Hi, I've now created a special task for attaching patches and other files (https://gna.org/task/index.php?6397). After acceptance by voting to become a relax developer, attaching files to this task will no longer be necessary.
Regards, Edward On Fri, Dec 12, 2008 at 2:46 PM, Pavel Kaderavek <[email protected]> wrote: > 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 > > > _______________________________________________ > 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 > _______________________________________________ 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
