IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

prettybox bug?

Peter Rice pmr at sanger.ac.uk
Thu May 23 05:26:28 EST 1996

In article <31A2AE86.22A9 at sgi.celgen.kuleuven.ac.be> Hugo Klaassen <hugo at sgi.celgen.kuleuven.ac.be> writes:
>   I have a prettybox problem. When I take an .msf file to shade the 
>   residues (protein) everything works fine except when I have a part of 
>   the .msf where only one sequence is present (for instance one of them is 
>   longer than the rest and "stick out"). What happens then is that the aa 
>   get colored as there was a 100% identity (black background). Anyone has 
>   an idea how to get rid of that miscoloring?

Sounds like a problem with the value of "plurality", allowing it to
build a consensus from just one sequence.

There is a problem with prettybox in the original EGCG 8.1 release.
To fix it:

% to egensourcevms

(or $ SET DEF EGENSOURCE on VMS systems)

... edit prettybox.for

change the lines:

         Call EGetReal ('Find consensus to what plurality',
     1          'PLUrality', 0.0,  900.0,  XPos, XPos)


         Call EGetReal ('Find consensus to what plurality',
     1          'PLUrality', 0.0,  900.0,  XPos, Plurality)

then rebuild prettybox with ebuildapp prettybox (Unix and VMS use the
same command here)

This is fixed in the current EGCG 8.1 distribution.

There are, of course, other versions of PRETTYBOX out there ...

Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr/   | England

More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net