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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
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