This menu is an aid to map interpretation. It allows one to make an estimate of what amino acid is to be associated with some electron density. The user enters a guess of the sequence based on the shape and position of the density that is then compared to the actual sequence via a look up table that must have been read into the users database. The guess may be accepted and may be entered into the database as a named entity. A number of guesses can later be combined together.
The guesses entered are one letter codes that usually appear to be the 20 amino acids. However, any one letter can be entered but it must exist in the 'slider matrix' that converts the entered symbol into a score relative to each of the 20 amino acids. The user is free to modify the file supplied in $ODAT/slider.o - it is NOT based simply on matching the size of the sequence to the guess.
This command defines which molecule is to be worked on and how long a scoring list is to be used.
O > slider
O > SLIDER is not a unique keyword.
O > SLider_Setup is a possibility.
O > Slider_guess is a possibility.
O > Slider_show is a possibility.
O > Slider_displ is a possibility.
O > Slider_combi is a possibility.
O > Slider_lego is a possibility.
O > SLIDER is not a visible command.
O > sl_setup
Slid> Slider molecule [A ] :
Slid> Maximum number on dial for Slider_guess [20] :
Allows one to enter a guess into the database. After getting a score, the user is asked if it should be associated with some coordinates. This allows one to first build a poly-alanine, for example, then later try to work out where one is in the sequence. Since one could have build the initial structure backwards, the program gives you the chance of associating the guess with a backwards model.
The 'slider matrix' must have been loaded.
O > sl_gues
Slid> There are 132 residues in molecule.
Slid> There is no slider matrix in the database.
O > read ../data/slider.o
Slid> There are 132 residues in molecule.
Slid> Estimated sequence: gvwa
Slid> Average= 0.43,rms= 0.14
Slid> GVWA
Slid> Fit 1 0.875 A6 GTWK
Slid> Fit 2 0.725 A33 GNLA
Slid> Fit 3 0.700 A84 VTLA
Slid> Fit 4 0.675 A26 GLAT
Slid> Fit 5 0.675 A55 SPFK
Slid> Fit 6 0.675 A122 VVCT
Slid> Fit 7 0.650 A99 GNET
Slid> Fit 8 0.650 A82 STVT
Slid> Fit 9 0.650 A111 GKMV
Slid> Fit 10 0.625 A28 ATRK
Slid> Fit 11 0.625 A89 GSLN
Slid> Fit 12 0.600 A62 ISFK
Slid> Fit 13 0.600 A40 VIIS
Slid> Fit 14 0.600 A72 ETTA
Slid> Fit 15 0.600 A24 GVGL
Slid> Fit 16 0.600 A50 TIRT
Slid> Fit 17 0.600 A22 ALGV
Slid> Fit 18 0.575 A102 TTIK
Slid> Fit 19 0.550 A79 KTKS
Slid> Fit 20 0.550 A73 TTAD
Slid> Do you want to associate with a residue ([Y],n)?
Slid> Molecule and residue name : a a6
Slid> Forwards or backwards ([F],b)?
The best fitting sequence is now shown on the display, and a dial controls which of the fits is displayed. To accept it into the database, type
O > yes
Slid> What name to associate with guess?g1
The guess text can be 1-6 characters in length and creates 4 items in the database. Which can be retrieved by other commands
O > dir *g1*
Heap> .SLIDER_XYZ_G1 R W 12
Heap> .SLIDER_SEQ_G1 T W 4
Heap> .SLIDER_POS_G1 I W 132
Heap> .SLIDER_FIT_G1 R W 132
Allows one to see on the display which guesses have been made.
Allows one to reactivate a guess that has been stored in the database. A dial controls which of the scores is shown.
O > sl_displ
Slid> Enter which one : g1
O > no
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!
People are often unsure about the size of a particular amino acid. This makes it rather difficult to make guess when one sees density. Even for experts, it helps to concentrate the mind to see which ones could actually fit. It is necessary to have built at least a poly-alanine before this command works. Then the first time one ID's an atom, 2 knobs get activated so that one controls which amino acid type gets displayed and one controls the rotamer for that residue type. If the Poly-alanine does not point into the density, then the side chain will not fit into the density. Making further ID's, transfers the activity to the new residue.
At present, some of the commands are a bit dumb when it comes to accepting the results. Future releases will have enhanced functionality in Slider_combine and Slider_lego.
.slider_integer, .slider_real, .slider_matrix should not be of interest to anyone.
The slider matrix is read in as a formatted T type data block. The first line contains the one letter symbolic names, then each following line scores how the amino acids are matched to the symbolic residue name.