Help & Tutorial for
ESPript 1.4

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 colored according to their degree of similarity.

The most simple case is shown below: the user has just to type in (green lines) the name of the file containing the aligned sequences.

> ESPript
1. Alignment file format CLUSTAL/GCG/PIR/FASTA/MAXHOM/THREADER
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 file.list
vp7.aln
-> File to open : vp7.aln

2. Secondary structure file from DSSP with accessibility(A)
or/and from PHD with access(A) and sec.s. reliability(9) :
file1.dssp A file2.phd A 9 (return or . if none)
<return>

3. Output postscript file with secondary structure written
with numbers(default), letters(L) or mixte(M) :
<return>
-> File to open : vp7.ps

4. Boxing using either BLOSUM62(B) Risler(R) PAM250(P) Identity(I)
similarity (id=1) differences (max=1) scoring matrix :
0.15 0.5 B
<return>
-> Parameters : 0.15 0.5 B

5. Presentation for output in colour(C) grey(G) B&W(B) with
orientation portrait or landscape, format A4(P/L) or A3(P3/L3)
fontsize width step top left colour paper :
7 70 4 0 0 C P
<return>
-> Parameters : 7 70 4 0 0 C P4

6. Special library (return or . if no use)
- Triangle up(U) triangle down(D) star(S) circle(C) dotted line(L) num.last(Z)
hydro(P) inter(R)
sec.str(X) sec.let(A) id.back(I) id.for(F) hom(H) hom.box(B) dif.box(O) non(N)
title(T) num(Y)
- Colour red(R) green(G) cyan(C) blue(B) yellow(Y) pink(P) black(D) white(W)
gold(O) skip(S) or (segID) if inter
- Position on sequence (based on first selected sequence)

Enter (Sign Colour Position), (%Comment) or replace (@Sec.Str.labels)
(return or . if finished) :
U R 2 9-39
<return>
-> End 


  [...]

 -> Mean similarity (blue box) : 0.28

 PostScript output of 1 page : vp7.ps
The following image is extracted from the PostScript file

Advanced features

Advanced features are explained on the next page