Updated Nov 18 2019

Welcome to MolProbity!!

MolProbity website source and installation instructions are provided with the
cautionary restriction and explicit understanding that user deployment occur
only on individual machines and restricted access private networks.
This code is not intended for deployment on world accessible public sites.

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.

32 BIT linux may not be supported.

Mac users: The Xcode app and xcode commandline tools may be needed to install
MolProbity.

0. Acquiring MolProbity

The MolProbity installation process is currently in flux.
Currently we recommend obtaining the installation script on its own:

svn --quiet --non-interactive --trust-server-cert export https://github.com/rlabduke/MolProbity.git/trunk/install_via_bootstrap.sh

Place this script at the top level of the directory where MolProbity is to be
installed.


1. Run install_via_bootstrap.sh. 

>>> ./install_via_bootstrap.sh

The script can accept a single integer argument to set the number of processors
to use.  We recommend 4 if possible.

>>> ./install_via_bootstrap.sh 4

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.

>>> cd/molprobity
>>> ./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

It may also be appropriate to set the script memory limit, thus:
memory_limit = 1280M