value" 2 1 2 > > stop_ > > save_ > > Jurgen, my question is how do you produce the correct File.datanodes > list using the SaveFrame and Tagtable objects to reproduce this when > calling File.write()? For example, how do you create the > _Heteronucl_T1_list.Sf_category entry? > > Cheers, > > Edward > > > P.S. It would be much appreciated if you could use reply-to-all > rather than simply replying, as this will include the relax-devel > mailing list in the CC list. Thanks. > -- Jurgen F. Doreleijers Centre for Molecular & Biomolecular Informatics, NCMLS & Protein Biophysics, Institute for Molecules & Materials Radboud University of Nijmegen Visitors: NCMLS Research building, room 0.25, Geert-Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands Mail: Protein Biophysics 260, PO Box 9101, 6500 HB Nijmegen, The Netherlands Tel: +31 24 3619674 _______________________________________________ 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
