See the documentation page for further information on this script, and data source references.



Select input files and output format
Output bargraph of secondary shifts
Output plaintext secondary shifts
Output comparison of secondary structure from shifts with that from dihedral angles***
Output plaintext torsion angles
Choose PDB file to upload:
Choose STR file to upload:
Choose source of random coil chemical shifts (SDB* format):
     Upload own random coil chemical shift file
     Correct random coil shifts from this data set for primary sequence**

Advanced Settings
PDB TM Shift Calculations
Consider only solvent-exposed or transmembrane segments****
Local Structure Averaging
Average PDB structure according to local consensus
Length of frame (residues)
Minimum frame agreement for structural averaging
Minimum agreement amongst ensemble members for defined secondary structure

Atom type and threshold selection
Shifts to consider in analysis (e.g. HA, CA, HB, and/or CB):
Shift significance thresholds for HA (For Helix, Sheet; d ppm):
Shift significance thresholds for CA (For Helix, Sheet; d ppm):
Shift significance thresholds for HB (For Helix, Sheet; d ppm):
Shift significance thresholds for CB (For Helix, Sheet; d ppm):
Plot Settings
Use own legends for bargraph
Scale of graph (1/d ppm):
    Suggested: 1 for C shifts, 10 for H shifts
Height of graphical output (in pixels):
Colour Settings
Bar colour (for first SDB selection)
    (RBG format: e.g. (255, 255, 255))
Iteration for subsequent SDBs
    (+/- to initial values):
Background colour:
Text colour:
Line colour:
Threshold colour:
* Please see script documentation for format of SDB files.
** Please see script documentation for references.
*** A locally-executable script is available to convert output from this option to a "percent agreement with PDB" and per-amino acid breakdown. **** Requires a PDB parsed with data from the PDB TM database. Please see script documentation for further information.

© 2009 Jan K. Rainey