prettyplot output

michael.baron at bbsrc.ac.uk michael.baron at bbsrc.ac.uk
Mon Jul 17 08:50:03 EST 1995

In article <1995Jul13.134532.9944 at reks.uia.ac.be>, przemko at reks.uia.ac.be 
(Przemko) says:
>prettyplot has finally arrived to our machine. Thankx to Peter Rice for 
>those color options etc.
>But, here is my problem.
>I would like to achieve the following
>-take file in msf format (BTW, why there is no conversion from Clustal 
.aln to 
>.msf format?. I know I can ask Clustal to give me .msf output but not 
all gcg 
>programs will recognize it)
>- color the aminoacids (including BACKGROUD - is it possible in the 
>- generate a .hgl (or any other VECTOR file).
>- import it into PowerPoint and make a slide of that (edit a bit if 
>Now, I can get the first and the second point to work. The problem 
starts with 
>the third point. If my default output is set to postscript, even if I 
>-plot=filename option in the prettyplot, I still get ps_file NOT a HPGL 
>Second problem arises when I get my .hpgl file (because of fiddling with 
>setplot) and get onto my pc. PowerPoint converts it very nicely BUT it 
puts a 
>multiple pages onto one. In other words, if my .msf is 1000bases long 
then I get 
>10 pages overlapped onto one (TOTTALY UNREADABLE). My VERY UNEDUCATED 
>that the end-of-page command (or something like that) is missing from 
that .hpgl 
>output of prettyplot.
>Anyone could help me on that?
>ThanX a lot!

I would like to suggest the latest version (version 3) of BOXSHADE. NOt 
only will it read either .msf or CLUSTAL files, but will also produce 
output in HPGL (amongst many others). The command line switch /SPLIT 
causes individual pages to be split into separate files. The program is 
currently available from the EMBL archive (at least the one at EBI). It 
has another vector-format output, XFIG (?) I think.

BOXSHADE v 3.0 has a number of improvements over 2.7, like threshold 
scores and consensus by similarity. I hope it's useful, but then I wrote 
those new bits, so I would, wouldn't I?

Michael D. Baron
michael.baron at bbsrc.ac.uk

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