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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.


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.pdb
This next line is the random number generator seed. You can ignore this.

seed 987384415
These 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    1.74
These 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     898.1
The '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    18
The 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 0
The 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-14

Finally, 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                              

Protein Engineering