Help & Tutorial for
E S P r i p t  1.9

Options and parameters for ESPript can be specified on the standard input. Thus, it is possible to group all the required values in an input file. Example files are held in the example directory.

ESPript is Easy to use

ESPript generates a pretty PostScript output from aligned sequences. Sequences are automatically coloured according to their degree of similarity. The most simple case is shown below: the user has just to type the name of the file (in maroon) containing the aligned sequences.
 
> ESPript
1. Alignment file from MULTALIN/CLUSTAL/GCG/SEAVIEW/MAXHOM/THREADER/PDB 
    with possibility PDB file for score in Bfac column 
    or list of intermolecular contacts generated with X-PLOR :
  file.aln [fragment(5-50)] [first residue(1)] [continue(+)] file.pdb xplor.list
vp7.aln
=> File to open : vp7.aln
2. Secondary structure file(s) with possibility chainID(chain_A)  
    accessibility(A) and reliability if from PHD(9) :
         file1.dssp A file2.phd A 9 (return or . if none)
<return>
3. Postscript output with sec.elements labeled
    with digits(default) letters(L) or mixte(M) :
<return>
=> File to open : vp7.ps 

4. Boxing similarities(id=1) group_differences(max=1)
    using RISLER(R) BLOSUM62(B) PAM250(P) Iden(I) %Strict(S) %Multa(M) %Equi(E)
    possibility line Consensus(C) : 
                                    0.7 0.5 R
<return>
=> Parameters : 0.7 0.5 R

5. Layout in colour(C) transfer(T) slide(S) B&W(B) flashy(F)
    with orientation portrait or landscape format A4(P/L) or A3(P3/L3)
    Possibility all sequences numbered(N)
    fontsize width step top left colour paper :
                                   7 70 6 0 0 C P
<return>
=> Parameters : 7 70 6 0 0 C P4

6. Special library (return or . if no use)
    - Triangle up(U) down(D) go(G) jam(J) star(S) circle(C)  
       open(E) dotted line(L) stroke(K) num.last(Z) hydro(P)
       inter(R) do_box(Q) do_char(V) do_fram(W)
       sec.str(X) sec.let(A) id.box(I) id.char(F) hom.box(M) 
       hom.char(H) hom.fram(B) dif.box(O) none(N) title(T) num(Y) 
       NMR : NHslow(s) J<6(t) J>7(u)
                   dNNweak(a) dNNmedium(b) dNNstrong(c)
                   dANw(d) dANm(e) dANs(f) dBNw(g) dBNm(h) dBNs(i)
                   dNN2(j) dAN2(k) dAN3(l) dAB3(m) dAN4(n)
    - Colour black(D) blue(B) red(R) pink(P) green(G) cyan(C)
       gold(O) yellow(Y) white(W) skip(S) or (segID) if inter
    - Position in sequence (based on first displayed sequence)

  Enter a Sign Colour Position such as U R 2 9-39
  or a %Comment or a @Special(sec.lab nott min plus ruler skip col seq pp top) :
<return>
=> End 
  [...]

  -> Mean identity : 0.11      Mean similarity : 0.75
 Number of columns : 360

 Top seq.numbering matches 1 displayed sequence: vp7_btv1s 
 PostScript output of 1 page : vp7.ps

Excerpt from the generated PostScript

Advanced features

Advanced features are explained on the next page