Hi, Thanks for the quick response. I've used the SaveFrameTest.py test code as an example but also found that using pystarlib to read a full BMRB record, such as Sebasian Morin's http://www.bmrb.wisc.edu/cgi-bin/explore.cgi?format=raw&bmrbId=6838 data, helps to explain the python data structure design. Using this I've worked out the 'free' argument to TabTable and the significance of a few other arguments. relax is now outputting relaxation data in STAR format, and the pystarlib code seems to be working perfectly. Apart from the import issues that I fixed in the relax copy of pystarlib (https://mail.gna.org/public/relax-commits/2009-01/msg00155.html), it looks like the code requires zero modification to read and write these BMRB files. This is perfect!
Cheers, Edward On Mon, Jan 12, 2009 at 11:33 AM, Jurgen F. Doreleijers <[email protected]> wrote: > 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
