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DC: Servers for Dipolar Coupling Calculations

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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:

[ Hide Advanced Error Analysis Options ]

Error Analysis by Randomized Couplings
Number of Trials with Randomized Couplings.
Number of Standard Deviations for Randomizing Coupling Values.
Error Analysis by Randomized Coordinates
Number of Trials with Randomized Coordinates. DI Values will be held fixed.
Standard Deviation for Randomized Coordinates, Angstroms.
Error Analysis by Cross-Validation (CV) with Randomized Deletion
Number of Cross-Validation Trials.
Approximate Fraction of Data to Keep for Each Trial.
Select by ResID Use this option to select couplings according to Residue ID during randomized cross-validation. In this mode, when a coupling is randomly selected for deletion, all couplings for that residue will be deleted as well.
Error Analysis by Systematic Cross-Validation (CV)
Systematic CV Use this option to perform error analysis by systematically selecting each coupling one at a time for cross-validation.
Select by ResID 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.

[ Hide Advanced Error Analysis Options ]


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last update: Apr 2 2012