| title | author | tags | |
|---|---|---|---|
Residual Dipolar Coupling SVD Fit Software for Python |
Justin L Lorieau |
|
The rdc_svd software fits residual dipolar couplings (RDCs) to a structure from the protein databank (PDB) using singular value decomposition (SVD).
- Conducts an SVD fit using the same input format as DC in NMRPipe.
- Capable of dealing with sum couplings, like in methylenes, using the '#' atom name. (ex: 'HA#' to fit both HA1 and HA2 of glycines.)
- Capable of fitting multiple conformers from multiple PDB files together.
- Custom weightings of RDC values in SVD fit.
- Detailed output of the Saupe tensor and fitting statistics.
- v1.1: 20160728. v1.1.tar.gz v1.1.zip
- v1.0: 20160727
$ ./rdc_svd.py -pdb test/*.pdb -dc test/hafp23_g8a.inp
Saupe(1): [ 1.24046551 0.30456653 -0.12318243 0.81267299 0.40941609]
Saupe(2): [ -7.93815366 6.16633859 6.11673696 -4.13554146 -10.0421545 ]
Saupe(3): [ 5.84082969 10.23609654 -9.57914833 13.20301772 9.35618703]
S_xyz(1): [ 1.6127692 -0.54233787 -1.07043132]
S_xyz(2): [ 14.63281043 -0.13731538 -14.49549505]
S_xyz(3): [-22.06437559 17.37816129 4.6862143 ]
Da(1): 0.806Hz, Dr(1): 0.176, Rh(1): 0.218
Da(2): 7.316Hz, Dr(2): 4.786, Rh(2): 0.654
Da(3): -11.032Hz, Dr(3): 4.231, Rh(3): 0.383
Q-factor: 3.5%
RMS (Hz): 0.450861536825
================================================================================================
conformer: atom(i) / atom(j) D_obs (Hz) D_pred (Hz) Delta (Hz) Scale
================================================================================================
test/2lwa_struc-a... F3-N / F3-H 4.700 5.059 -0.359 1.000
test/2lwa_struc-b... F3-N / F3-H
test/2lwa_struc-c... F3-N / F3-H
...
test/2lwa_struc-a... W21-CA / W21-HA 3.200 2.441 0.759 0.485
test/2lwa_struc-b... W21-CA / W21-HA
test/2lwa_struc-c... W21-CA / W21-HA
test/2lwa_struc-a... Y22-CA / Y22-HA -1.100 -2.686 1.586 0.485
test/2lwa_struc-b... Y22-CA / Y22-HA
test/2lwa_struc-c... Y22-CA / Y22-HA