Instructions for Using CDPro:
There are 10 reference sets (basis sets) in CDPro, and of these one (IBasis = 8) is created using CLUSTER program. These can be selected for analysis with any of the three softwares, SELCON3, CDSSTR and CONTINLL, by changing the IBasis (Basis_1) value in the INPUT file. [IBasis and Basis_1 are the same]
 
IBasis = 9 and 10 combine 13-MEMBRANE PROTEINS with 37- and 43-SOLUBLE proteins
 
All these programs and the output can now be accessed with ease in a browser environment (Netscape navigator, 4.7, frames compatible). Place the files in C:/CDPro directory and open RunCDPro.html in Navigator.

It also works in IE6.0 on a NT operating system.

 
IBasis
(Basis_1)
Wavelength Range
Number of Proteins
Secondary Structures
1
178-260 nm
29
6 (aR, aD, bR, bD, T, U)
2
178-260 nm
22
6 (a, 3/10, b, T, P2, U)
3
185-240 nm
37
6 (aR, aD, bR, bD, T, U)
4
190-240 nm
43
6 (aR, aD, bR, bD, T, U)
5
185-240 nm
37*
5 (a, b, T, P2, U)
6
185-240 nm
42
6 (aR, aD, bR, bD, T, U)
7
190-240 nm
48
6 (aR, aD, bR, bD, T, U)
8 190-240 nm various 6 (aR, aD, bR, bD, T, U)
9 185-240 nm 50 (37 SP and 13 MP)
6 (aR, aD, bR, bD, T, U)
10
190-240 nm 56 (43 SP and 13 MP) 6 (aR, aD, bR, bD, T, U)

List of proteins for IBasis = 3 and 5 are same; the secondary structure fractions are different -- option 3 splits the helix and sheet fractions, while option5 gives P2.

Results from IBasis values 1, 3, 4, 6 and 7, and 9 and 10, are comparable as the secondary structure fractions they estimate are identical (From DSSP assignments with regular and distorted helix and sheet structures). IBasis = 2 uses assignments from XTLSSTR program of King and Johnson and IBasis = 5 uses different types of structures from DSSP assignments (helix, sheet, turns, poly(Pro)II, and unordered) of secondary structure; results from these two options cannot be combined with those from others.
IBasis = 8 uses tertiary class specific protein set. Use CLUSTER to create the required files before using this option.

To analyze your CD spectrum: