README

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.

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

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_4.4 --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_4.4) over the master
development branch.  Just "git checkout molprobity_4.4" 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

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