*** NB.  This is a cut-down version of the UCL distribution for CCP4,
*** omitting the NMR component.  It may also not be up-to-date -- check out
*** the UCL ftp area for the latest.


PROCHECK v.3.5, incorporating PROCHECK-NMR and PROCHECK-COMP
------------------------------------------------------------

Introduction
------------

PROCHECK consists of 3 main components: the original PROCHECK programs for
assessing the overall geometrical quality of protein structures, the
extensions for analysing NMR ensembles (PROCHECK-NMR), and the version for
comparing related protein structures (PROCHECK-COMP, or PROCOMP).

PROCHECK itself is intended as a tool for highlighting regions of a
protein structure where the geometry is unusual and hence which may need
closer examination.

PROCHECK-NMR is an extension for ensembles of NMR structures (where all
models are in a single PDB file, delimited by MODEL and ENDMDL records).
As well as analysing the geometry of the structures in the ensemble, the
programs also produce analyses of the NMR restraint violations. The
violations are calculated by a program called AQUA, written by Ton Rullmann
of Utrecht University. AQUA requires the restraints be supplied in a
standard file format, but also has scripts for converting DISGEO, X-PLOR,
etc restraint files into this format. AQUA produces detailed listing of all
its analyses.

PROCHECK-COMP is for comparing the residue-by-residue geometry of a set of
closely-related structures, such as separate members of a family, or models
of the same structure saved during different stages of refinement. It
outputs a number of PostScript files showing the comparisons, including
residue-by-residue Ramachandran plots and comparison of the different
secondary structure elements in each PDB file.


THE SOURCE CODE
---------------

The latest versions (v.3.5) of the PROCHECK programs are in two
directories, available via anonymous ftp on 128.40.46.11, as follows:-

pub/procheck/tar3_5
-------------------
This contains the following compressed tar files:-

    procheck.tar.Z   - The source code for PROCHECK v.3.5 (which includes
                       PROCHECK-NMR and PROCHECK-COMP).

    manual.tar.Z     - Operating Instructions for PROCHECK, in HTML format.

    aqua.tar.Z       - The source code for AQUA.

    nmr_manual.tar.Z - Operating Instructions for AQUA and PROCHECK-NMR,
                       in HTML format.

For unix systems, transfer these four files across to your machine and then
uncompress and untar them.

pub/procheck/source3_5
----------------------
This contains all the individual PROCHECK source files, script files,
command files, and documentation files (excluding the AQUA programs and the
AQUA and HTML-format documentation). If yours is a VAX/VMS system, you
will need to transfer all these files using "mget". Remember to change the
transfer mode from BINARY to ASCII.



CONFIDENTIALITY AGREEMENT
-------------------------

Before using the programs you must first sign a Confidentiality Agreement.
This is in a file called confid.doc which you will find both in the
pub/procheck/ directory and in amongst the source files when you uncompress
procheck.tar.Z. If you are a new PROCHECK user and have not already
returned this document, please print it off (Note: it is an ASCII text
file), fill in the details, sign it and send it to the address given at the
bottom.




INSTALLATION INSTRUCTIONS
-------------------------

The PROCHECK installation instructions are in a file called
maninst.ps. This is a PostScript file, so send it to a PostScript printer
and follow the instructions carefully before doing anything else.

The AQUA programs are in the compressed tar file called aqua.tar.Z which
contains all the source code, script files and documentation. When you have
uncompressed and untarred the file, read the README file for installation
instructions.

Note that, the AQUA scripts that run the programs are currently available
for unix machines only.


OPERATING INSTRUCTIONS
----------------------

1. PROCHECK
   --------
   The operating instructions for PROCHECK are in a set of HTML format
   files in manual.tar.Z. Create a directory for the documentation and
   uncompress and untar this file. Then use Netscape or Mosaic to view the
   documentation by calling up the contents page index.html.

   For example, with Netscape, type

             netscape index.html &


2. AQUA and PROCHECK-NMR
   ---------------------
   The operating instructions for AQUA and PROCHECK-NMR are in a set of
   HTML format files in nmr_manual.tar.Z. Create a directory for
   the documentation and uncompress and untar this file. Note that the
   directory should be separate from that where the PROCHECK documentation
   (above) is stored, as many of the files have the same file-names in the
   two sets of documentation.

   Use Netscape or Mosaic to view the documentation by calling up the
   contents page index.html.

   For example, with Netscape, type

             netscape index.html &

   IMPORTANT. For existing users, please note that the method of running
              the new PROCHECK-NMR programs has altered slightly in that
              the name of the restraints file is no longer required as the
              second parameter (which is now used for the ranges file
              instead - see Operating Instructions).

3. PROCHECK-COMP
   -------------
   There is no documentation for PROCHECK-COMP at present, but the program
   will be further developed (and proper documentation produced) later in
   1997.

   To run, enter:

                    procheck_comp  filelist

       where   filelist   =   file containing the list of structures
                              to be compared

   For example:-
                    procheck_comp  globins.list

   At present, this program assumes that the residue-numbering between the
   PDB files to be compared corresponds to equivalent residues (though
   allowance is made for insertions and deletions). The program also
   assumes that the structures have already been fitted and superposed on
   the equivalent residues. Future versions will allow an alignment between
   the structures to be supplied so that equivalent residue-numbering will
   no longer be a requirement, and will also perform the fitting.

4. GFAC2PDB
   --------
   A new program called gfac2pdb is supplied with the latest version of the
   PROCHECK programs. This can be run to generate a PDB file of your
   protein structure with all torsion-angle G-factors converted into
   B-values (scaled from 0.0 to 80.0). The new PDB file (called
   <filename>_gfact.pdb, where <filename> is the original rootname of your
   coordinates file) can be viewed using any molecular modelling package
   with the atoms coloured according to B-factor. The high B-value regions
   will then highlight the regions with unusual G-factor scores.

   See section 6 of the PROCHECK Operating Manual for further details.




IMPORTANT NOTE for existing PROCHECK and PROCHECK-NMR users
-----------------------------------------------------------
If you have been using a version of the programs earlier than v.3.3 you
will find that the current version of PROCHECK has a number of extensions
in the parameter files (procheck.prm and procheck_nmr.prm). If you run
either PROCHECK and PROCHECK-NMR in a directory which contains an old
version of one of these parameter files you may get an error message about
the version numbers being incompatible. In this case, just delete your old
parameter file before running the program again. A new version of the file
will be created in its place.




If you have any problems either installing or using the software, please
write to me at the following e-mail address:-

      roman@bsm.bioc.ucl.ac.uk

Questions about AQUA should be directed to Ton Rullmann at

      rull@nmr.chem.ruu.nl



Roman Laskowski.
