Bax Group DC Server - Fit Dipolar Couplings of Helix Using SVD

Dipolar Coupling Input and Options Limited to RDCs collected in a single alignment medium. Better to include RDCs for only the residues in the desired single ɑ-helix, otherwise the residues in the desired ɑ-helix can be specified in the Residue Selection option. Note that the residue numbers of the helix are limited to 1-999. Example for the ɑ-helix of Ubiquitin (residues I23 to E34): dObsA_H1.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_H1.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 Select residues in the helix for alignment tensor calculation, as a list of residue numbers or ranges separated by comma. [More Info] Residue Selection: Graphical Output: Select this option to generate graphs of the DC results. Example DC graphics: dcp_viewer.html tensor.gif Generate DC Graphics
PDB Input (Optional) Target Type: Select whether the structure input should be treated as a protein helix or as a nucleic acid duplex. Proteins Nucleic Acids PDB Input: Atom names in the PDB format file must exactly match names used in the RDC input file. If not specified, the Helix-Fit is performed only using the refined ideal helix by the server. Example: ubiq.pdb PDB Input: Atom names in the PDB format file must exactly match names used in the RDC input file. The PDB input is optional for nucleic acids; if omitted, the server can generate an ideal duplex from the strand sequence and nucleic acid type specified below. PDB Ensemble Input: Must be preprared in a single PDB file and with the `MODEL/ENDMDL` keywords to indicate multiple conformers. 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 Select this option to run Helix-Fit using the refined ideal helix, for which the coordinates are aligned to input helix coordinates. (optional: download ideal helix coordinates here) Replace helix coordinates by idealized helix coordinates When Nucleic Acids is selected, specify the input strand sequence and the nucleic acid type below. These values will be submitted to the server for ideal duplex generation and RDC fitting. Input Strand Sequence: Enter the strand sequence in the 5' to 3' direction using one-letter base codes. Nucleic Acid Type: B-form DNA A-form RNA
Submission Details Email Confirm Email Calculation results will be sent by Email (results typically will be sent in less than a few minutes).

	From the Bax Group at the National Institutes of Health DC: Servers for Residual Dipolar Coupling Calculations Helix-Fit: Fit RDCs To Ideal ɑ-Helix