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Rasmol Script
The rasmol script is provided to help you visualize
the aligned structures. If you don't have rasmol,
go get it.
Once you've installed rasmol you can use it to view these scripts. If your script is named 'test.rs', simply type 'rasmol -script test.rs' to view it.
The script will color Protein 1 in red and Protein 2 in blue. All of the aligned regions will have thick backbones, while the unaligned regions will have skinny backbones.
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Output File
Below you'll find the output from a sample alignment and a description of what everything means. This example uses the alpha and beta chains of 2HHB, a hemoglobin.These first two lines are the names of the input files .
file1 2hhba.pdb file2 2hhbb.pdbThis next line is the random number generator seed. You can ignore this.
seed 987384415These next few lines describe the results of the rms-fit-search routine. You can see that after the 0th round, there were 27 matches at an rmsd of 2.15 Angstroms. You can probably ignore this as well.
rms fit round 0 matches 27 rmsd 2.15 rms fit round 1 matches 77 rmsd 1.94 rms fit round 2 matches 108 rmsd 1.71 rms fit round 3 matches 116 rmsd 1.74These lines describe the final statistics of the alignment. This example had 118 aligned residues at 1.74 Angstroms rmsd. The final score was 898.1
final rmsd 1.74 final matches 118 final score 898.1The 'ss pair' lines describe the number of aligned residues for each secondary structure. The secondary structure labels can be found below. The label '0000' indicates a loop or turn. In this example, protein 1 SSE 0200 and protein 2 SSE 0300 were aligned over 18 residues.
ss pair 0000 0000 22 ss pair 0000 0300 2 ss pair 0000 0400 1 ss pair 0000 0500 2 ss pair 0000 0600 1 ss pair 0100 0000 3 ss pair 0100 0100 8 ss pair 0100 0200 13 ss pair 0200 0000 1 ss pair 0200 0300 18 ss pair 0300 0400 3 ss pair 0400 0400 9 ss pair 0500 0500 17 ss pair 0600 0600 18The next few lines describe how many SSEs from each protein were aligned. A SSE is said to be aligned iff three or more of its residues are aligned.
aligned h1 6 aligned h2 6 total aligned h 6 aligned s1 0 aligned s2 0 total aligned s 0The pvalue is an estimate of the probability of obtaining an alignment of these two proteins with a score equal to or greater than this score by chance alone. In general, p-values less than 1.0e-2 are pretty good.
pvalue 2.92e-14Finally, the alignment. Protein 1's residues are shown in the first and second columns, protein 2's residues are in the third and fourth columns. The fifth and sixth columns describe describe the secondary structure assignments ('H' for helix, 'E' for strand).
Each SSE is assigned a 4-digit code. Helix codes end in '00', so the code '0100' indicates that the first secondary structure in the protein is a helix. The code '0201' indicates that the second secondary structure is a strand. The '01' in '0201' corresponds to the first strand in sheet '02'. Likewise '0305' corresponds to the fifth strand in sheet '03'.
Residues appearing in the first or fourth column were not aligned to anything. Residues in the second were aligned to residues in the fourth.
In this example, Protein 1 residues 1-6 and Protein 2 residues 1-7 were no aligned to *any* other residues. Protein 1 residues 7-17 were aligned to Protein 2 residues 8-18.
------ protein 1 ------- ------ protein2 -------
|non-aligned | aligned | aligned |non-aligned | SS1 | SS2 |
-----------------------------------------------------------------
VAL A 1 VAL B 1
LEU A 2 HIS B 2
SER A 3 LEU B 3
PRO A 4 THR B 4 H 0100
ALA A 5 PRO B 5 H 0100 H 0100
ASP A 6 GLU B 6 H 0100 H 0100
GLU B 7 H 0100
LYS A 7 LYS B 8 H 0100 H 0100
THR A 8 SER B 9 H 0100 H 0100
ASN A 9 ALA B 10 H 0100 H 0100
VAL A 10 VAL B 11 H 0100 H 0100
LYS A 11 THR B 12 H 0100 H 0100
ALA A 12 ALA B 13 H 0100 H 0100
ALA A 13 LEU B 14 H 0100 H 0100
TRP A 14 TRP B 15 H 0100 H 0100
GLY A 15 GLY B 16 H 0100
LYS A 16 LYS B 17 H 0100
VAL A 17 VAL B 18 H 0100
GLY A 18 ASN B 19 H 0100
ALA A 19 VAL B 20 H 0100 H 0200
ASP B 21 H 0200
HIS A 20 GLU B 22 H 0100 H 0200
ALA A 21 VAL B 23 H 0100 H 0200
GLY A 22 GLY B 24 H 0100 H 0200
GLU A 23 GLY B 25 H 0100 H 0200
TYR A 24 GLU B 26 H 0100 H 0200
GLY A 25 ALA B 27 H 0100 H 0200
ALA A 26 LEU B 28 H 0100 H 0200
GLU A 27 GLY B 29 H 0100 H 0200
ALA A 28 ARG B 30 H 0100 H 0200
LEU A 29 LEU B 31 H 0100 H 0200
GLU A 30 LEU B 32 H 0100 H 0200
ARG A 31 VAL B 33 H 0100 H 0200
MET A 32 VAL B 34 H 0100 H 0200
PHE A 33 H 0100
LEU A 34 H 0100
SER A 35 H 0100
PHE A 36 TYR B 35
PRO A 37 PRO B 36
THR A 38 TRP B 37
THR A 39 THR B 38
LYS A 40 GLN B 39
THR A 41 ARG B 40
TYR A 42 PHE B 41
PHE A 43 PHE B 42
PRO A 44 GLU B 43
HIS A 45 SER B 44
PHE A 46 PHE B 45
ASP A 47 GLY B 46
LEU A 48 ASP B 47
SER A 49 LEU B 48
HIS A 50 SER B 49
THR B 50
PRO B 51 H 0300
ASP B 52 H 0300
ALA B 53 H 0300
VAL B 54 H 0300
MET B 55 H 0300
GLY A 51 GLY B 56 H 0300
SER A 52 ASN B 57 H 0300
ALA A 53 PRO B 58 H 0200 H 0300
GLN A 54 LYS B 59 H 0200 H 0300
VAL A 55 VAL B 60 H 0200 H 0300
LYS A 56 LYS B 61 H 0200 H 0300
GLY A 57 ALA B 62 H 0200 H 0300
HIS A 58 HIS B 63 H 0200 H 0300
GLY A 59 GLY B 64 H 0200 H 0300
LYS A 60 LYS B 65 H 0200 H 0300
LYS A 61 LYS B 66 H 0200 H 0300
VAL A 62 VAL B 67 H 0200 H 0300
ALA A 63 LEU B 68 H 0200 H 0300
ASP A 64 GLY B 69 H 0200 H 0300
ALA A 65 ALA B 70 H 0200 H 0300
LEU A 66 PHE B 71 H 0200 H 0300
THR A 67 SER B 72 H 0200 H 0300
ASN A 68 ASP B 73 H 0200 H 0300
ALA A 69 GLY B 74 H 0200 H 0300
VAL A 70 LEU B 75 H 0200 H 0300
ALA A 71 ALA B 76 H 0200
HIS A 72 HIS B 77
VAL A 73 LEU B 78
ASP A 74 ASP B 79
ASP A 75 ASN B 80
MET A 76 LEU B 81 H 0300 H 0400
PRO A 77 LYS B 82 H 0300 H 0400
ASN A 78 GLY B 83 H 0300 H 0400
ALA A 79 THR B 84 H 0300 H 0400
LEU A 80 PHE B 85 H 0400
SER A 81 ALA B 86 H 0400 H 0400
ALA A 82 THR B 87 H 0400 H 0400
LEU A 83 LEU B 88 H 0400 H 0400
SER A 84 SER B 89 H 0400 H 0400
ASP A 85 GLU B 90 H 0400 H 0400
LEU A 86 LEU B 91 H 0400 H 0400
HIS A 87 HIS B 92 H 0400 H 0400
ALA A 88 CYS B 93 H 0400 H 0400
HIS A 89 ASP B 94 H 0400 H 0400
LYS A 90 LYS B 95
LEU A 91 LEU B 96
ARG A 92 HIS B 97
VAL A 93 VAL B 98
ASP A 94 ASP B 99
PRO A 95 PRO B 100
VAL A 96 GLU B 101 H 0500 H 0500
ASN A 97 ASN B 102 H 0500 H 0500
PHE A 98 PHE B 103 H 0500 H 0500
LYS A 99 ARG B 104 H 0500 H 0500
LEU A 100 LEU B 105 H 0500 H 0500
LEU A 101 LEU B 106 H 0500 H 0500
SER A 102 GLY B 107 H 0500 H 0500
HIS A 103 ASN B 108 H 0500 H 0500
CYS A 104 VAL B 109 H 0500 H 0500
LEU A 105 LEU B 110 H 0500 H 0500
LEU A 106 VAL B 111 H 0500 H 0500
VAL A 107 CYS B 112 H 0500 H 0500
THR A 108 VAL B 113 H 0500 H 0500
LEU A 109 LEU B 114 H 0500 H 0500
ALA A 110 ALA B 115 H 0500 H 0500
ALA A 111 HIS B 116 H 0500 H 0500
HIS A 112 HIS B 117 H 0500 H 0500
LEU A 113 PHE B 118 H 0500
PRO A 114 GLY B 119 H 0500
ALA A 115 LYS B 120 H 0500
GLU A 116 GLU B 121 H 0500
PHE A 117 PHE B 122
THR A 118 THR B 123
PRO A 119 PRO B 124 H 0600 H 0600
ALA A 120 PRO B 125 H 0600 H 0600
VAL A 121 VAL B 126 H 0600 H 0600
HIS A 122 GLN B 127 H 0600 H 0600
ALA A 123 ALA B 128 H 0600 H 0600
SER A 124 ALA B 129 H 0600 H 0600
LEU A 125 TYR B 130 H 0600 H 0600
ASP A 126 GLN B 131 H 0600 H 0600
LYS A 127 LYS B 132 H 0600 H 0600
PHE A 128 VAL B 133 H 0600 H 0600
LEU A 129 VAL B 134 H 0600 H 0600
ALA A 130 ALA B 135 H 0600 H 0600
SER A 131 GLY B 136 H 0600 H 0600
VAL A 132 VAL B 137 H 0600 H 0600
SER A 133 ALA B 138 H 0600 H 0600
THR A 134 ASN B 139 H 0600 H 0600
VAL A 135 ALA B 140 H 0600 H 0600
LEU A 136 LEU B 141 H 0600 H 0600
THR A 137 ALA B 142 H 0600
SER A 138 HIS B 143
LYS A 139 LYS B 144
TYR A 140 TYR B 145
ARG A 141 HIS B 146
