Bax Group DC Server - Fit Dipolar Couplings to PDB Structure Using SVD

Dipolar Coupling Input RDC Input File: Limited to RDCs collected in a single alignment medium. Example: dObsA.tab [More Info] RDC Input(s) [Multiple Files Allowed]: RDCs measured from collected in different alignment media should be stored in separate input files (press and hold the Ctrl key to select multiple files in Windows or the Command key in MacOS) Input table of dipolar couplings associated with a given alignment medium. Examples: inD_GB1_B.tab (Bicelle GB1 Sample). [More Info] Input table of dipolar couplings associated with a given alignment medium. Examples: inD_apoMBP.tab (apo-MBP Sample). [More Info] Use Standard Dipolar Interaction(DI) Values: Unselect to use DI values from the input table ('DI' column; dObsA.tab). If unselected while lacking DI values in input table, DI is calculated from PDB file coordinates. [More Info] Use standard DI Values Override Error Limit: If the input table (dObsA.tab) lacks experimental errors ('DD' column), or the input error is unrealistically small, the default lower limit of [DI_pq/DI_HN] Hz is used. Select this option to overwrite the lower limit. Override Error Limit Use C-C Bond for Methyl: Select this option to use ¹³C-¹³CH₃ bond rather than the ¹³C-¹H vectors for RDCs of methyl groups. (Example RDC input: inD_methyl_msg.tab) Use Methyl CC RDCs
PDB Input PDB Input: Atom names in the PDB format file must exactly match names used in the RDC input file. Example: ubiq.pdb PDB Ensemble Input: Must be preprared in a single PDB file and with the `MODEL/ENDMDL` keywords to indicate multiple conformers. Example: 2mjb.pdb PDB Ensemble Input: Must be preprared in a single PDB file and with the `MODEL/ENDMDL` keywords to indicate multiple conformers. Example: 3gb1.pdb PDB Ensemble Input: Must be preprared in a single PDB file and with the `MODEL/ENDMDL` keywords to indicate multiple conformers. Example: 1omp_3mbp_ens.pdb Select this option to add H atoms to the input PDB file, hydrogen atoms will be replaced if already present. [More Info] Add hydrogens to PDB
Options Select residues for alignment tensor calculation, as a list of residue numbers or ranges separated by comma. [More Info] Residue Selection: Use same selection for validation Select residues for validating/evaluating the fitting performance (RMS, Q-factors, etc.). If not specified, the same Selection of Residues for tensor calculation is used. Residue Selection for Validation: Fit RDCs to ensemble of conformers in PDB file (click to display options). Ensemble Fit (Single Tensor) SVD ensemble fit with all conformers equally weighted. Unweighted SVD Fit Variable weight ensemble fit (VWFit), with conformer weights Monte-Carlo optimized. Variable Weight Fit (VWFit) Increasing scale factor C reduces the number of significantly populated conformers. Constant Coefficient C Align conformers to the first one (for CA, C, N atoms). See more alignment options here. Align Ensemble Conformers Select residues for coordinate alignment, as multiple residue numbers or ranges separated by comma, e.g., `2-8, 11, 13-72` for residues 2 to 8, 11, and 13 to 72. All residues are used if left blank Residue Selection Range: Select a maximal subset of the residues clustered within a given distance cutoff. The maximal subset is selected by an iterative MaxSub procedure. ^[reference] MaxSub Selection Distance cutoff: Å For each Input Ensemble conformer, a separate alignment tensor will be used for the fit. Multi-Tensor Multi-conformer Fit Using SVD-fitted tensors. Note that multi-tensor multi-conformer SVD fits with > 2 tensors often results in overfitting!. SVD-optimized conformer weight is reflected in Da. Using SVD-Fitted Tensors Using alignment tensors calculated from the hydrodynamic shape of each conformer. ^[reference] Using Hydrodynamic Shape Tensors Graphical Output: To generate graphs of the DC results. Examples: tensor.gif, dcp_viewer.html Generate DC Graphics
Advanced Error Analysis Options [More Info] Evaluates how random RDC errors impact the fitted alignment tensor (adds random error to exp values). [example output] Randomized Couplings Number of Trials with Randomized Couplings [0:5000]. Standard Deviations (in Hz) for Randomizing Coupling Values [0:100]. Evaluates how uncertainties in the atomic coordinates impact the alignment tensor and fit quality. Adds coordinate noise to the PDB input file. [example output] Randomized Coordinates Number of Trials with Randomized Coordinates [0:5000]. Standard Deviation [in Angstroms] for Randomized Coordinates [0:100]. Jackknifed cross-validated fits: For N RDCs, one of the couplings is deleted in each of N trials, with the fit performed on the remaining N-1 RDCs. [example output] "Jackknifed" Cross-Validation Use this option to select couplings according to Residue ID during systematic cross-validation. In this mode, when a coupling is selected for deletion, all couplings for that residue will be deleted as well. Select by ResID Evaluates reproducibility of alignment tensor when randomly omitting of a small percentage of the RDCs. [example output] Cross-Validation by Randomized Deletion Number of Cross-Validation Trials. [0:5000]. Approximate Fraction of Data to Keep for Each Trial. [0:1.0]. Select RDCs according to Residue ID during randomized cross-validation. In this mode, all RDCs for a selected residue are deleted. Select by ResID
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