link to RWJMS home page
About the FacilityAbout the FacilityAbout the Facility
About Circular DichroismAbout Circular DichroismAbout Circular Dichroism
moreFee Schedule and Policies
Experimental GuidelinesExperimental GuidelinesExperimental Guidelines
moreContact Us

Experimental Guidelines

Data Analysis

Other Programs

The following information about the use of programs and links to the programs are provided by Norma J. Greenfield.

Two self extracting files, which contain programs for estimating protein secondary structure from CD data, can be downloaded from this web site. They are: CD1.EXE and CD2.EXE (right click on file names to download.) These files are DOS files. The programs run under DOS, or in DOS windows in Windows 95, 98, XP or OS/2. Make a directory to house the files - e.g. type "mkdir cd" copy CD1.EXE to the directory e.g. type "copy cd1.exe cd" enter the cd directory by typing "cd cd" Type "CD1 -d" to unzip the file. The "-d" is necessary to keep the correct paths. The files can also be unzipped using WinZip. Make a subdirectory to house the K2D program. e.g. type mkdir \cd\k2d. Copy the CD2 file to the k2d subdirectory e.g. type "copy cd2.exe \cd\k2d" Unzip the k2d program by typing CD2) The files created by CD1.EXE and CD2.EXE are described more fully below. Please read the instructions before using these files. Occasionally these files do not download properly. Some web browsers download them as ASCII files.

A program deconvoluting sets of data into its components using singular value decomposition can also be downloaded from this site. This program runs under Windows 95/98 or NT. The file is a gift from Takashi Konno. The file is called SVD1.EXE (right click on file name to download.) Instructions for the SVD program are in the file README.SVD (right click on the file name to download.)

Instructions for using the programs in CD1.EXE and CD2.EXE

The computer programs created by running CD1.EXE and CD2.EXE are compiled programs which will run on IBM compatible computers. In addition the files create programs to convert data collected on AVIV, JASCO and OLIS, instruments to the required format for each program.

Instructions and references for each program are in the files named README.1ST in each subdirectory.

In most cases the source code is included in FORTRAN, QBASIC or C. The FORTRAN programs can be compiled and run on UNIX based machines. The programs are all very primitive. To use the programs one first must convert the CD data into the proper format for each program using the programs called CDCONVRT or RAW2XXX, where XXX are the first three letters of the name of the subdirectory with the programs of interest. (Note at present only the CDCONVRT program can be used with OLIS data.) The easiest method of converting the data is to enter the subdirectory containing the analysis program of interest and run the conversion programs from that directory. That way the files needed for each program will be in the proper directory.

After converting the data one runs the analysis program. Then one reads the output files with a text editor. (Note that most of the output files have different names, e.g. output, out.out, etc. ) In some cases, the calculated best fit curves can be viewed using programs called PLOTXXX. Complete directions and references are in the files called README.TXT in each subdirectory.

CD1.EXE will create the following subdirectories: CCA, CONTIN, JOBIN, LINEAR, SELCON, USEFUL and VARSLC

LINEAR contains three programs for fitting data using least squares regression.

MLR.EXE is a non-constrained least squares analysis program.

LINCOMB.EXE is a constrained least squares analysis program of Fasman.

Perczel, A., Park, K., and Fasman, G.D. (1992) Anal. Biochem. 203, 83-93.

G&F.EXE is the original method of Greenfield and Fasman.

Greenfield, N., and Fasman, G.D. (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8, 4108-4116.

CONTIN contains the ridge regression procedure of Provencher and Glöckner.

S.W. Provencher & J. Glöckner: Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20, 33 (1981).

Link to Provencher

SELCON contains programs to estimate protein conformation using the self-consistent method of Sreerama and Woody.

Sreerama, N and Woody, R.W. A self-consistent method for the analysis of protein secondary structure from circular dichroism.
Anal Biochem. 1993 Feb 15;209(1):32-44.

Sreerama N and Woody, R.W. Protein secondary structure from circular dichroism spectroscopy. Combining variable selection principle and cluster analysis with neural network, ridge regression and self-consistent methods. J Mol Biol. 1994 Sep 30;242(4):497-507.

Sreerama N, Woody RW. Poly(pro)II helices in globular proteins: identification and circular dichroic analysis. Biochemistry. 1994 Aug 23;33(33):10022-5.

VARSLC contains the variable selection program of Manavalan and Johnson.

Manavalan, P., and Johnson, W.C. Jr.
Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra.
Anal Biochem. 1987 Nov 15;167(1):76-85.

Link to Johnson

CCA contains the convex constraint algorithm of Perczel et al.

References for the CCA program:

Perczel, A., Holl¢si, M., Tusnady, G., and Fasman, G.D. (1991) Prot. Eng. 4, 669-679.
Perczel, A., Park, K., and Fasman, G.D. (1992) Anal. Biochem. 203, 83-93.

Link to Perczel

CD2.EXE is a self extracting file containing the K2D program of Andrade et al .

Andrade, M.A., Chacon, P., Merolo, J.J., and Moran, F. (1993) Prot. Engin. 6, 383-390.

Link to Andrade

USEFUL is a subdirectory with files containing protocols for protein determination and for estimating the helical content of proteins from the ellipticity at 222 nm and 208 nm. JOBIN contains programs for converting files from JOBIN spectrometers to a format which can be used by the analysis programs (The Jobin conversion programs have not been debugged since I did not have access to the raw data files.)

The installation disks will also create the program called CDCONVRT.EXE that can convert any x,y file of CD data, where x is wavelength in nm and y is ellipticity in millidegrees or mean residue ellipticity, to the proper formats for the SELCON, VARSLC, CONTIN, K2D, LINCOMB, MLR and G&F programs. The intervals between the data points must be even and the data file may not have spaces between lines. Data sets must begin and end at integer values of wavelengths, e.g. 180.0 nm, not 180.5. The x and y values may be separated by commas, spaces or tabs but each x,y pair must be on a separate line. The order of the wavelengths does not matter, they may either increase or decrease. When the output is for the SELCON program, the output file must be named or renamed test.dat before the SELCON program is run.

Home Pages

Other Useful Files

  • THERMODYNAMICS contains useful files in SigmaPlot formats for calculating thermodynamic properties of the folding of peptides and proteins from CD data.
  • BINDING CONSTANTS contains useful files in SigmaPlot formats for calculating binding constants from changes in CD as a function of ligand concentration.