CD Analysis Using CDPro via the Internet Browser
Some of the frequently asked questions are available in FAQ.html
Old readme file is accessed here


1. Create INPUT:

The INPUT file looks like:
 

#
# PRINT    IBasis   
      0         1       
#
# 1 Title Line
 SAMPLE INPUT:  Lactate Dehydrogenase CD DATA (178-260 nm)
#
#    WL_Begin     WL_End       Factor
     260.00000    178.00000    1
#
# CD DATA (Long-Wavelength to Short-wavelength; 260-178 nm LIMITS)
  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -0.03 -0.07
 -0.12 -0.18 -0.25 -0.33 -0.43 -0.54 -0.67 -0.82 -0.99 -1.19 -1.41 -1.65 -1.92 -2.20 -2.49
 -2.79 -3.11 -3.43 -3.71 -3.93 -4.10 -4.22 -4.29 -4.32 -4.31 -4.28 -4.22 -4.15 -4.06 -3.97
 -3.87 -3.78 -3.71 -3.67 -3.64 -3.60 -3.53 -3.36 -3.05 -2.60 -2.04 -1.40 -0.68  0.22  1.38
  2.68  4.00  5.32  6.63  7.74  8.46  8.91  9.20  9.27  9.02  8.45  7.60  6.63  5.69  4.80
  3.95  3.15  2.40  1.71  1.11  0.58  0.12 -0.30
#
#  IGuess  Str1   Str2   Str3   Str4    Str5    Str6
        0
  • The lines starting with # are required and the data is read free of formatting. Please do not have more than required values in the INPUT file. The CD data should be with in 260 - 178 nm (examples: (1) 260 - 178 nm; (2) 250 - 182 nm; (3) 240 - 180 nm; (4) 240 - 193 nm; (5) 255 - 188 nm; etc.)
  • CD Data should be in per residue De (M-1 cm-1) units.
  • A driver program, CRDATA written in FORTRAN, is provided to convert the ASCII data (wavelength, CD data on each line)--a text file -- to INPUT file is provided. For details of INPUT file check out INPUT.htm file.

Execute the CRDATA program
 

The INPUT file can be edited (changing the Print Option and Reference set Option) using a text editor. Be sure to save as a text file with no extensions!

Multiple sets of DATA can be analyzed in one run. All data sets should be contained in the INPUT file, sequentially.

OUTPUT files will contain results for all data sets contained in the INPUT file.



2. Analyze CD data using CDPro suite of programs
 
  • Before proceeding please check the INPUT file. If you need to change certain values, such as IBasis, please do so using a text editor and save the file.
  • CDPro has three programs for CD analysis (SELCON3, CDSSTR and CONTINLL) and one program for determining the tertiary class (CLUSTER).
  • Excuting CLUSTER determines the tertiary class of the protein from the CD spectrum and creates a reference set, specific to the protein, for analysis. The input file will also be modified accordingly (IBasis = 8).
  • You may use the reference set of proteins determined by CLUSTER and execute the other three programs.
  • Alternatively, you can change the IBasis value to choose one of the reference sets (largest protein set depending on the wavelength range; for example, if the wavelength range is 250 - 187 nm, then the 37-protein set or if the wavelength range is 250 - 195 nm then the 43 protein set) by editing the INPUT file and run the analysis.
  • Everytime the analysis is performed the output files are written over, so be sure to save them with a different name or print them.
Execute Program (Click on the name)
 
CLUSTER SELCON3 CDSSTR CONTINLL

Program CLUSTER determines the tertiary class and creates the reference set based on that information. It also modifies the INPUT file (IBasis = 8). If interested in that analysis, you will need to run the three CD analysis programs with the newly created INPUT file.



3. Results: Check OUTPUT files (Click on the name)
 
SELCON3 CDSSTR CONTINLL CLUSTER
SELCON3.OUT
PROTSS.OUT
CALCCD.OUT
BASIS
 CDSSTR.OUT
PROTSS.OUT
RECONCD.OUT
CONTINLL.OUT
PROTSS.OUT
CONTIN.OUT
BASIS.PG
SUMMARY.PG
CONTIN.CD
CLUSTER.OUT
INPUT

Files:
 
Selcon3.out OUTPUT from Selcon3 Program
ContinLL.out OUTPUT from ContinLL program
CDsstr.out OUTPUT from CDsstr program
ProtSS.out Final result from each of the three programs, APPENDED!
CalcCD.out Calculated CD spectra from Selcon3 program
ReconCD.out Calculated & Reconstructed CD spectra from CDsstr program
Basis Details of the reference set used in Selcon3
Basis.PG Details of the reference set used in ContinLL
Summary.PG Detailed output from each of LL combinations in ContinLL
Contin.out Output from CONTIN in the final iteration from ContinLL
Contin.CD Calculated CD spectra from CONTINLL program


4. How to read the results?
 
 

Compare final results from each program, summarized in ProtSS.out. ProtSS.out is appended; be sure to check the last three lines. 
If the results from three programs are similar then the analysis is reliable, and  you can average the secondary structure fractions. 

If the results from the three programs differ considerably, then they are unreliable. There may be a problem with the Input data or the Input CD spectrum may not be well-represented in the reference proteins.

One can also check the output from individual programs and look for problems in the analysis.

Calculated CD spectra from the three programs are given in files: CalcCD.OUT (SELCON3), reconCD.OUT (CDSSTR), and CONTIN.CD (CONTINLL)