addenda-3.0

mfold

1. 7/2/99

"ENERGY =" has been changed to "dG =" throughout. The mfold script now
creates a $FILE_PREFIX.dh file by running 'efn' to compute (RNA or
DNA) enthalpies of the original ct file, when enthalpies are
available.

The new add-dHdSTm program reads a text output file (.out or
.out.html) or a detailed out put file (.det or .det.html) and then
reads in a corresponding .dh file, which should already be
computed. The output file is identical to the input file, except that
"dG = " records have enthalpies, entropies and Tm's appended. Note
that Tm is computed from a simple 2 state model and should only be
used for oligos.

2. 7/19/99

John SantaLucia spent July 12-16 in St. Louis. During this time, we
added [Na+] and [Mg++] corrections for DNA folding. This is done
entirely through the newtemp program, so changes were
minimized. However, it was necessary to go from single decimal to 2
decimal precision for all the free energy fules. This affected all the
".dat", ".dg", ".dh", ".dgd" and ".dhd" files. In addition, nafold had
to be altered to read the more precise energy files. Makefile now
automatically creates 2 versions on nafold. The nafold2 version
uses full integers and the free energies are stored as 100ths of a
kcal/mol. This version will fold up to 500 bases. nafold2 can be
made to fold more or fewer than 500 bases, depending on the value of
'MAXN2' in Makefile. The value of 'MAXN' controls the number of bases
that nafold can handle. This program continues to use 16 bit (short)
integers and stores free energies in 10ths of a kcal/mole. 

The changes affected other programs as well. sav2plot and sav2p-num
have 2 new versions, sav2plot2 and sav2p-num2, corresponding to nafold
and nafold2, respectively.