Hi,

`we have embodied into the Relax program possibility to perform the
``analysis with consideration of the asymmetric character of the CST and
``also all dipole-dipole interactions arising from the spins in the
``proximity to the studied S-I spin pair.
``This should be taken into the account for the dynamic studies of the
``fully labeled nucleic acid (Poster 118 at 23rd ICMBRS meeting in San
``Diego) and we would like to add this feature to the public version of
``the Relax program.
`

`These changes can be done by the addition of new terms into the
``equations for the relaxation rates. The description of the relaxation
``due to the fully anisotropic CST can be written in concordance with the
``article by Goldman M, J magn. Reson 60, 437-452 (1984). The CST tensor
``is splitted into two axially symmetric subtensors which both contribute
``to the relaxation. Such approach has advantage that the spectral density
``function do not change the form used in Relax program. The calculation
``is done in the same manner using only different input orientation. The
``function for chi^2 calculation and minimalization procedure is not
``affected.
`
Definition additional input information:

`The orientation of the CS tensor is defined in the new input file
``containing for each studied nucleus three Euler angles in separate
``columns defining the orientation of the CS tensor with respect to the
``PDB frame (these values are then stored in the variable called CSEA).
``Separate file contains three columns with the eigenvalues of the
``chemical shielding tensor (these values are then stored in the variable
``called CST).
``The choice of atom responsible for the significant dipole-dipole
``interaction with the studied nuclei is done in the PDB file. Atoms,
``which are to be considered in the calculations, should be marked in the
``PDB file by adding the distance to the studied nuclei (in the 1e-10m
``unit) after the z coordinate. Other atoms should have zero distance
``instead. So far only atoms from the same residuum may be taken into the
``account.
`
Suggested changes in the code:

` generic_fns/nuclei.py added function for setting gyromagnetic ratios
``for selected atoms Y (atoms dipole-dipole interaction should be
``considered in the calculation) and ratio of gyromagnetic ratios of atoms
``Y and X (nucleus which relaxation is studied)
`` generic_fns/pdb.py added function for calculating XY unit vector
``from the structure
` generic_fns/runs.py added 'mf_csa' model name

` prompt/interpreter and other files in prompt directory added code
``for accessing Csa_data and Model_free_csa functions
`` prompt/model_free_csa.py added csa extended model_free code
``(according to model_free.py)
` prompt/csa_data.py Class for manipulating CST and CSEA csa data.

` specific_fns/model_free_csa.py added csa extended model_free code
``(according to model_free.py)
` specific_fns/csa_data.py Class for manipulating CST and CSEA csa data.

`Instead of the only jw_mf.py file in the original version of the Relax
``program we added files:
`` jw_mf_csa1.py (calculate the spectral density function for the first
``CS subtensor)
`` jw_mf_csa2.py (calculate the spectral density function for the
``second CS subtensor)
`` jw_mf_csacross.py (calculate the cross correlation spectral density
``function between both CS subtensors)
`` jw_mf_dipY.py (calculate the vector of the spectral density
``functions for the dipole-dipole interactions to all nuclei Y, i.e. each
``component of vector correspond to the individual dipole-dipole interaction)
`

` direction_cosine_csa.py (calculate direction cosines of the
``principal axis of the two CS pseudo tensors and first and second
``derivations of the directions cosines with respect to the angles
``defining the orientation of the diffusion tensor)
`` direction_cosine_dipY.py (calculate direction cosines of the
``principal axis of the dipole-dipole interactions to atoms Y and first
``and second derivations of the directions cosines with respect to the
``angles defining the orientation of the diffusion tensor, data are store
``as a vector, in which each component correspond to the individual
``dipole-dipole interaction)
`

` weights_csa1.py (calculate the coefficient necessary to calculate
``the spectral density function for the first CS subtensor)
`` weights_csa2.py (calculate the coefficient necessary to calculate
``the spectral density function for the second CS subtensor)
`` weights_csaC.py (calculate the coefficient necessary to calculate
``the cross correlation spectral density function of the first and second
``CS subtensor ... the form of the equation is slightly different to previous)
`` weights_dipY.py (calculate the coefficient necessary to calculate
``the spectral density function for the first CS subtensor)
`

` mf_csa.py (analogy of mf.py, redirect the calculation according to
``the setup and initialize all necessary parameter)
``ri_comps_csa_dipY.py (analogy to ri_comps.py, prepare the linear
``combination of the spectral density functions and the constants
``corresponding to the each type of the relaxation mechanism
`i.e. instead of only
data.dip_jw_comps_func[i] ("i" goes over residues)
data.csa_jw_comps_func[i] ("i" goes over residues)
is necessary to introduce:
data.dip_jw_comps_func[i] ("i" goes over residues)

` data.dipY_jw_comps_func[j][i] ("i" goes over residues, "j" over
``atoms Y interacting with atom X)
` data.csa1_jw_comps_func[i] ("i" goes over residues)
data.csa2_jw_comps_func[i] ("i" goes over residues)
data.csaC_jw_comps_func[i] ("i" goes over residues)
and similarly for constants:
data.dip_const_func by function comp_dip_const_func

` data.dipY_const_func[i] by function comp_dipY_const_func ("j" over
``atoms Y interacting with atom X)
`` data.csa1_const_func[i] by function comp_csa1_const_func ("i" goes
``over spectrometer frequencies)
`` data.csa2_const_func[i] by function comp_csa2_const_func ("i" goes
``over spectrometer frequencies)
`` data.csaC_const_func[i] by function comp_csaC_const_func ("i" goes
``over spectrometer frequencies)
``similarly for gradients and Hessian. So far the fitting the distance to
``the selected neighbouring nuclei and the fitting of parameters of CS
``tensor is not included.
`

` ri_prime_csa_dipY.py (analogy of ri_prime.py, but relaxation rates,
``gradients and Hessians comprises all terms calculated by mf_csa.py )
`

` ri_csa_dipY.py (analogy to ri.py, but again the number of variables
``is enlarged by those introduced previously)
``
`All comments or suggestions are welcomed.
Pavel Kaderavek, Petr Novak