Updated May 20 2015
Installing MolProbity:

32 BIT linux may not be supported.

Welcome to MolProbity!!

Installation

Installation is fairly straightforward. First move the MolProbity
directory (the directory that this README file is in) to a location
where you want it to reside. Note that Apache will have to see
MolProbity/public_html if you are interested in setting up a web
service. Once the MolProbity directory is in the proper location, you
are redy to install. Open a terminal and go to the MolProbity
directory.

Linux users: ensure that gawk is on a path that the server can read
(gawk may need to be installed).

Linux users: python-dev is a dependency of one of MolProbity's cctbx
dependencies, and may need to be installed. The build script will warn
you about this if it fails for this reason.

0. Acquiring MolProbity

Currently the only way to get MolProbity is from GitHub. For users, we suggest:

git clone https://github.com/rlabduke/MolProbity.git --branch molprobity_4.3.1 --single-branch --depth 1

This will check out just the most recent release of the code. If you
did a whole-repository checkout instead, let us suggest you swap to a
stable release branch (currently molprobity_4.2) over the master
development branch.  Just "git checkout molprobity_4.2" from the
directory containing this readme.

1. Run configure.sh. 

If your machine has less than 2 GB memory per processor, you may wish
to edit configure.sh by commenting out "make" and commenting in the
nearby line "./bin/libtbx.scons -j 1".  This causes the underlying
cctbx code to compile on only one processor instead of all processors
- it's slower (an hour?) but less likely to bog down your computer.

>>> ./configure.sh

This will install cctbx_project and needed components in MolProbity/sources:

    build list:
     annlib
     annlib_adaptbx
     boost
     cbflib
     ccp4io
     ccp4io_adaptbx
     cctbx_project
     chem_data
     lapack_fem
     probe
     reduce
     scons
     tntbx

and then will compile and configure in MolProbity/build.

2. Run setup.sh to configure the webserver.

>>> ./setup.sh

If setting up a webserver, make sure that the machine's Apache
configuration can point to the MolProbity/public_html directory.

Note that it is not necessary to setup a webserver if you are only
interested in running the command-line tools.

Note that it is not necessary to set up an externally-accessible
webserver like Apache to get MolProbity served as a website available
only on your computer (via localhost). You will need to install
php-cli or a similar package, then run "php -S localhost:8000" in the
MolProbity main directory. This sets up a non-public webserver. In a
browser, navigate to http://localhost:8000/public_html/index.php , and
you will have a functioning local MolProbity site.

3. Tweak Apache settings as needed

We have provided two files in public_html/, .user.ini and .htaccess,
which attempt to preclude the need for users to do system-wide server
reconfigurations.  In particular, .htaccess should override the global
php.ini for an Apache MolProbity server, and .user.ini should do the
same for a local PHP-CLI server.

If that doesn't work, you may need to edit Apache settings for proper
MolProbity performance.  The settings file is often called php.ini,
e.g. /etc/php5/???/php.ini, but it will vary on different computers.
Two such defaults are:

upload_max_filesize = 2M
post_max_size = 8M

Something like 50M (for both) may be more appropriate.

An external explanation:
http://stackoverflow.com/questions/24377403/maximum-upload-size-in-php-and-apache
http://stackoverflow.com/questions/2184513/php-change-the-maximum-upload-file-size