Installation

1. Get the tar file. It is called whatcheck_<version>.tar.bz2. So you must uncompress it with the command bunzip2 whatcheck_<version>.tar.bz2.
2. It would be nice if you can create a user "vriend" with as home directory "/home/vriend/". In that case, you put the tarfile whatcheck.tar (or whatcheck.*.tar) in the "/home/vriend/" directory and unpack it. After that, the command:
   /home/vriend/whatcheck/DO_WHATCHECK.COM <PDB-file> will validate the PDB file named PDB-file.
3. Make sure the whatcheck directory is in your path (needed for the picture software). This is not important if you are only interested in the check.db computer readable WHAT_CHECK output file.
4. If you install WHAT_CHECK at some other location, it will work just as well, but there is some code in WHAT_CHECK that looks for the (location of the) databases. You will need to adjust the paths in the files DO_WHATCHECK.COM and WHATIF.FIG to properly indicate the location of WHAT_CHECK on your system.
5. In the whatcheck directory you find a sub-directory "dssp". This directory holds DSSP.EXE, which is an executable of the DSSP program by Kabsch and Sander. This software can only be used in the context of WHAT_CHECK. If you want to use it for other purposes, you need a license. DSSP is here. If this executable does not work (and it is highly unlikely that it will work...), then go to the http://swift.cmbi.ru.nl/gv/dssp/ DSSP site and get an executable that suites your needs (or get the source and compile it). Make sure you call the executable DSSP.EXE and that you place it in the directory .../whatcheck/dssp/.
6. Make an alias:
   alias WHAT_CHECK /home/vriend/whatcheck/DO_WHATCHECK.COM
   or any other path if you installed WHAT_CHECK elsewhere.
7. Log off and log on again (or source your .cshrc or equivalent file) and test WHAT_CHECK. In the directory /home/vriend/whatcheck/junk you find all files produced by what_checking 1crn with the actual WHAT_CHECK version. Go to any directory (neither run WHAT_CHECK in the whatcheck directory, nor in any whatcheck sub-directory, but always in any other directory) and copy 1crn.pdb there. Now type WHAT_CHECK. This will copy some files from whatcheck subdirectories local and starts the whatcheck executable. It will ask you for the name of the PDB file. Answer 1crn.pdb, or, if you have set your PDB directory in the CCONFI.FIG file (see below) just say 1crn. After some seconds the validation is done. Now type
   latex pdbout
   dvipdf pdbout
   acroread pdbout.pdf (or evince pdbout.pdf)
   and you have the validation report. Now check that the report is the same as the one I made for you and that is in the /home/vriend/whatcheck/junk directory. If that is the case you are all set.
   Some people might only be interested in the check.db file. They can skip the latex etc steps.
8. After running WHAT_CHECK you find several files in your directory. The important ones are: pdbout.txt which is the WHAT_CHECK result in ASCII text format.
   pdbout.tex which is the WHAT_CHECK result file in Latex format.
   check.db which holds all warnings, errors, etc., is in a format that is easy to parse by other programs.
   

Additional software needed

WHAT_CHECK doesn't really need any additional software, but it works much nicer if a few things are additionally available. Some of these come default with certain Linux variants, though, so don't start installing things before checking if it is really needed.

• If you encounter an "empty scatter plot" problem you need fig2dev (which is part of the transfig package). I have added a fig2dev in the directory scatterdir. In this directory you also find the scatter software that is used for some of the WHAT_CHECK plots. I guess it is easiest to either make sure that this directory is in your path, or to copy the two executables to the directory in which you run WHAT_CHECK routinely.
• DSSP has been mentioned above already.
• PRODRUG is Daan van Aalten's software (now maintained by Alex Schuettelkopf) that makes topology entries for ligands, substrates, drugs, etc. WHAT_CHECK can work without it, but works better with. You find the files DAVADRUG.TOP and prodrg in the sub-directory .../whatcheck/prodrug/. If prodrug failes (you see that the first time you run into a non-standard ligand because 'Ligand without topology' is a standard error message) you need to obtain a version that is commensurate with your hardware/firmware situation.

Tuning WHAT_CHECK

You can modify WHAT_CHECK's behaviour in many ways. The first one is to look in the file /home/vriend/whatcheck/dbdata/CCONFI.FIG because in this file you can modify the standard location of your PDB files. The rest of this file is mainly for WHAT IF and has little influence on WHAT_CHECK.

If you are a Latex specialist, look in /home/vriend/whatcheck/dbdata/HEADER.TEX if you want to change/correct some of my Latex work.

If you don't like my Dutchlish and want proper English warnings, search for the printed text in /home/vriend/whatcheck/dbdata/MESSAGES.TXT and correct it. This file can also be used if you want to make a French or Russian version, for example.

And finally, the most difficult thing: /home/vriend/whatcheck/dbdata/PRARAMS.FIG holds actual WHAT_CHECK operational parameters. May I suggest you don't change these unless you really know what you are doing?

Good luck (you will need it).