This is a file of default parameters for use with BOXSHADE there are several sections, one for GENERAL parameters and one for each output device. The parameters may be edited freely, they reflect the input expected from the keyboard if BOXSHADE is run interactively. The purpose of each parameter is documented briefly within the respective line. When editing, one has to regard: - one parameter per line (background/foreground shading = one parameter) - parameters of a section (labeled :SECTION) start in the first line after the label - there may be no empty (or comment) lines between the parameters of a section. These lines are allowed only between sections - only the leftmost part of every parameter line is looked at. Comments are allowed starting at row 10 - don't change the section header :GENERAL 1 input type (1: PRETTY) 1 output device (1: ANSI Terminal) N consensus to single sequence? 60 sequence chars per line Y sequence names to be printed? N sequence numbers to be printed? 1 No of empty lines between blocks Y special shading for similar residues N special shading for conserved residues N consensus output LU consensus display pattern N split output to multiple files N default numbering (starting at 1) 0.5 default threshold fraction :HTML WB normal residues BW identical residues 1B similar residues B2 globally conserved residues :POSTSCRIPT WB normal residues BW identical residues 1B similar residues B2 globally conserved residues 10 character size (in Pts.) n landscape mode :CRT LD normal residues BL identical residues LR similar residues BW globally conserved residues :RTF WK normal residues WR identical residues WB similar residues WM globally conserved residues 10 character size (in pts) :ANSI N normal residues R identical residues B similar residues E globally conserved residues :ASCII L normal residues - identical residues l similar residues . globally conserved residues :HPGL 0F1N normal residues (bgnd/fgnd) 2F1N identical residues 3F1N similar residues 2F4N globally conserved residues 8 character size (in Pts.) N landscape mode :LJ250 B normal residues R identical residues L similar residues M globally conserved residues :FIG WB normal residues BW identical residues 1B similar residues BY globally conserved residues 12 0=Tms,12=Cour,16=Helv,28=Palat 10 character size (in Pts.) :ReGIS WB normal residues BW identical residues LW similar residues BY globally conserved residues :VT N normal residues R identical residues B similar residues E globally conserved residues :PICTFILE WB normal residues BW identical residues 1B similar residues B2 globally conserved residues 10 character size (in Pts.) T shade only ? n landscape mode