Date: Thu Nov  3 14:54:27 EST 2005
Name: Jonathan Foley
Email: jonefoley@gmail.com
Remote Host: 169-229-7-53.sph.berkeley.edu
Subject: mfold RNAml and RNAMLVIEW error

When I try to open a mfold generated rnaml structure file with
rnamlview I get the following error:

a base-pair with the base n4 at the 5' side for the helix n infinity 1
is not found in the base-pair list of your RnaML file

M. Zuker replies:

Thank you for reporting this problem. I have been aware for a while
that rnaml files were not being parsed properly by web browsers. I
looked into the
http://www-lbit.iro.umontreal.ca/rnaml/current/rnaml.dtd file at the
University of Montreal and found an error in it. We are working to
resolve the problem.

November 18, 2005: There is no error in the rnaml.dtd file. The rnaml
files from my web site are properly formatted and are parsed correctly
if renamed to have the suffix "xml". It's a matter of browser
settings. This has nothing to do with your problem. It turns out that
"rnamlview" is not intelligent enough to read our rnaml files that
contain all of the necessary information. I will contact the author of
the rnamlview program as well as the Major group at the University of
Montreal. When we specify a helix, we do not specify the individual
base pairs as well. They are implied by the helix. I will pursue this
problem until it is resolved, but I cannot promise a quick solution.