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 |
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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. |
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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.
SELCON3 CDSSTR CONTINLL CLUSTER SELCON3.OUT
PROTSS.OUT
CALCCD.OUT
BASISCDSSTR.OUT
PROTSS.OUT
RECONCD.OUTCONTINLL.OUT
PROTSS.OUT
CONTIN.OUT
BASIS.PG
SUMMARY.PG
CONTIN.CDCLUSTER.OUT
INPUTFiles:
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.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) |