XEasy input supported by PISTACHIO

Sequence Input

Two forms of sequence input is supported by PISTACHIO.  Single letter Amino Acid names or the three letter version of the names must be listed in order.  For the XEasy output "prot" file to match correctly with the one user may have created, all charges must be indicated - for example, ARG+.

Table shows sequence data format for PISTACHIO

MET   
THR   
GLU   
VAL   
TYR   
ASP   
LEU   
GLU   
ILE   
THR   
THR   
ASN   
ALA
.......
.......



Peak List Input Format

The peak list input format is the XEasy format.  An example is shown below.

Table shows HNCA peak-list in XEasy format

# Number of dimensions 3
#INAME 1 1H
#INAME 2 13C
#INAME 3 15N
 269   8.739  58.660 117.280 1 U          2.434e+03  0.00e+00 m   0    0    0    0 0
 270   8.127  54.606 131.974 1 U          1.928e+03  0.00e+00 m   0    0    0    0 0
 271   8.694  54.247 131.717 1 U          2.799e+03  0.00e+00 m   0    0    0    0 0
 272   7.943  62.714 129.837 1 U          3.834e+03  0.00e+00 m   0    0    0    0 0
 273   7.920  56.659 128.408 1 U          1.472e+04  0.00e+00 m   0    0    0    0 0
 274   9.239  58.660 128.144 1 U          3.032e+03  0.00e+00 m   0    0    0    0 0
 275   9.189  53.887 127.284 1 U          2.630e+03  0.00e+00 m   0    0    0    0 0
 276   7.661  57.069 127.125 1 U          4.806e+03  0.00e+00 m   0    0    0    0 0
 278   8.604  54.606 126.467 1 U          4.260e+03  0.00e+00 m   0    0    0    0 0
 281   9.062  54.554 126.825 1 U          1.064e+04  0.00e+00 m   0    0    0    0 0
 282   9.386  57.993 126.065 1 U          3.398e+03  0.00e+00 m   0    0    0    0 0
 283   8.000  62.714 125.755 1 U          4.618e+03  0.00e+00 m   0    0    0    0 0
 284   8.342  62.355 125.379 1 U          3.601e+03  0.00e+00 m   0    0    0    0 0
 285   8.157  55.889 125.551 1 U          1.588e+03  0.00e+00 m   0    0    0    0 0
 286   8.612  55.068 125.258 1 U          4.607e+03  0.00e+00 m   0    0    0    0 0



XEasy Output supported by PISTACHIO

Xeasy output format is supported by PISTACHIO.  An example output format with atom numbers filled in according to the "prot" file is shown below.


Xeasyhnca.peaks

# Number of dimensions 3
#INAME 1 1H
#INAME 2 13C
#INAME 3 15N
 269   8.739  58.660 117.280 1 U          2.434e+03  0.00e+00 m   0    0        0        0     0
 270   8.127  54.606 131.974 1 U          1.928e+03  0.00e+00 m   0    400      391      399   0
 271   8.694  54.247 131.717 1 U          2.799e+03  0.00e+00 m   0    1337     1321     1336  0
 272   7.943  62.714 129.837 1 U          3.834e+03  0.00e+00 m   0    0        0        0     0
 273   7.920  56.659 128.408 1 U          1.472e+04  0.00e+00 m   0    1964     1939     1963  0
 274   9.239  58.660 128.144 1 U          3.032e+03  0.00e+00 m   0    1320     1300     1319  0
 275   9.189  53.887 127.284 1 U          2.630e+03  0.00e+00 m   0    1299     1272     1298  0
 276   7.661  57.069 127.125 1 U          4.806e+03  0.00e+00 m   0    0        0        0     0
 278   8.604  54.606 126.467 1 U          4.260e+03  0.00e+00 m   0    931      914      930   0
 281   9.062  54.554 126.825 1 U          1.064e+04  0.00e+00 m   0    764      747      763   0
 282   9.386  57.993 126.065 1 U          3.398e+03  0.00e+00 m   0    813      793      812   0
 283   8.000  62.714 125.755 1 U          4.618e+03  0.00e+00 m   0    390      375      389   0
 284   8.342  62.355 125.379 1 U          3.601e+03  0.00e+00 m   0    33       21       32    0
 285   8.157  55.889 125.551 1 U          1.588e+03  0.00e+00 m   0    1878     1851     1877  0
 286   8.612  55.068 125.258 1 U          4.607e+03  0.00e+00 m   0    1000     987      999   0
 287   8.920  54.247 125.294 1 U          3.141e+03  0.00e+00 m   0    98       89       97    0
 288   8.734  55.991 125.037 1 U          3.726e+03  0.00e+00 m   0    299      286      298   0
 289   9.107  54.657 124.801 1 U          3.641e+03  0.00e+00 m   0    792      765      791   0


1 999.000 0.000 N 1
2 999.000 0.000 HN 1
3 55.632 0.000 CA 1
4 999.000 0.000 HA 1
5 32.706 0.000 CB 1
6 999.000 0.000 HB2 1
7 999.000 0.000 HB3 1
8 999.000 0.000 QB 1
9 999.000 0.000 CG 1
10 999.000 0.000 HG2 1
11 999.000 0.000 HG3 1
12 999.000 0.000 QG 1
13 999.000 0.000 QE 1
14 999.000 0.000 CE 1
15 999.000 0.000 HE1 1
16 999.000 0.000 HE2 1
17 999.000 0.000 HE3 1
18 176.310 0.000 C 1
19 116.300 0.000 N 2
20 8.107 0.000 HN 2
21 62.355 0.000 CA 2
22 999.000 0.000 HA 2
23 69.576 0.000 CB 2
24 999.000 0.000 HB 2
25 999.000 0.000 QG2 2
26 999.000 0.000 HG1 2
27 999.000 0.000 CG2 2
28 999.000 0.000 HG21 2
29 999.000 0.000 HG22 2
30 999.000 0.000 HG23 2
31 174.053 0.000 C 2
32 125.379 0.000 N 3
33 8.342 0.000 HN 3
34 56.761 0.000 CA 3
35 999.000 0.000 HA 3
36 30.508 0.000 CB 3
37 999.000 0.000 HB2 3
38 999.000 0.000 HB3 3
39 999.000 0.000 QB 3
40 999.000 0.000 CG 3
41 999.000 0.000 HG2 3
42 999.000 0.000 HG3 3
43 999.000 0.000 QG 3
44 999.000 0.000 CD 3
45 175.521 0.000 C 3
46 123.660 0.000 N 4
47 8.376 0.000 HN 4
48 60.354 0.000 CA 4
49 999.000 0.000 HA 4



PISTACHIO Native assignment output

PISTACHIO also outputs the assignment in the format that is supported by NMR-STAR.   Note that this is not the entire NMR-STAR file format.  It is only the portion of NMR-STAR that deals with the specification of chemical shifts.  An example is shown below.


1 1 MET C 176.310 1.000 0
2 1 MET CA 55.632 1.000 0
3 1 MET CB 32.706 1.000 0
4 2 THR N 116.300 1.000 0
5 2 THR H 8.107 1.000 0
6 2 THR C 174.053 1.000 0
7 2 THR CA 62.355 1.000 0
8 2 THR CB 69.576 1.000 0
9 3 GLU N 125.379 1.000 0
10 3 GLU H 8.342 1.000 0
11 3 GLU C 175.521 1.000 0
12 3 GLU CA 56.761 1.000 0
13 3 GLU CB 30.508 1.000 0
14 4 VAL N 123.660 1.000 0
15 4 VAL H 8.376 1.000 0
16 4 VAL C 174.603 1.000 0
17 4 VAL CA 60.354 1.000 0
18 4 VAL CB 35.704 1.000 0
19 5 TYR N 123.645 1.000 0
20 5 TYR H 8.855 1.000 0
21 5 TYR C 174.900 1.000 0
22 5 TYR CA 53.682 1.000 0
23 5 TYR CB 40.700 1.000 0
24 6 ASP N 123.887 1.000 0
25 6 ASP H 9.245 1.000 0
26 6 ASP C 175.171 1.000 0
27 6 ASP CA 54.247 1.000 0
28 6 ASP CB 41.299 1.000 0
29 7 LEU N 125.294 1.000 0
30 7 LEU H 8.920 1.000 0
31 7 LEU C 176.352 0.995 0
32 7 LEU CA 56.197 0.995 0
33 7 LEU CB 32.706 0.995 0
34 8 GLU N 124.010 0.995 0
35 8 GLU H 8.210 0.995 0
36 8 GLU C 176.262 1.000 0
37 8 GLU CA 59.430 1.000 0
38 8 GLU CB 30.108 1.000 0
39 9 ILE N 122.211 1.000 0
40 9 ILE H 8.156 1.000 0



Native Backbone output format generated by PISTACHIO

PISTACHIO produces a probabilistic assignment for every residue.  This means that it is possible for some residues to have more than one candidate system for their chemical shifts.   In this case, there is an associated probability to each system assigned to a residue.  The sum of all probabilities always add to one.  For the remainder of this discussion consult the sample output shown in the table below.

The probability for the system is shown in the third column marked with P(H,N).  A value of -999 indicates that a value for the given slot could not be found that would match the given residue.  When all values for the backbone are -999, then the probability is set to -999 as well to indicate that the probability in this case is undefined.  When more than one possibility is detected (row 11), the structure in the columns 2-7 for the given residue is repeated and the alternative values and their probabilities are specified.


The table shows portions of the backbone assignment with computed probabilities.

 Residue Name P(H,N) H(i) N(i) CO(i) CA(i) CB(i) P(H,N) H(i) N(i)
1 MET -999 -999 -999 -999 -999 -999 -999 -999 -999
2 GLY -999 -999 -999 -999 -999 -999 -999 -999 -999
3 HIS -999 -999 -999 -999 -999 -999 -999 -999 -999
4 HIS -999 -999 -999 -999 -999 -999 -999 -999 -999
5 HIS -999 -999 -999 -999 -999 -999 -999 -999 -999
6 HIS -999 -999 -999 -999 -999 -999 -999 -999 -999
7 HIS -999 -999 -999 -999 55.886 29.896 -999 -999 -999
8 HIS 0.99952 8.556 122.15 173.92 55.863 29.616 -999 -999 -999
9 LEU 1 8.269 125.68 176.17 54.378 42.826 -999 -999 -999
10 GLU 1 8.015 124.49 174.76 55.943 31.394 -999 -999 -999
11 GLU 0.9999 8.194 122.84 175.46 55.24 31.394 0.00010321 8.139 120.93
12 PHE 1 8.857 121.87 176.73 56.303 43.397 -999 -999 -999
13 THR 1 8.752 113.97 999 60.569 71.377 -999 -999 -999
14 ALA 1 9.563 125.93 181.27 55.926 17.496 -999 -999 -999
15 GLU 1 8.787 120.07 180.26 59.839 29.213 -999 -999 -999
16 GLN 1 8.106 123.25 179.74 58.948 29.392 -999 -999 -999
17 LEU 1 8.829 121.31 177.8 57.86 42.217 -999 -999 -999
18 SER 1 7.539 112.02 175.11 60.986 63.55 -999 -999 -999
19 GLN 1 7.254 118.66 177.03 56.616 28.726 -999 -999 -999
20 TYR 1 8.105 124.31 175.67 57.211 35.967 -999 -999 -999
21 ASN 1 7.304 116.24 176.28 52.19 39.111 -999 -999 -999
22 GLY 1 9.016 109.5 174.37 45.361 999 -999 -999 -999
23 THR 1 7.825 113.87 174.63 64.229 69.573 -999 -999 -999
24 ASP 1 8.691 124.28 178.22 52.273 41.362 -999 -999 -999
25 GLU 1 9.185 128.21 176.64 58.602 29.505 -999 -999 -999
26 SER 1 8.822 116.15 174.27 59.462 64.103 -999 -999 -999
27 LYS 1 7.553 124.33 999 999 999 -999 -999 -999
28 PRO 1 999 999 175.86 62.222 33.256 -999 -999 -999
29 ILE 1 8.203 121.8 174.16 60.716 39.537 -999 -999 -999
30 TYR 1 7.916 125.38 178.45 56.555 37.723 -999 -999 -999
31 VAL 0.99012 8.378 121.63 173.85 61.819 37.239 0.0098837 8.375 121.68
32 ALA 1 8.824 129.35 175.23 48.944 22.174 -999 -999 -999
33 ILE 1 8.601 117.58 176.91 60.66 41.578 -999 -999 -999
34 LYS 1 9.77 128.82 176.66 57.395 30.043 -999 -999 -999
35 GLY 1 8.101 103.72 172.91 46.144 999 -999 -999 -999

































































































An Overall Picture of  The Assignment

A jpg figure is also sent to the user that demonstrates the overall picture of the assignment. For those residues that the best assignment has a probability higher than 99% a green bar is presented. For those with probabilities between 85%-99% a cyan bar, between 50%-85% a yellow bar, and for those with less than 50% a red bar is presented. For those residues that the probability on having no assignment with the included data is higher than any other assignment, a grey bar is presented with  the related probability of no assignment .

image