Bax Group DC Server - Constrained least-squares fit of RDCs to atomic coordinates

Dipolar Coupling Input

Dipolar Coupling Input: Limited to RDCs collected in a single alignment medium. Example: dObsA.tab [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

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, see example: 2mjb.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 constrained least-squares fit, as multiple residue numbers or ranges separated by comma. [More Info]

Residue Selection:

Fit RDCs to ensemble of conformer in PDB file (click to display options).

Ensemble Fit

Restraints for Tensor Magnitude (Da) [Hz] [ More Info ]
Select the Fixed checkbox to ignore Min/Max limits and hold the corresponding parameter fixed during the fit.
Da is usually in the range of -100 to 100 Hz.

Da:	Da Min::	Da Max:

Fixed Da:

Restraints for Rhombicity (Rh) [ More Info ]
Select the Fixed checkbox to ignore Min/Max limits and hold the corresponding parameter fixed during the fit.
Rh can vary from 0.0 to 2/3.

Rh:	Rh Min::	Rh Max:

Fixed Rh:

Restraints for Tensor Rotations RX RY RZ [ More Info ]
RX, RY and RZ are the angles in degrees which rotate the PDB coordinates onto the alignment tensor frame. Select the Fixed checkbox to ignore Min/Max limits and hold a given angle fixed during the fit:

Rotation RX:	RX Min::	RX Max:

Fixed RX:
Rotation RY:	RY Min::	RY Max:

Fixed RY:
Rotation RZ:	RZ Min::	RZ Max:

Fixed RZ:

Graphical Output: To generate graphs of the DC results. Examples: tensor.gif, dcp_viewer.html

Generate DC Graphics

Submission Details

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	From the Bax Group at the National Institutes of Health DC: Servers for Residual Dipolar Coupling Calculations Constrained Least-Squares (CLS) Fit of RDCs to Atomic Coordinates