############################################################################### # NOTE: Output options can be "turned off" by placing a "#" symbol in front # # of the line declaring the location of the output file. # # Output locations are by default a directory. However, you can ouptut to # # a file name by entering the name in this config file, i.e.: # # change log dir = # # to log = # # Important: DIRECTORY NAMES should end with the character "/". # ############################################################################## # The scoring methods include: MultiCoil, PairCoil, NEWCOILS, HMMCoil # # For more advanced users (me) using pos mode, is also ActualCoil. # method = MultiCoil prn = .5 #The bound controls what is classified as a coiled coils. no GUI #Including the "no GUI" option allows for the creation of #ouput files without going through the on screen interface. ############################################################################## # The window length determines how many residues contribute to each # # score computation. # # If the window lengths are changed, then different conversion files # # will be used from the conversion directory (see below). # # Currently sizes 28 and 21 are allowed. Size 28 is recommended. # window length = 28 ############################################################################## # These values determine which distances are used as scoring # # dimensions by the programs. MultiCoil only allows at most 6 scoring # # dimensions total for the 2 scoring tables (1=dimer, 2=trimer). # multi_lib dim 1 = 3 4 5 multi_lib dim 2 = 2 3 4 #pair_lib = 1 2 4 ############################################################################## # The printfile is the postscript file for a hard copy of the # # graphical display (obtained by pressing the "print" button. # # The default size of the printed display holds 300-350 residues per # # line, but the user can increase this by entering the number with the # # residues per line command. The "one print line" command can also be # # used to fit the entire # the display is around 300-350, but that can be changed with the # # "ps res per line" option or the "one print line" option to customize # # your hard copy (the output picture will be fit to the page). # ############################################################################## # Sequences scoring above the bound (set above) are output to the log # # file. The "Show Seq" option causes the sequence and the predicted # # coiled coil registers to be printed out. Otherwise, only the scores # # and locations of the high scoring regions are output. # Show Seq ############################################################################## # Sequence scores (seq scores) give a single dimeric and trimeric # # to the entire sequence (based on a weighted average or residue # # scores). If the "Just Scores" option is enabled, then the scores # # will NOT be labelled by the identification tags (seq code and name). # ############################################################################# # Only one method for outputting "out" file can be done at a time. # # Using "out" method, gives a file of positions, scores, and registers. # # Using "sparse_out" gives a list of the dimer and trimer probabilities # # scoring above the bound without any labels (useful for plotting).# #out dir = ~/MULTICOIL/TEST_RUNS/ #sparse_out dir = ~/MULTICOIL/TEST_RUNS/ ############################################################################## # Gaussian files are precomputed data files used to convert the # # MultiCoil scores into prediction probabilities. # # The likelihood files convert the PairCoil Scores into Probabilities. # ############################################################################## # Table 1 is the table of data to estimate the residues probabilities # # in DIMERIC coiled coils. Table 2 is for TRIMERIC coiled coils. # table1 = ../cgi-bin/lib/dimer28.txt table2 = ../cgi-bin/lib/trimer28.txt genbnk = ../cgi-bin/lib/genbnk.txt gauss_param combo = ../cgi-bin/lib/gauss_parameters_combo28 log = data.log out = data.out