According to the What's New in 2.1:
2. New threading programs are integrated.
LOMETS in I-TASSER V1.0 includes five threading programs for protein fold-
recognition and template identification. In I-TASSER V2.0, three new
threading programs with a novel sequence profile generation stratagy are
added.
Indeed, runI-TASSER.pl does run 8 threading programs, in the following order:
PPA
dPPA
dPPA2
sPPA
MUSTER
wPPA
wdPPA
wMUSTER
However, when I look in my init.dat, only the following 5 threading program are included:
MUSTER
dPPA
wdPPA
wMUSTER
wPPA
Here is a sample output from a init.dat (first 15):
152 4.228 1 4mh6A MUSTER
147 4.384 2 1dk8A dPPA
127 4.830 3 3hefB wdPPA
149 3.845 4 1axnA2 wMUSTER
126 4.201 5 2crwA wPPA
153 3.620 6 4kqtA MUSTER
146 4.308 7 4mh6A dPPA
110 4.562 8 2c5uA2 wdPPA
149 3.517 9 4mh6A wMUSTER
112 4.110 10 3o47A1 wPPA
150 3.597 11 1axnA2 MUSTER
137 4.188 12 3rauA2 dPPA
125 4.562 13 2crwA wdPPA
149 3.480 14 3du6A3 wMUSTER
118 3.785 15 2crrA wPPA
runI-TASSER.pl uses mkinit.pl to generate the init.dat.
I believe the following bold line in mkinit.pl might be the guilty one:
#!/usr/bin/perl
use Math::Trig;
$datadir="$ARGV[1]";
$librarydir="$ARGV[0]";
$M=5; #### in an order of confidence
%NAME=(
1=>"MUSTER",
2=>"dPPA",
3=>"wdPPA",
4=>"wMUSTER",
5=>"wPPA",
6=>"dPPA2",
7=>"PPA",
8=>"sPPA",
);
...
########## read templates #############
$M0=0;
for($m=1;$m<=$M;$m++)
What do you think?