Problems, Workarounds, Clarifications (FAQ)

1. When attempting to Create a HintMap or HintTable, Hint tells you to partition the molecule first even though you already have. This problem seems to occur when the InsightII object name for the molecule is particularly long. The workaround is to shorten the object name to no more than 9 characters and repeat the partition step.

2. Many Hint errors are currently reported only in the text window. We continue to supplement the Hint error reporting with upcoming releases. The obvious workaround is to monitor the text window for error messages from the Hint executable.

3. There have been some comments on the difficulty of getting all of the atom types correctly set for small molecule (i.e., calculate method) partition calculations. This is a major bore, but it is of utmost importance to get the best partitioning results. We would like to point out that there are few other properties as sensitive to small changes in structure as the LogP. For example, adding one methyl to a molecule adds 0.8-0.9 log units to its hydrophobicity, or in other words changes its solubility by nearly an order of magnitude!

Hint 2.35I Installation Instructions

The Hint 2.35I installation consists of two components: 1) installing the Hint software and 2) setting up user accounts to give them access to Hint. Although it is not strictly necessary, the installation of Hint is best performed as the "superuser".

Note: This installation creates a new "dynamic shared object" (DSO) libuser.so that contains both original (MSI) InsightII 970/972/980/2000 functionality and the new Hint functionality. The user must be cautioned that any problems with Hint routines are NOT the responsibility of MSI. Errors and/or questions about Hint should be directed to eduSoft, LC. MSI WILL NOT HELP YOU! If, in the course of using Hint, problems develop that are apparently unrelated to the Hint module, the user is asked to reproduce the problem with the original InsightII before calling MSI to ensure that the problem is not Hint related.

1. Make a root directory for the eduSoft products. We recommend /usr/eduSoft, but any location will work. The unix command for this step is: mkdir /usr/eduSoft

2. Unload the Hint 2.35I tape or tar file into this directory:
   • cd /usr/eduSoft
   • tar xov

3. Make sure that the Biosym environment is defined. If you are not sure, check to see if the environment variable BIOSYM is defined:
   • echo $BIOSYM
   If $BIOSYM is not defined, you will have to perform the steps you usually undertake to run InsightII up to the point where you enter insightII to the unix prompt.

4. Change the current directory to the eslc directory.
   • cd eslc

5. One of the Hint definition files must be "sourced" to define the appropriate Hint variables and code. There are three definition files, keyed to the SGI processor and O/S you are using (see the release notes for more explicit information.) These are detailed in the table below. Edit the appropriate config/cshrc_?? so that the proper location of $EDUSOFT_ROOT is set (assumed above to be /usr/eduSoft).
   • vi config/cshrc_hint
   • make appropriate changes...

   (All other HINT environment variables are defined relative to $EDUSOFT_ROOT.) If you are on a mixed network of processors, you may have to add some shell logic here to call the correct definition files. Note that there is not an r8000/r10000 executable for HINT; however, there is for the background program used for batch calculations.

   Product(s)	Platform	config/cshrc
   Hint 2.35I	r4000	cshrc_hint
   	r8000/r10000/r12000	cshrc_hint_r8

6. Install the HINT License Keys(s) as described on-line.

7. Enable Hint 2.35I for users. All users who want to use the insightII+Hint DSO must modify their individual .cshrc files to define the Hint environment. The line "source /usr/eduSoft/eslc/config/cshrc_hint" needs to be after any reference to files that define the InsightII program and environment.
   • vi ~user/.cshrc
   • make appropriate changes (for each user)...

8. Try it out. Typing "DEFINE_HINT" will select the InsightII+Hint DSO rather than the original. To return to the original MSI DSO environment type "INSIGHT_RESET". In either case entering "insightII" to the unix prompt activates the program. Alternatively you can add the line "setenv LD_LIBRARY_PATH ${HINT_SO}:{LD_LIBRARY_PATH}" to your/users .cshrc file if you believe that you will always want to use the Hint DSO when using InsightII.

Special Notes for "Customized" InsightII Sites

If there are questions or difficulties with the Hint installation, please feel free to give us a call.