Re: BMRB diffusion tensor saveframes. -- November 13, 2009 - 16:26

Hi,

Supergroup 3: Molecular assembly is for canonical data. Although there 
are tables for torsion angles, and others, at the assembly level note 
that there are no values provided for the torsion angles. They are just 
defined so that the ID for the angle can be used in other places, if 
wanted. At the chem_comp level internal angle values are provided, but 
these are library or canonical values to be taken from high resolution 
X-ray studies.

The interatomic distance information might fit in the Supergroup 8: 
structure, especially if the distances are derived from a PDB structure. 
However, if they are specific to the calculation of kinetic/dynamic data 
and could have various sources, I would argue to keep the information in 
the same Supergroup as the information they are used to derive.

Eldon

Edward d'Auvergne wrote:
> Hi,
>
> Considering that CSA and shielding tensors go into "Supergroup 5 : NMR
> parameters", that the optimised model-free values go into "Supergroup
> 7 : Thermodynamic data", or that the tensor could be measured (people
> do this but it is rubbish) or optimised, is "Supergroup 6 : Kinetic
> data" the best for the _Tensor saveframe?  Kinetic sounds correct to
> me though.  Also for the Interatomic_distance saveframe, this could be
> kinetic/dynamic, but would it not be better to go with the other
> structural data in "Supergroup 3 : Molecular assembly"?  Note this is
> inconsequential for bmrblib (https://gna.org/projects/bmrblib/) or for
> relax (https://nmr-relax.com, here useless links are for improving
> search engine rankings :P), and I am only asking to help keep the new
> saveframes and tags consistent.
>
> Cheers,
>
> Edward
>
>
> 2009/11/12 Eldon Ulrich <elu@xxxxxxxxxxxxx>:
> > Hi,
> >
> > I was thinking this would all still go in the 'kinetics' super-category.
> >
> > Eldon
> >
> > Edward d'Auvergne wrote:
> > > Hi,
> > >
> > > Thank you, this will help a lot!  I will rename General_relaxation to
> > > Auto_relaxation, and use this to start generating the diffusion tensor
> > > saveframe and the interatomic distance list for the dipolar relaxation
> > > mechanism.  For the new Tensor and Interatomic_dist saveframes, would
> > > you know what saveframe super-category they would belong to?  This
> > > will help with the file layout and placing these new files into
> > > http://svn.gna.org/viewcvs/bmrblib/trunk/bmrblib/.
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > > 2009/11/12 Eldon Ulrich <elu@xxxxxxxxxxxxx>:
> > > > Hi,
> > > >
> > > > Below are the draft saveframes for auto-relaxation, tensors, and
> > > > interatomic distances as of July based on our ENC discussions. You could
> > > > use these as a starting point. I will be trying to refine them, but your
> > > > active help where you are working with real data will be great.
> > > >
> > > > Eldon
> > > >
> > > > save_<auto_relaxation>
> > > > _Auto_relaxation_list.Sf_category
> > > > _Auto_relaxation_list.Sf_framecode
> > > > _Auto_relaxation_list.Entry_ID
> > > > _Auto_relaxation_list.Sf_ID
> > > > _Auto_relaxation_list.ID
> > > > _Auto_relaxation_list.Data_file_name
> > > > _Auto_relaxation_list.Sample_condition_list_ID
> > > > _Auto_relaxation_list.Sample_condition_list_label
> > > > _Auto_relaxation_list.Temp_calibration_method
> > > > _Auto_relaxation_list.Temp_control_method
> > > > _Auto_relaxation_list.Spectrometer_frequency_1H
> > > > _Auto_relaxation_list.Common_relaxation_type_name
> > > > _Auto_relaxation_list.Relaxation_coherence_type
> > > > _Auto_relaxation_list.Relaxation_val_units
> > > > _Auto_relaxation_list.Rex_units
> > > > _Auto_relaxation_list.Details
> > > > _Auto_relaxation_list.Text_data_format
> > > > _Auto_relaxation_list.Text_data
> > > >
> > > > loop_
> > > > _Auto_relaxation_experiment.Experiment_ID
> > > > _Auto_relaxation_experiment.Experiment_name
> > > > _Auto_relaxation_experiment.Sample_ID
> > > > _Auto_relaxation_experiment.Sample_label
> > > > _Auto_relaxation_experiment.Sample_state
> > > > _Auto_relaxation_experiment.Sf_ID
> > > > _Auto_relaxation_experiment.Entry_ID
> > > > _Auto_relaxation_experiment.Auto_relaxation_list_ID
> > > >
> > > > stop_
> > > >
> > > > loop_
> > > > _Auto_relaxation_software.Software_ID
> > > > _Auto_relaxation_software.Software_label
> > > > _Auto_relaxation_software.Method_ID
> > > > _Auto_relaxation_software.Method_label
> > > > _Auto_relaxation_software.Sf_ID
> > > > _Auto_relaxation_software.Entry_ID
> > > > _Auto_relaxation_software.Auto_relaxation_list_ID
> > > >
> > > > stop_
> > > >
> > > > loop_
> > > > _Auto_relaxation.ID
> > > > _Auto_relaxation.Assembly_ID
> > > > _Auto_relaxation.Assembly_atom_ID
> > > > _Auto_relaxation.Entity_assembly_ID
> > > > _Auto_relaxation.Entity_ID
> > > > _Auto_relaxation.Comp_index_ID
> > > > _Auto_relaxation.Seq_ID
> > > > _Auto_relaxation.Comp_ID
> > > > _Auto_relaxation.Atom_ID
> > > > _Auto_relaxation.Atom_type
> > > > _Auto_relaxation.Atom_isotope_number
> > > > _Auto_relaxation.Auto_relaxation_val
> > > > _Auto_relaxation.Auto_relaxation_val_err
> > > > _Auto_relaxation.Rex_val
> > > > _Auto_relaxation.Rex_val_err
> > > > _Auto_relaxation.Resonance_ID
> > > > _Auto_relaxation.Auth_entity_assembly_ID
> > > > _Auto_relaxation.Auth_seq_ID
> > > > _Auto_relaxation.Auth_comp_ID
> > > > _Auto_relaxation.Auth_atom_ID
> > > > _Auto_relaxation.Sf_ID
> > > > _Auto_relaxation.Entry_ID
> > > > _Auto_relaxation.Auto_relaxation_list_ID
> > > >
> > > >
> > > > stop_
> > > >
> > > > save_
> > > >
> > > > save_<tensor>
> > > > _Tensor_list.Sf_category
> > > > _Tensor_list.Sf_framecode
> > > > _Tensor_list.Entry_ID
> > > > _Tensor_list.Sf_ID
> > > > _Tensor_list.ID
> > > > _Tensor_list.Data_file_name
> > > > _Tensor_list.Details
> > > >
> > > > loop_
> > > > _Tensor.ID
> > > > _Tensor.Shieldings_calc_type_ID
> > > > _Tensor.Assembly_ID
> > > > _Tensor.Assembly_atom_ID
> > > > _Tensor.Entity_assembly_ID
> > > > _Tensor.Entity_ID
> > > > _Tensor.Comp_index_ID
> > > > _Tensor.Seq_ID
> > > > _Tensor.Comp_ID
> > > > _Tensor.Atom_ID
> > > > _Tensor.Atom_type
> > > > _Tensor.Atom_isotope_number
> > > > _Tensor.Isotropic_comp_1_1_val
> > > > _Tensor.Isotropic_comp_2_2_val
> > > > _Tensor.Isotropic_comp_3_3_val
> > > > _Tensor.Anti_sym_comp_1_2_val
> > > > _Tensor.Anti_sym_comp_1_3_val
> > > > _Tensor.Anti_sym_comp_2_3_val
> > > > _Tensor.Sym_traceless_comp_1_1_val
> > > > _Tensor.Sym_traceless_comp_1_2_val
> > > > _Tensor.Sym_traceless_comp_1_3_val
> > > > _Tensor.Sym_traceless_comp_2_2_val
> > > > _Tensor.Sym_traceless_comp_2_3_val
> > > > _Tensor.Euler_angle_alpha
> > > > _Tensor.Euler_angle_beta
> > > > _Tensor.Euler_angle_gamma
> > > > _Tensor.Isotropic_val
> > > > _Tensor.Anisotropic_val
> > > > _Tensor.Rhombic_val
> > > > _Tensor.Reduceable_matrix_1_1_val
> > > > _Tensor.Reduceable_matrix_1_2_val
> > > > _Tensor.Reduceable_matrix_1_3_val
> > > > _Tensor.Reduceable_matrix_2_1_val
> > > > _Tensor.Reduceable_matrix_2_2_val
> > > > _Tensor.Reduceable_matrix_2_3_val
> > > > _Tensor.Reduceable_matrix_3_1_val
> > > > _Tensor.Reduceable_matrix_3_2_val
> > > > _Tensor.Reduceable_matrix_3_3_val
> > > > _Tensor.Auth_entity_assembly_ID
> > > > _Tensor.Auth_seq_ID
> > > > _Tensor.Auth_comp_ID
> > > > _Tensor.Auth_atom_ID
> > > > _Tensor.Sf_ID
> > > > _Tensor.Entry_ID
> > > > _Tensor.Tensor_list_ID
> > > >
> > > > stop_
> > > >
> > > > save_
> > > >
> > > > save_<interatomic_distances>
> > > > _Interatomic_distance_list.Sf_category
> > > > _Interatomic_distance_list.Sf_framecode
> > > > _Interatomic_distance_list.Entry_ID
> > > > _Interatomic_distance_list.Sf_ID
> > > > _Interatomic_distance_list.ID
> > > > _Interatomic_distance_list.Details
> > > > _Interatomic_distance_list.Text_data_format
> > > > _Interatomic_distance_list.Text_data
> > > >
> > > > loop_
> > > > _Interatomic_dist.ID
> > > > _Interatomic_dist.Set_ID
> > > > _Interatomic_dist.Assembly_atom_ID_1
> > > > _Interatomic_dist.Entity_assembly_ID_1
> > > > _Interatomic_dist.Entity_ID_1
> > > > _Interatomic_dist.Comp_index_ID_1
> > > > _Interatomic_dist.Seq_ID_1
> > > > _Interatomic_dist.Comp_ID_1
> > > > _Interatomic_dist.Atom_ID_1
> > > > _Interatomic_dist.Atom_type_1
> > > > _Interatomic_dist.Assembly_atom_ID_2
> > > > _Interatomic_dist.Entity_assembly_ID_2
> > > > _Interatomic_dist.Entity_ID_2
> > > > _Interatomic_dist.Comp_index_ID_2
> > > > _Interatomic_dist.Seq_ID_2
> > > > _Interatomic_dist.Comp_ID_2
> > > > _Interatomic_dist.Atom_ID_2
> > > > _Interatomic_dist.Atom_type_2
> > > > _Interatomic_dist.Auth_asym_ID_1
> > > > _Interatomic_dist.Auth_entity_assembly_ID_1
> > > > _Interatomic_dist.Auth_seq_ID_1
> > > > _Interatomic_dist.Auth_comp_ID_1
> > > > _Interatomic_dist.Auth_atom_ID_1
> > > > _Interatomic_dist.Auth_asym_ID_2
> > > > _Interatomic_dist.Auth_entity_assembly_ID_2
> > > > _Interatomic_dist.Auth_seq_ID_2
> > > > _Interatomic_dist.Auth_comp_ID_2
> > > > _Interatomic_dist.Auth_atom_ID_2
> > > > _Interatomic_dist.Sf_ID
> > > > _Interatomic_dist.Entry_ID
> > > > _Interatomic_dist.Interatomic_distance_list_ID
> > > >
> > > > stop_
> > > >
> > > > save_
> > > >
> > > >
> > > > Edward d'Auvergne wrote:
> > > > > Hi Eldon,
> > > > >
> > > > > I'm ready to place the diffusion tensor data into the file for BMRB
> > > > > deposition.  This, from memory of our discussions at the 2009 ENC,
> > > > > will require a new saveframe as there is currently no capacity to
> > > > > store such data.  Would the 'Diffusion_tensor' name be reasonable?
> > > > > Did we come up with any tag names?  Maybe I can generate something,
> > > > > attach it to task #6438 (https://gna.org/task/?6438), and then you
> > > > > advise on all the tag name changes or other fundamental changes?
> > > > >
> > > > > Cheers,
> > > > >
> > > > > Edward
> > > > _______________________________________________
> > > > relax (http://nmr-relax.com)
> > > >
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