Normally one enters a number of guesses into the system and then tries to combine them in some way. The order in which guesses are specified to be combined is vital since this implies that the first guess comes before the second one in the sequence, and so on. When combining them, one specifies a maximum size gap between guesses. These values are important since they act as constraints in forming the scores. In the following examples, a few more guesses are added to the system. The first one is actually starting at residue A38 and has quite a worse fit when compared to the top score.
O > sl_gues Slid> There are 132 residues in molecule. Slid> Estimated sequence: vavvlv Slid> Average= 0.54,rms= 0.16 Slid> VAVVLV Slid> Fit 1 0.883 A82 STVTLA Slid> Fit 2 0.833 A80 TKSTVT Slid> Fit 3 0.783 A23 LGVGLA Slid> Fit 4 0.767 A38 PRVIIS Slid> Fit 5 0.733 A122 VVCTRI Slid> Fit 6 0.733 A89 GSLNQV Slid> Fit 7 0.717 A81 KSTVTL Slid> Fit 8 0.717 A83 TVTLAR Slid> Fit 9 0.717 A120 KDVVCT Slid> Fit 10 0.717 A25 VGLATR Slid> Fit 11 0.717 A88 RGSLNQ Slid> Fit 12 0.717 A48 IITIRT Slid> Fit 13 0.700 A100 NETTIK Slid> Fit 14 0.700 A123 VCTRIY Slid> Fit 15 0.700 A45 KGDIIT Slid> Fit 16 0.683 A98 NGNETT Slid> Fit 17 0.683 A11 VSSENF Slid> Fit 18 0.683 A37 KPRVII Slid> Fit 19 0.683 A73 TTADNR Slid> Fit 20 0.667 A27 LATRKL Slid> Do you want to associate with a residue ([Y],n)? Slid> Molecule and residue name : a a38 Slid> Forwards or backwards ([F],b)? O > yes Slid> What name to associate with guess? g2
Now the next strand is added, the correct answer is fit 12, residue A48
O > sl_gues Slid> There are 132 residues in molecule. Slid> Estimated sequence: vltfal Slid> Average= 0.52,rms= 0.15 Slid> VLTFAL Slid> Fit 1 0.817 A90 SLNQVQ Slid> Fit 2 0.767 A83 TVTLAR Slid> Fit 3 0.750 A61 EISFKL Slid> Fit 4 0.750 A22 ALGVGL Slid> Fit 5 0.733 A63 SFKLGQ Slid> Fit 6 0.717 A85 TLARGS Slid> Fit 7 0.717 A92 NQVQKW Slid> Fit 8 0.700 A114 VVECKM Slid> Fit 9 0.700 A103 TIKRKL Slid> Fit 10 0.700 A29 TRKLGN Slid> Fit 11 0.683 A5 LGTWKL Slid> Fit 12 0.683 A48 IITIRT Slid> Fit 13 0.683 A123 VCTRIY Slid> Fit 14 0.667 A7 TWKLVS Slid> Fit 15 0.667 A81 KSTVTL Slid> Fit 16 0.650 A11 VSSENF Slid> Fit 17 0.650 A59 NTEISF Slid> Fit 18 0.650 A99 GNETTI Slid> Fit 19 0.650 A54 ESPFKN Slid> Fit 20 0.633 A24 GVGLAT Slid> Do you want to associate with a residue ([Y],n)? Slid> Molecule and residue name : a a48 Slid> Forwards or backwards ([F],b)? O > yes
Now they can all be combined, or in pairs
O > sl_com Slid> Slider guess : G1 Slid> Slider guess : G2 Slid> Slider guess : G3 Slid> Enter which ones : g2 g3 Slid> There will be a search for 2 Slid> Enter gap sizes : 4 Slid> Fit 1 = 0.850 82 90 Slid> Fit 2 = 0.825 80 90 Slid> Fit 3 = 0.800 82 92 Slid> Fit 4 = 0.767 81 90 Slid> Fit 5 = 0.767 83 90 Slid> Fit 6 = 0.742 23 29 Slid> Fit 7 = 0.725 84 90 Slid> Fit 8 = 0.725 73 83 Slid> Fit 9 = 0.725 38 48 Slid> Fit 10 = 0.717 82 88 Slid> Fit 11 = 0.717 83 92 Slid> Fit 12 = 0.708 82 89 Slid> Fit 13 = 0.708 55 61 Slid> Fit 14 = 0.708 82 91 Slid> Fit 15 = 0.700 55 63 Slid> Fit 16 = 0.700 80 86 Slid> Fit 17 = 0.692 53 61 Slid> Fit 18 = 0.692 89 99 Slid> Fit 19 = 0.692 80 88 Slid> Fit 20 = 0.683 80 89 O > no
Because of the relatively poor guessing, the correct answer is a little way down the list at position 9.
Lets add some more, the next strand. The error message `` Residue FA not in matrix'' comes because the A molecule includes a fatty acid that is not in the slider matrix.
The guess is a good one, the top score is correct.
O > sl_gues Slid> There are 132 residues in molecule. Slid> Estimated sequence: siqlqf Slid> Residue FA not in matrix. Slid> Residue FA not in matrix. Slid> Residue FA not in matrix. Slid> Residue FA not in matrix. Slid> Residue FA not in matrix. Slid> Residue FA not in matrix. Slid> Average= 0.53,rms= 0.15 Slid> SIQLQF Slid> Fit 1 0.833 A59 NTEISF Slid> Fit 2 0.817 A90 SLNQVQ Slid> Fit 3 0.783 A114 VVECKM Slid> Fit 4 0.750 A67 GQEFEE Slid> Fit 5 0.750 A12 SSENFD Slid> Fit 6 0.733 A89 GSLNQV Slid> Fit 7 0.717 A91 LNQVQK Slid> Fit 8 0.717 A14 ENFDEY Slid> Fit 9 0.717 A50 TIRTES Slid> Fit 10 0.700 A65 KLGQEF Slid> Fit 11 0.700 A92 NQVQKW Slid> Fit 12 0.700 A63 SFKLGQ Slid> Fit 13 0.700 A124 CTRIYE Slid> Fit 14 0.700 A13 SENFDE Slid> Fit 15 0.683 A10 LVSSEN Slid> Fit 16 0.683 A61 EISFKL Slid> Fit 17 0.683 A47 DIITIR Slid> Fit 18 0.667 A123 VCTRIY Slid> Fit 19 0.667 A82 STVTLA Slid> Fit 20 0.667 A15 NFDEYM Slid> Do you want to associate with a residue ([Y],n)? Slid> Molecule and residue name : a a59 Slid> Forwards or backwards ([F],b)? O > yes Slid> What name to associate with guess? g4
Now include this one and the first guess which is also well defined.
O > sl_com Slid> Slider guess : G1 Slid> Slider guess : G2 Slid> Slider guess : G3 Slid> Slider guess : G4 Slid> Enter which ones : g1 g2 g3 g4 Slid> There will be a search for 4 Slid> Enter gap sizes : 40 5 5 Slid> Fit 1 = 0.782 6 38 48 59 Slid> Fit 2 = 0.764 55 82 90 99 Slid> Fit 3 = 0.759 6 37 48 59 Slid> Fit 4 = 0.755 55 82 90 101 Slid> Fit 5 = 0.755 33 38 48 59 Slid> Fit 6 = 0.750 40 82 90 99 Slid> Fit 7 = 0.750 72 82 90 99 Slid> Fit 8 = 0.750 55 80 90 99 Slid> Fit 9 = 0.750 33 73 83 90 Slid> Fit 10 = 0.750 50 82 90 99 Slid> Fit 11 = 0.750 62 82 90 99 Slid> Fit 12 = 0.745 6 50 61 67 Slid> Fit 13 = 0.745 26 38 48 59 Slid> Fit 14 = 0.741 40 82 90 101 Slid> Fit 15 = 0.741 62 82 90 101 Slid> Fit 16 = 0.741 6 38 49 59 Slid> Fit 17 = 0.741 50 82 90 101 Slid> Fit 18 = 0.741 72 82 90 101 Slid> Fit 19 = 0.741 6 23 29 40 Slid> Fit 20 = 0.741 55 80 90 101 O > no
The correct answer is at the top. Notice that there are clusters of correct answers in the top scores. The gap values are important since they are restraints in evaluating the scores. In the above example, we check all possibilities that are separated by less then 40 residues between guess G1 and G2; by 5 between G2 and G3, and by 5 between G3 and G4. In the next example, the gaps are all less then 200 residues, i.e. the gap restraints are not of any use (there are only 131 residues in the protein).
O > sl_set Slid> Slider molecule [A ] : Slid> Maximum number on dial for Slider_guess [20] : 30 O > sl_comb Slid> Slider guess : G1 Slid> Slider guess : G2 Slid> Slider guess : G3 Slid> Slider guess : G4 Slid> Enter which ones : g1 g2 g3 g4 Slid> There will be a search for 4 Slid> Enter gap sizes : 200 200 200 Slid> Fit 1 = 0.836 6 82 90 114 Slid> Fit 2 = 0.823 6 80 90 114 Slid> Fit 3 = 0.814 6 82 90 124 Slid> Fit 4 = 0.809 6 23 90 114 Slid> Fit 5 = 0.809 33 82 90 114 Slid> Fit 6 = 0.809 6 82 92 114 Slid> Fit 7 = 0.805 6 38 90 114 Slid> Fit 8 = 0.805 6 82 90 123 Slid> Fit 9 = 0.805 6 82 103 114 Slid> Fit 10 = 0.805 6 23 83 90 Slid> Fit 11 = 0.800 6 82 90 99 Slid> Fit 12 = 0.800 6 23 61 90 Slid> Fit 13 = 0.800 55 82 90 114 Slid> Fit 14 = 0.800 6 82 90 122 Slid> Fit 15 = 0.800 6 82 90 108 Slid> Fit 16 = 0.800 6 38 83 90 Slid> Fit 17 = 0.800 6 82 90 112 Slid> Fit 18 = 0.800 6 82 90 103 Slid> Fit 19 = 0.800 26 82 90 114 Slid> Fit 20 = 0.800 6 80 90 124 Slid> Fit 21 = 0.795 6 23 83 114 Slid> Fit 22 = 0.795 33 80 90 114 Slid> Fit 23 = 0.795 6 80 92 114 Slid> Fit 24 = 0.795 6 23 63 90 Slid> Fit 25 = 0.795 6 38 61 90 Slid> Fit 26 = 0.791 6 23 61 114 Slid> Fit 27 = 0.791 6 82 90 125 Slid> Fit 28 = 0.791 6 38 83 114 Slid> Fit 29 = 0.791 6 23 29 59 Slid> Fit 30 = 0.791 28 82 90 114 O > no
Now the correct answer does not show in the top 30!