Release Notes for HINT 2.35I

1. HINT 2.35I has been optimized to work with insightII 98.0 and 2000.
   HINT was compiled:
   • Under Irix 6.5 on a R4400 SGI using the -mips3 compiler directive with the MIPSpro^TM 7.2.1 compilers.
   There is no R8000/R10000 (64 bit) insightII/HINT executable available. However, the background executable, which is used for non-interactive HINT jobs, has been compiled with the mips4/-64 option and can be used by those with r8000/r10000/r12000 processors. (See the Installation instructions for more information.) Also note that there is no further support for Irix5.x and R3000 processors forthcoming from MSI, so we cannot provide it either.

2. An error has been discovered in the interaction matrix for classifying and setting the sign of interactions for Interaction Tables and Interaction Maps. This particular error was only a problem when interacting two species that were (both) partitioned with the "ALL" Hydrogens Option. Interactions between hydrophobic (apolar) hydrogens and polar heavey atoms were being misclassified and assigned the wrong sign. (They should be unfavorable hydrophobic-polar). We have fixed the error. It should be pointed out that we have generally recommended using POLAR_ONLY hydrogen paritioning when perfori=ming interaction calculations, for several reasons: 1) apolar hydrogens are never explicitly located in experimental structures of biomacromolecules, so using their locations in sensitive distance-based calculations may be overextending the actual structure data; 2) the HINT parameterization for splitting, for example a methyl, into four separate atoms is uncertain, and 3) this would appear to add unneccessary complications to the calculation. A methyl-methyl interaction would become 16 separate calculations. We have added some text in the Theory section of the manual to more explicitly define the interaction matrix and its effect on HINT interaction calculations. (Through extensive calculations, Andrea Mozzarelli, Anna Marabotti, Pietro Cozzini, and Lara Balestreri of the University of Parma have located and characterized this problem.)

3. We have revised the HINT partition dictionary for nucleic acid bases, particularly for RNA.

4. There was an error in the Solvent Optimization algorithm for cases of 3 "site" molecules. This has been corrected. Also, there was a problem with the "speed" parameter which also has been fixed. (James Burnett of Virginia Commonwealth University reported these problems.)

5. Two aliases are defined in the Hint (2.35I) cshrc file:
   • DEFINE_HINT - sets the library path to use Hint.
   • RESET_INSIGHT - returns the library path to the original.
   Enter one of these two choices before starting InsightII. In either case InsightII is activated by entering "insightII" to the unix prompt.

6. Previous versions of HINT will not operate after this end of this year due to a date rollover in the License Manager.