1 ###############################################################################
2 # NOTE: Output options can be "turned off" by placing a "#" symbol in front #
3 # of the line declaring the location of the output file. #
4 # Output locations are by default a directory. However, you can ouptut to #
5 # a file name by entering the name in this config file, i.e.: #
6 # change log dir = <DIRECTORY NAME> #
7 # to log = <FILE NAME> #
8 # Important: DIRECTORY NAMES should end with the character "/". #
12 ##############################################################################
13 # The scoring methods include: MultiCoil, PairCoil, NEWCOILS, HMMCoil #
14 # For more advanced users (me) using pos mode, is also ActualCoil. #
16 prn = .5 #The bound controls what is classified as a coiled coils.
17 no GUI #Including the "no GUI" option allows for the creation of
18 #ouput files without going through the on screen interface.
21 ##############################################################################
22 # The window length determines how many residues contribute to each #
23 # score computation. #
24 # If the window lengths are changed, then different conversion files #
25 # will be used from the conversion directory (see below). #
26 # Currently sizes 28 and 21 are allowed. Size 28 is recommended. #
30 ##############################################################################
31 # These values determine which distances are used as scoring #
32 # dimensions by the programs. MultiCoil only allows at most 6 scoring #
33 # dimensions total for the 2 scoring tables (1=dimer, 2=trimer). #
34 multi_lib dim 1 = 3 4 5
35 multi_lib dim 2 = 2 3 4
40 ##############################################################################
41 # The printfile is the postscript file for a hard copy of the #
42 # graphical display (obtained by pressing the "print" button. #
43 # The default size of the printed display holds 300-350 residues per #
44 # line, but the user can increase this by entering the number with the #
45 # residues per line command. The "one print line" command can also be #
46 # used to fit the entire
47 # the display is around 300-350, but that can be changed with the #
48 # "ps res per line" option or the "one print line" option to customize #
49 # your hard copy (the output picture will be fit to the page). #
52 ##############################################################################
53 # Sequences scoring above the bound (set above) are output to the log #
54 # file. The "Show Seq" option causes the sequence and the predicted #
55 # coiled coil registers to be printed out. Otherwise, only the scores #
56 # and locations of the high scoring regions are output. #
59 ##############################################################################
60 # Sequence scores (seq scores) give a single dimeric and trimeric #
61 # to the entire sequence (based on a weighted average or residue #
62 # scores). If the "Just Scores" option is enabled, then the scores #
63 # will NOT be labelled by the identification tags (seq code and name). #
66 #############################################################################
67 # Only one method for outputting "out" file can be done at a time. #
68 # Using "out" method, gives a file of positions, scores, and registers. #
69 # Using "sparse_out" gives a list of the dimer and trimer probabilities #
70 # scoring above the bound without any labels (useful for plotting).#
72 #out dir = ~/MULTICOIL/TEST_RUNS/
73 #sparse_out dir = ~/MULTICOIL/TEST_RUNS/
77 ##############################################################################
78 # Gaussian files are precomputed data files used to convert the #
79 # MultiCoil scores into prediction probabilities. #
80 # The likelihood files convert the PairCoil Scores into Probabilities. #
83 ##############################################################################
84 # Table 1 is the table of data to estimate the residues probabilities #
85 # in DIMERIC coiled coils. Table 2 is for TRIMERIC coiled coils. #
86 table1 = ../cgi-bin/lib/dimer28.txt
87 table2 = ../cgi-bin/lib/trimer28.txt
88 genbnk = ../cgi-bin/lib/genbnk.txt
90 gauss_param combo = ../cgi-bin/lib/gauss_parameters_combo28