WHAT_CHECK will run on Linux machines, but be aware that it was tested on only two of them, so be in for
a bit of creativity (for a Mac OSX version,
see: https://trac.macports.org/browser/trunk/dports/science/whatcheck/Portfile). Follow the series
of steps listed below in that order. Things in < > brackets
are place holders that need to be replaced in their entirity. So, for example, <PDB-file> should,
for example, become 1CRN and not <1CRN>.
- Get the tar file. It is called whatcheck.tar or whatcheck.tar.bz2.
If you take the latter, you must uncompress it with
the command bunzip2 whatcheck_<version>.tar.bz2.
- Create a new, empty directory. Try to keep the path a bit short, so preferably make a dirctory
like /home/yourname/whatcheck and not /usr/imported_software_products/three_dimensional_related/Xray/whatcheck or so.
- 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 and/or the pdbout.txt files.
- Untar the whatcheck.tar file with ′tar -xvf whatcheck.tar′. This will generate a bunch of
directories that will be explained further down this writeup.
- In the whatcheck directory type twice ′make clean′ and once ′make′. If you have
many cores you can replace ′make′ by ′make -j<X>′ in which X is two times
the number of cores available to you.
- Make an alias <whatcheck> that points at <.../whatcheck/bin/whatcheck>
- Make sure whatcheck can see your CCP4 suite because whatcheck uses Acedrug and DSSP from the CCP4. Check
that DSSP.EXE in the .../whatcheck/dssp directory points at the DSSP executable in CCP4. If you don't
have CCP4 installed, replace the DSSP.EXE link by the the DSSP executable (available from this same site)
and call it DSSP.EXE. If you don't have CCP4 available, you either have to live with sub-optimal
results for the hydrogen bond network calculations, or run the ProDrug server in Dundee for each
ligand unknown to whatcheck.
- Somewhere, but neither in the whatcheck directory, nor in any of its sub-directories, type:
- Now type
acroread pdbout.pdf (or evince pdbout.pdf)
- Some people might only be interested in the check.db file. They can skip the latex etc steps.
- 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
I have added a fig2dev in the directory scatter. 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.
On some machines scatter doesn't work (properly). In those cases recompiling scatter (a Makefile
is present in the scatter directory) can help. You might also need to remove the BSLASH1 precompiler
directive on some machines.
- 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. If you make a ligand topology with ProDrug, you need to add the
resulting WHAT IF topology in the TOPOLOGY.FIL file in the .../whatcheck/dbdata directory.
I think it is easier to just install the CCP4 suite...
You can modify WHAT_CHECK's behaviour in many ways.
If you are a Latex specialist, look in .../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 .../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/PARAMS.FIG holds actual
WHAT_CHECK operational parameters. May I suggest you don't change these unless you really know
what you are doing?
However, if I made a mistake and messages pop up that start with DBG> you can set parameter 1012
to zero (in PARAMS.FIG).
The present WHAT_CHECK is more meant for X-ray crystallographers than for NMR spectroscopists (albeit
that I don't expect it to fail on an NMR ensemble). If you don't like the suggestions for
crystallographers that are listed after the summary, you can put parameter 105 at zero (in PARAMS.FIG).
Be aware that CING holds all WHAT_CHECK
results that are relevant for NMR validation, and CING uses them in a NMR-friendly context (contact
Geerten Vuister (email@example.com) for access to cing
Good luck (you will need it).