automar 248x110
Edited on May 04, 2009

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Installation

1. Supported Operating Systems

The executables in the automar distribution have been compiled and are available for the following operating systems:

Name OS Version
Linux RedHat, SuSE 9.x, 10.x
Apple Mac OS X 10.4.x 10.5.x

Note: Apple Mac OS X requires X11 that must be obtained and installed separately. For further information on how to do protein crystallography on Mac OS X, please refer to: Crystallography on OS X by W Scott et al. from UC Santa Cruz, CA, USA.

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2. How to Get It

The automar distribution is available free of charge by FTP from the anonymous FTP-server at marresearch.de from directory ftp://ftp.marresearch.de/pub/automar. Alternatively, you may use the Download Page of the Marresearch web site.

To reduce download time, the package has been split into several parts. For a new installation, all packages should be downloaded. For future upgrades, in most cases it will be sufficient to only update the binary executable distributions. All tgz-packages have the same file structure with a top level directory called "automar". For further instructions on how to install the software, see below .

Programs that do not belong to Marresearch GmbH, i.e. all CCP4 programs including MOSFLM and SCALA must be obtained from the CCP4 web site. Programs denzo, scalepack, XDS and XSCALE are are commercial programs and are therefore NOT included within this distribution.

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3. Environment

The environment should best be defined within the shell startup scripts, i.e. files $HOME/.cshrc (C-shell) or $HOME/.tcshrc (TC-shell) or $HOME/.bashrc (Bourne-shell) using the usual nomenclature. When executing the installation script (setup), the additions to the corresponding login scripts will be done automatically. This scipt also takes care about the CCP4-environment settings which are needed for the additional programs from the CCP4-suite.

Name Description
MARPRCDOCDIR Location of directory tree with documentation.
MARPRCDATDIR Directory where to save current session parameters (automar.mix).
MARPRCDEFDIR Directory where to find default session parameters (automar.defaults) and executable file cleanup.com
AUTOMARDOCDIR Location of directory tree with documentation. Only used if MARPRCDOCDIR is not defined.
AUTOMARDATDIR Directory where to save current session parameters (automar.mix). Only used if MARPRCDATDIR is not defined.
AUTOMARDEFDIR Directory where to find default session parameters (automar.defaults) and executable file cleanup.com Only used if MARPRCDEFDIR is not defined.
AUTOMARDIR Root directory of the automar distribution with subdirectories $AUTOMARDIR/man for the documentation and $AUTOMARDIR/dat containing session files. Only used if others are not defined.
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4. Directory Structure

The automar program suite directory ($AUTOMARDIR) contains the following directories.

Directory Contents
bin/linux Binary executables for Linux (RedHat, SuSE, etc.)
bin/ppc Binary executables for Mac OS X (Power PC)
bin/osx86 Binary executables for Mac OS X (Intel)
ccp4 Stuff required for defining the environment of CCP4-programs
man/man Unformatted man pages for programs written by marresearch
man/html HTML conversions of unformatted man pages
man/css Style sheets used by HTML pages
man/layout Design elements used by HTML pages
man/automar HTML documentation of automar program suite
man/automar/img Graphics files used by HTML pages
man/ccp4 HTML documentation of mosflm and the some CCP4-programs
dat Startup file for program automar (automar.mix).
tmp Temporary files used by some CCP4-programs

When installing the automar program suite, make sure to create these directories.

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5. Description of Programs

Name man page html page Description
automar yes yes GUI for data processing
marPeaks yes yes Spot search in images
marIndex yes yes Autoindexing
marPredict yes yes Predicts patterns from matrix of marIndex
marStrategy yes yes Obtains best data collection strategy
marProcess yes yes Integrates images
marPost yes yes Postrefinement and addition of partials
marScale yes yes Scales and merges data from marProcess-run
sortmtz/binsort no yes Sorts "mtz"-file from mosflm-run
scala no yes Scales and merges data from mosflm-run
truncate no yes Converts intensities to structure factors
mar2mtz no yes Converts output from marScale into "mtz"-file
mtz2various no yes Converts binary "mtz"-files into other formats
mtzdump no yes Lists contents of binary "mtz"-files
mtzutils no yes Various data manipulation tools for "mtz"-files
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6. Installation

6.1 Download


6.2 Setup

The "automar-install"-installation script is a text based shell script that will ask you a couple of questions. Defaults (in [brackets]) will be applied when just typing return. The default location of the automar program suite should be $HOME/automar.

The "setup"-procedure will modify your login scripts (either .cshrc or .tcshrc) and append the new path names and environment parameters at the end of the file.

After finishing the "setup"-procedure, source the .cshrc or .tcshrc file and start work, e.g. by typing: automar

If for some reasons the automar-install script fails, it is easy enough to do the setup manually. The installation consists of:

In the login shell initialization scripts you will have to set some environment parameters, in particular AUTOMARDIR and AUTOMARDOCDIR, if you like also AUTOMARDATDIR. Then, you have to add the location of the executables to the binary search path.

Example for .cshrc:

	setenv AUTOMARDIR        $HOME/automar
	setenv AUTOMARDOCDIR     $AUTOMARDIR/man
	set path                = ( $path $AUTOMARDIR/bin/linux/glibc-2.5 )

Example for .bashrc: 

	export AUTOMARDIR='${HOME}/automar'
	export AUTOMARDOCDIR='${AUTOMARDIR}/man'
	auto='${AUTOMARDIR}/bin/linux/glibc-2.5'
	if [ ${PATH} ]; then              
	     export PATH="${PATH}:${auto}"
	else
	     pub=".:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/bin"
	     export PATH="${pub}:${auto}"
	fi

Some programs out of this software suite make use of a license key mechanism. Please refer to the following section for more details.

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7. License Key

The automar software suite is NOT public-domain software. Marresearch GmbH, however, does NOT charge license fees for the programs contained within this suite, but users must get registered in order to continue using the programs after a compilation-date coupled period of usage has expired.

License keys will be supplied to customers of Marresearch GmbH and Rayonix, LLC, only.

The following programs require a license key:

License keys are platform specific. A license key file must be installed on each computer in order to be able to run the programs.

Run program marlicense on each platform where you want to install the corresponding programs. marlicense is contained within the automar software suite. This program requires simple terminal input and produces an ASCII type output file named "marlicense.hostname" that must be mailed to 'license@marresearch.com'. Mailing can be done automatically from within program marlicense.

marresearch will return a crypted license file that must be installed in one of the following locations on the target host computer.

Note, that the returned license file will be void when modified in any single byte. Note also, that $HOST is the computer's hostname as returned by the UNIX command 'uname -n' but without the domain name. Each of the programs tries to read the license files in the given order. This mechanism can be overwritten by defining an environment parameter MARLICENSE, e.g. like this:

setenv MARLICENSE directory/marlicense.XXX

As a last resort, if there is no license key installed at all the programs have a limited lifetime coupled to the date of compilation.

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