Download Instructions for CDPro:

These g-factor reference set files are formatted for use with the CDPro Circular Dichroism Deconvolution Software Package. Before they can be used, CDPro must be downloaded and installed, according to the instructions here.

Download Instructions for g-Factor Reference sets:

Right-click, and select "Save Target As..." on each of the download links on the top of this page. Unzip each file, and copy both the files (g6_26.ss and g6_26.cd) to the directory C:\CDPro\ .

These data files, archived under the filenames g6_26.ss and g6_26.cd, are also available from the laboratory of Prof. Robin L. Garrell, University of California, Los Angeles, P.O. Box 951569, Los Angeles, CA, 90095-1569, garrell@chem.ucla.edu.

Installation Instructions for g-Factor Reference sets:

It is recommended that the CDPro files Cddata.23 and Ssdata.23 be renamed and archived before creating g-factor reference set files, or else they will be overwritten and lost. The first reference set file, g6_26.ss, contains secondary structure assignments and should be named Ssdata.23 and placed in the CDPro directory. The second file, g6_26.cd, contains g-factor spectra and should be named Cddata.23 and placed in the CDPro directory.

The text files must be formatted exactly as they appear here. Ssdata.23 contains rows of protein names (1 space followed by up to 4 letters followed by carriage return) and rows of secondary structure fractions (3 spaces followed by alpha helix, 3₁₀ helix, beta sheet, beta turn, polyproline type II helix, and unordered fractions formatted as X.XXX with 3 spaces between each fraction and with a carriage return after the sixth fraction). Cddata.23 contains two lines of comments followed by rows of protein names (1 space followed by up to 4 letters followed by carriage return) and rows of g-factor spectra from 260 to 179 nm (1 data point per nm, with 2 spaces at beginning of the line followed by g-factor values multiplied by 1000 formatted as X.XX with 2 spaces between each value with 15 values per line and with a carriage return at the end of each line). Only spectral data for 240 to 185 nm is used in our reference set. (Other entries are filled with zeroes.) When using CRDATA in CDPro, IBASIS=2 should be chosen to select this g-factor reference set. The entries for these reference set files are composed of g-factor spectra from Peter McPhie (24 proteins) and of poly(L-proline) and poly(L-hydroxyproline).

Instructions:

1. Acquire CD and UV absorbance spectra from 185-240 nm, with resolution of one data point per nm or better, for the sample and background solutions.

2. Convert HT voltages to absorbance, and subtract background CD and UV spectra from the sample spectra.

3. Convert the CD spectrum to A_L-A_R (or DeltaOD) units.

4. Divide the DeltaOD spectrum by the absorbance spectrum to obtain the g-factor spectrum.

5. Multiply the g-factor spectrum by 1000. Reference set g-factor spectra have also been multiplied by 1000, and calculated g-factor spectra from SELCON3, CDSSTR, and CONTIN/LL will also be multiplied by 1000. This is necessary only for numerical formatting during the deconvolution.

6. Save the g-factor spectrum as a text file (tab-delimited). The text file should contain only wavelength (nm) and g-factor data (unitless, multiplied by 1000) in column format.

7. Copy the g-factor spectrum text file to the CDPro directory.

8. Launch CDPro and run the CRDATA program.

9. Answer the CRDATA questions as follows:

QUESTION	ANSWER
“Do you want to create a new INPUT file?”	0 (make new)
“Enter title for your data”	(<40 character description)
“Enter the number of CD values per nm”	5 (depends on resolution)
“Input INITIAL wavelength”	240 (the larger wavelength)
“Input FINAL wavelength”	185 (the smaller wavelength)
“Is the CD in molar ellipticity units?”	0 (no. no conversion performed.)
“ASCII file-name”	sample.txt (text file with g-factor data)
“Select a REFERENCE SET”	2 (for g-factor ref. set)

10. Run SELCON3, CDSSTR, and/or CONTIN/LL, included in CDPro.