SeqApp PrettyPrint problem
I'm using SeqApp-1.9a166 (and -1.9a159) on a Mac II FX under System 7.1.
When I open a PIR file of aligned amino acid sequences, I can appropriately
highlight selected amino acids in colors (for example, I can assign blue for
basic residues, etc.). However, when I then use PrettyPrint to generate an
aligned display that has identical residues shaded at each position of the
aligned sequences, the previously selected amino acid color coding is lost,
and the coding reverts to default color coding (A is red, C is blue, G is
green, T is orange). I'm able to alter the shading of conserved residues and
select the level of conservation that triggers the shading (boxing); however,
I've been unable to select any alternative residue color schemes in the
PrettyPrint display. I wished to check with the SeqApp "satisfied user"
population, to see whether this is a general problem, or is it specific to my
To summarize, PrettyPrint has exactly the display modalities that I need, I
just can't seem to alter the residue color display in that window, despite
having full control over residue color coding in the initial filename-Align
Kudos to Don Gilbert for his efforts in providing this software to the
research community, and in his efforts to provide a central exchange point
for software and data at bio.indiana.edu.
Philip C. Ross