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View Code? Open in Web Editor NEWProgram to calculate alpha-helical propensities
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Min flag not working
Example input:
helix --seq="{D,E,I,Q,A,L,E,E,E,N,A,Q,L,E,Q,E,N,A,A,L,E,E,E,I,A,Q,L,E,Y,G}" --pH=7.0 --salt=L --findAll --min
Output:
No. of command line parameters: 5
argument 1: --seq={D,E,I,Q,A,L,E,E,E,N,A,Q,L,E,Q,E,N,A,A,L,E,E,E,I,A,Q,L,E,Y,G}
Input sequence: {D,E,I,Q,A,L,E,E,E,N,A,Q,L,E,Q,E,N,A,A,L,E,E,E,I,A,Q,L,E,Y,G}
argument 2: --pH=7.0
pH: 7.000000
argument 3: --salt=L
Salt concentration: L
argument 4: --findAll
Looking up all features
argument 5: --min
Writing minimal output only
----------------
The sequence and initial parameters are:
w' w vN vC N C
1 D- 0.360 0.340 0.060 0.050 6.500 1.500
2 E- 0.790 0.700 0.045 0.042 2.100 0.710
3 I 0.730 0.470 0.050 0.050 1.250 0.660
4 Q 0.830 0.540 0.050 0.046 0.360 0.890
5 A 1.540 1.580 0.041 0.037 0.900 1.000
6 L 1.100 0.940 0.040 0.040 0.900 1.100
7 E- 0.790 0.700 0.045 0.042 2.100 0.710
8 E- 0.790 0.700 0.045 0.042 2.100 0.710
9 E- 0.790 0.700 0.045 0.042 2.100 0.710
10 N 0.410 0.360 0.064 0.050 6.900 2.000
11 A 1.540 1.580 0.041 0.037 0.900 1.000
12 Q 0.830 0.540 0.050 0.046 0.360 0.890
13 L 1.100 0.940 0.040 0.040 0.900 1.100
14 E- 0.790 0.700 0.045 0.042 2.100 0.710
15 Q 0.830 0.540 0.050 0.046 0.360 0.890
16 E- 0.790 0.700 0.045 0.042 2.100 0.710
17 N 0.410 0.360 0.064 0.050 6.900 2.000
18 A 1.540 1.580 0.041 0.037 0.900 1.000
19 A 1.540 1.580 0.041 0.037 0.900 1.000
20 L 1.100 0.940 0.040 0.040 0.900 1.100
21 E- 0.790 0.700 0.045 0.042 2.100 0.710
22 E- 0.790 0.700 0.045 0.042 2.100 0.710
23 E- 0.790 0.700 0.045 0.042 2.100 0.710
24 I 0.730 0.470 0.050 0.050 1.250 0.660
25 A 1.540 1.580 0.041 0.037 0.900 1.000
26 Q 0.830 0.540 0.050 0.046 0.360 0.890
27 L 1.100 0.940 0.040 0.040 0.900 1.100
28 E- 0.790 0.700 0.045 0.042 2.100 0.710
29 Y 0.640 0.700 0.038 0.041 3.000 1.150
30 G 0.130 0.080 0.068 0.028 2.000 0.800
No Tyr interactions are found and accepted!
No Arg or His are found at C-terminus!
An N-capping box is found between: E-(9) and Q(12)
An N-capping box is found between: E-(23) and Q(26)
The parameters after adjustments are:
w' w vN vC N C
7 E- 0.632000 0.700000 0.045000 0.042000 2.100000 0.710000
8 E- 0.553000 0.560000 0.045000 0.042000 1.680000 0.710000
9 E- 0.395000 0.560000 0.045000 0.042000 2.520000 0.710000
11 A 1.663200 1.580000 0.041000 0.037000 0.900000 1.000000
21 E- 0.632000 0.700000 0.045000 0.042000 2.100000 0.710000
22 E- 0.553000 0.560000 0.045000 0.042000 1.680000 0.710000
23 E- 0.395000 0.560000 0.045000 0.042000 2.520000 0.710000
24 I 0.730000 0.470000 0.072000 0.050000 1.250000 0.660000
25 A 4.989600 1.580000 0.041000 0.037000 0.900000 1.000000
A C-cap is found at: Y(29)
The parameters after adjustments are:
w' w vN vC N C
29 Y 0.640000 0.700000 0.038000 0.041000 3.000000 1.680818
End effect is found between: E-(28) and COO-(30)The parameters after adjustments are:
w' w vN vC N C
28 E- 0.790000 0.588000 0.045000 0.037800 2.100000 0.710000
29 Y 0.640000 0.700000 0.038000 0.032800 3.000000 1.546353
30 G 0.130000 0.080000 0.068000 0.028000 2.000000 0.640000
Lipophillic interaction is found between:
I(3) and L(6)
L(20) and I(24)
I(24) and L(27)
The parameters after adjustments are:
w' w vN vC N C
2 E- 0.790000 0.700000 0.054000 0.042000 2.100000 0.710000
3 I 0.773800 0.498200 0.050000 0.050000 1.250000 0.660000
6 L 1.166000 0.996400 0.040000 0.040000 0.900000 1.100000
20 L 1.342000 1.146800 0.040000 0.040000 0.900000 1.100000
22 E- 0.641480 0.649600 0.045000 0.042000 1.680000 0.710000
24 I 0.944036 0.607804 0.072000 0.050000 1.250000 0.660000
27 L 1.166000 0.996400 0.040000 0.040000 0.900000 1.100000
Hydrogen-bonding effect is found between:
Q(4) and E-(8)
Q(12) and E-(16)
The parameters after adjustments are:
w' w vN vC N C
5 A 1.540000 1.896000 0.041000 0.037000 0.900000 1.000000
7 E- 0.632000 0.840000 0.045000 0.042000 2.100000 0.710000
13 L 1.100000 1.128000 0.040000 0.040000 0.900000 1.100000
15 Q 0.830000 0.648000 0.050000 0.046000 0.360000 0.890000
Columbic interaction is found between:
E-(2) and E-(8)
E-(8) and E-(14)
E-(16) and E-(22)
E-(22) and E-(28)
The parameters after adjustment are:
w' w vN vC N C
2 E- 0.742600 0.700000 0.054000 0.042000 2.100000 0.710000
5 A 1.386000 1.706400 0.041000 0.037000 0.900000 1.000000
8 E- 0.519820 0.504000 0.045000 0.042000 1.680000 0.710000
11 A 1.496880 1.422000 0.041000 0.037000 0.900000 1.000000
14 E- 0.790000 0.630000 0.045000 0.042000 2.100000 0.710000
16 E- 0.742600 0.700000 0.045000 0.042000 2.100000 0.710000
19 A 1.386000 1.422000 0.041000 0.037000 0.900000 1.000000
22 E- 0.602991 0.584640 0.045000 0.042000 1.680000 0.710000
25 A 4.490640 1.422000 0.041000 0.037000 0.900000 1.000000
28 E- 0.790000 0.529200 0.045000 0.037800 2.100000 0.710000
Starting matrix calculation: . . . . . . . . . . . . . . . . . . . . . . . . . . . . done!
1 D- 0.000 0.000 0.000 0.000 0.000 0.000
2 E- 0.000 0.000 0.060 0.000 0.000 0.060
3 I 0.060 0.000 0.021 0.000 0.060 0.082
4 Q 0.070 0.000 0.011 0.011 0.070 0.093
5 A 0.070 0.000 0.002 0.012 0.070 0.083
6 L 0.025 0.033 0.002 0.013 0.058 0.073
7 E- 0.009 0.036 0.003 0.015 0.045 0.063
8 E- 0.005 0.030 0.005 0.013 0.035 0.052
9 E- 0.006 0.014 0.009 0.019 0.021 0.048
10 N 0.013 0.009 0.041 0.007 0.022 0.071
11 A 0.052 0.009 0.042 0.003 0.061 0.106
12 Q 0.079 0.008 0.008 0.016 0.087 0.112
13 L 0.071 0.011 0.002 0.013 0.082 0.097
14 E- 0.037 0.027 0.007 0.020 0.064 0.091
15 Q 0.014 0.045 0.013 0.013 0.058 0.084
16 E- 0.018 0.030 0.002 0.023 0.048 0.073
17 N 0.015 0.023 0.042 0.012 0.038 0.092
18 A 0.053 0.024 0.046 0.004 0.076 0.126
19 A 0.083 0.027 0.004 0.013 0.109 0.126
20 L 0.069 0.022 0.001 0.022 0.090 0.114
21 E- 0.027 0.033 0.002 0.031 0.061 0.094
22 E- 0.004 0.038 0.014 0.020 0.042 0.077
23 E- 0.016 0.030 0.044 0.010 0.046 0.100
24 I 0.057 0.021 0.118 0.011 0.078 0.208
25 A 0.171 0.018 0.006 0.007 0.190 0.202
26 Q 0.121 0.015 0.003 0.059 0.136 0.198
27 L 0.071 0.032 0.000 0.037 0.103 0.140
28 E- 0.002 0.015 0.000 0.086 0.017 0.103
29 Y 0.000 0.000 0.000 0.017 0.000 0.017
30 G 0.000 0.000 0.000 0.000 0.000 0.000
<P(w'+w)>(n-4) = 0.0680 <P(w'+w)>(n-3) = 0.0655
*************** End of the Output ****************
Done!
Program crash with combination of cmd arguments
This two command lines cause the program to crash
helix --seq="{Ac,E,N,A,A,L,E,E,K,I,A,Q,L,K,Q,E,A,E,A,L,E,Q,K,N,A,A,L,K,E,E,I,Q,A,L,E,Y,G,NH2}" --pH=7.0 --salt=L --out=X9URL3U6T8.out --findAll --min
helix --seq="{Ac,K,N,A,A,L,K,E,E,I,Q,A,L,E,E,K,A,E,A,L,K,Q,E,N,Q,A,L,E,E,K,I,A,Q,L,K,Y,G,NH2}" --pH=7.0 --salt=L --out=CU816IWA2W.out --findAll --min
All other examples work fine, for example
helix --seq="{Ac,K,N,S,Q,L,K,Q,E,I,Q,S,L,E,E,E,N,R,R,L,E,S,K,I,S,Q,L,K,Y,G,C,NH2}" --pH=7.0 --salt=L --out=D1TJ9IZSPH.out --findAll --min
helix --seq="{Ac,E,N,S,Q,L,E,E,K,I,S,Q,L,K,Q,K,N,S,Q,L,K,Q,E,I,R,R,L,E,Y,G,C,NH2}" --pH=7.0 --salt=L --out=OP9CXFPIOX.out --findAll --min
helix --seq="{Ac,K,N,S,Q,L,K,E,E,I,Q,Q,L,E,E,E,N,Q,S,L,E,Q,K,I,Q,Q,L,K,Y,G,C,NH2}" --pH=7.0 --salt=L --out=020AYPPYFJ.out --findAll --min
helix --seq="{Ac,K,N,E,R,L,K,E,E,I,Q,R,L,E,Q,E,N,Q,Q,L,E,E,K,I,Q,R,L,K,Y,G,C,NH2}" --pH=7.0 --salt=L --out=9MZUI9YN99.out --findAll --min
helix --seq="{Ac,E,I,Q,Q,L,E,E,E,I,S,Q,L,E,Y,K,N,Y,A,L,K,A,K,N,E,E,L,K,R,G,C,NH2}" --pH=7.0 --salt=L --out=M1PSWLFX12.out --findAll --min
helix --seq="{Ac,K,I,S,Q,L,K,Q,K,I,Q,Q,L,K,Q,E,N,Q,R,L,E,E,E,N,R,R,L,E,Y,G,C,NH2}" --pH=7.0 --salt=L --out=BLRR49OAB3.out --findAll --min
helix --seq="{Ac,E,I,Q,Q,L,E,E,E,I,R,Q,L,E,Q,K,N,S,Q,L,K,E,K,N,Q,Q,L,K,Y,G,C,NH2}" --pH=7.0 --salt=L --out=14TZE9M4W2.out --findAll --min
helix --seq="{Ac,K,I,E,E,L,K,Q,K,I,E,Q,L,K,Q,E,N,Q,Q,L,E,E,E,N,S,Q,L,E,Y,G,C,NH2}" --pH=7.0 --salt=L --out=RS9BBOVFMP.out --findAll --min
helix --seq="{Ac,E,I,Q,R,L,E,Q,E,I,Q,R,L,E,Q,K,N,R,R,L,K,Q,K,N,R,R,L,K,Y,G,NH2}" --pH=7.0 --salt=L --out=R5CLHIJ09P.out --findAll --min
helix --seq="{Ac,K,I,R,R,L,K,E,K,I,R,R,L,K,Q,E,N,R,R,L,E,Q,E,N,R,R,L,E,Y,G,NH2}" --pH=7.0 --salt=L --out=NG5SHCTQIN.out --findAll --min
helix --seq="{Ac,D,E,I,E,K,L,E,R,E,I,E,K,L,E,E,K,N,E,E,L,K,E,K,N,E,E,L,K,Y,G,NH2}" --pH=7.0 --salt=L --out=FNEYPY8H94.out --findAll --min
helix --seq="{Ac,D,E,I,E,E,L,E,E,E,I,E,E,L,E,Q,K,N,E,E,L,K,E,K,N,E,E,L,K,Y,G,NH2}" --pH=7.0 --salt=L --out=WQJW6HNT58.out --findAll --min
helix --seq="{Ac,D,K,I,E,E,L,K,Q,K,I,E,E,L,K,Q,E,N,E,E,L,E,E,E,N,E,E,L,E,Y,G,NH2}" --pH=7.0 --salt=L --out=PSJT2NMYT5.out --findAll --min
helix --seq="{Ac,R,M,K,Q,L,E,D,K,I,E,E,L,L,S,K,I,Y,H,L,E,N,E,I,A,R,L,K,K,L,I,G,E,R,NH2}" --pH=7.0 --salt=L --out=L3PRLMMHMG.out --findAll --min
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