Bax Group DC Server - Restrained Fit of Dipolar Couplings Using Non-Linear Least-Squares

From the Bax Group at the National Institutes of Health ...
DC: Servers for Dipolar Coupling Calculations

Restrained Fit of Dipolar Couplings to a PDB Structure
Using Non-Linear Least-Squares

See Also:

About DC: Server-Based Tools for Dipolar Coupling Calculations
NMR Server PDB Utilities to Add Protons, Align Structures, etc
NMRPipe Table Format

Contacts:

Frank Delaglio delaglio@nih.gov

Ad Bax bax@nih.gov

	PDB Input: Input PDB file of the protein structure. Atom names in the PDB file must exactly match the names used in the dipolar coupling input. Example: ubiq.pdb
	Dipolar Coupling Input: Input table of dipolar couplings associated with a given alignment medium. DC Web Page. Examples: dObsA.tab (Neutral Bicelle Sample) \| dObsB.tab (Charged Bicelle Sample). [ More Info ]
Keep Existing DI Values	Dipolar Interaction Values: Select this option to use existing Dipolar Interaction (DI) values in the input table. Otherwise, DI values will be calculated according to information in the PDB file. [ More Info ]
	Residue Selection: Selection of Residues for the DC calculation, as a list of residue IDs or ranges separated by spaces. Use keywords `First` and `Last` for the lowest and highest residue IDs, respecively. To specify a range of residues, use the keyword `to`, for example: `22 to 34`. [ More Info ]
Generate DC Graphics	Graphical Output: Select this option to generate graphs of the DC results. Example DC graphics for a protein: dc.pdf tensor.gif Example DC graphics for a small molecule: dcmol.pdf tensormol.gif

Tensor Magnitude (Da) and Rhombicity (Rh) Values and Ranges [ More Info ]
Select the `Fixed` checkbox to ignore Min/Max limits and hold the corresponding parameter fixed during the fit. Da can vary from -1.0 to 1.0, but is usually in the range of -1.0e-3 to 1.0e-3. Rh can vary from 0.0 to 2/3.
Magnitude Da:	Da Min:	Da Max:	Fixed Da:
Rhombicity Rh:	Rh Min:	Rh Max:	Fixed Rh:

Tensor Rotation Values and Ranges [ More Info ]
These 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:

[ Show Advanced Error Analysis Options ]

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last update: Apr 2 2012