TUD Organische ChemieImmelMolArch+ (no frames)InstallationView or Print this frame onlyView or Print (this frame only)

MolArch+ - Download and Installation

This page gives detailed instructions on how to download MolArch+ and its interfaced external applications.

You may also use the frames version of this documentation.

Top of Page MolArch+ - Introduction
Program Name
The name of the MolArch+ program ("Molecular Architecture") was derived from the well-known German Journal "Zeitschrift für Architektur und Städtebau" for Architects named "Arch+".
General Remarks
The MolArch+ program (current version V7.35 09.MAY.2003) is suitable for the representation and animation of simple wire-, capped-, ball-and-stick-, and CPK-type molecular models. It is written almost completely in FORTRAN with some minor parts in C, and features a very simple graphics display and a command line only, but no graphical menus. However, MolArch+ is fully interfaced to produce high-quality models with the POVRAY ("Persistence of Vision") ray-tracing program or any VRML ("Virtual Reality Modeling Language") viewing program. The program can be used to visualize organic and inorganic structures, solid-state crystal structures, molecular orbitals imported e.g. from GAUSSIAN, and different types of molecular surfaces with mapped properties. The command line interface and the batch-processing capabilities make it a highly versatile tool for the visualization, animation, and automated geometry analysis of a wide range of molecular scenarios; a large number of different file types may be imported and exported. The program runs on LINUX systems only, development is done on LINUX Redhat 7.2 and 8.0, but MolArch+ may also be used with other LINUX distributions.
Basic Knowledge
Some advanced knowledge on LINUX systems and the command line (bash) execution environment is crucial for successfully using MolArch+ and its various sub-components. I will not provide any LINUX-related basic support. In particular the animations (as shown in the "movies" section of this web-site) require advanced knowledge on how to create, modify, and run shell scripts. C and FORTRAN compilers are required, and you should know how to modify and adapt "Makefiles" to fit your system.
Top of Page MolArch+ - License Agreement
LICENSE
PLEASE READ THIS LICENSE AGREEMENT CAREFULLY BEFORE USING THE PROGRAM. BY PROCEEDING, DOWNLOADING, INSTALLING, AND USING THE PROGRAM YOU AGREE TO THESE TERMS.
THE PROGRAM IS OWNED BY DR. STEFAN IMMEL, AND NEITHER THE WHOLE PROGRAM NOR PARTS OF IT MAY BE REDISTRIBUTED OR SOLD BY OTHER PARTIES. THE TERM "PROGRAM" MEANS THE ORIGINAL PROGRAM AND ALL WHOLE OR PARTIAL COPIES OF IT. A PROGRAM CONSISTS OF MACHINE-READABLE INSTRUCTIONS, ITS COMPONENTS, DATA, AUDIO-VISUAL CONTENT (SUCH AS IMAGES, TEXT, RECORDINGS, OR PICTURES), AND RELATED MATERIALS.
ONLY NONEXCLUSIVE LICENSES TO USE THE PROGRAM ARE GRANTED. YOU MAY MAKE AND INSTALL COPIES OF THE PROGRAMS ON YOUR OWN COMPUTER, BUT YOU MAY NOT REDISTRIBUTE ANY PARTS OF IT. YOU WILL ENSURE THAT ANYONE WHO USES THE PROGRAM DOES SO ONLY IN COMPLIANCE WITH THE TERMS OF THIS AGREEMENT.
INDIVIDUALS OF ACADEMIC AND EDUCATIONAL INSTITUTIONS MAY DOWNLOAD AND USE THE PROGRAM IN COMPLIANCE WITH THE CONDITIONS MADE HERE FREE OF CHARGE; OTHERS, INCLUDING ALL PERSONS RELATED TO COMMERCIAL INSTITUTIONS OR COMPANIES MUST CONTACT ME BEFORE PROCEEDING TO THE DOWNLOAD SECTION.
YOU MAY NOT 1) USE, COPY, MODIFY, OR DISTRIBUTE THE PROGRAM EXCEPT AS PROVIDED IN THIS AGREEMENT; 2) REVERSE ASSEMBLE, REVERSE COMPILE, OR OTHERWISE TRANSLATE OR MANIPULATE THE PROGRAM.
NO WARRANTIES OR CONDITIONS EITHER EXPRESS OR IMPLIED ARE MADE, INCLUDING WITHOUT LIMITATION, THE WARRANTY OF NON-INFRINGEMENT AND THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, REGARDING THE PROGRAM OR TECHNICAL SUPPORT, IF ANY.
NO WARRANTY REGARDING THE CAPABILITY OF THE PROGRAM TO CORRECTLY PROCESS DATA IS MADE. THE OWNER OF THE PROGRAM WILL NOT BE LIABLE FOR ANY DIRECT OR INDIRECT DAMAGES, INCLUDING WITHOUT LIMITATION, LOST PROFITS, LOST SAVINGS, OR ANY INCIDENTAL, SPECIAL, OR OTHER ECONOMIC CONSEQUENTIAL DAMAGES, EVEN IF THE OWNER IS INFORMED OF THEIR POSSIBILITY.
BY PROCEEDING TO THE DOWNLOAD SECTION YOU DECLARE THAT YOU HAVE READ AND ACCEPTED THESE LISCENCE CONDITIONS.
TECHNICAL SUPPORT MAY BE PROVIDED ONLY ON A PURELY VOLUNTARILY BASIS BY THE OWNER.
Top of Page MolArch+ - Prerequisites
Libraries

(Currently disabled)

MolArch+ uses the public domain VOGLE ("Very Ordinary Graphics Learning Environment") as a portable 3D graphics library and its basic interface. This library must be installed first on your system:
  • Download the archive "libvogle-1.3.0.tar.gz" (approx. 412 KBytes) to a local directory on your system.

    MD5 checksums are as follows: 

    	ls -l libvogle-1.3.0.tar.gz

	-rw-r--r--    1       414060 Apr  8 09:33 libvogle-1.3.0.tar.gz

	md5sum libvogle-1.3.0.tar.gz

	d3d6684020a90ff7fc935ebfdcd78b2d  libvogle-1.3.0.tar.gz
  • Login as "root", unarchive, compile and install "libvogle" and the "hershey" fonts (included with this archive). The default locations are "/usr/local/lib/libvogle.a" and "/usr/local/lib/hershey/", if you want to install these to other locations you must edit the Makefile. For further informations you may refer to the "README" file distributed with this archive. 
    	gunzip -c libvogle-1.3.0.tar.gz | tar -xvf -
    Then compile and install the VOGLE library (you must be logged in as "root"): 
    	cd libvogle-1.3.0
        make
        make install
POVRAY
MolArch+ uses the external program POVRAY ("Persistence of Vision Raytracer") to produce high quality graphics; it is recommended to install this free program on your local system. Download POVRAY V3.5 or latter and follow the corresponding installation instructions. You need not to install the source code, but you must install the POVRAY "include" files as MolArch+ will use for example the color definitions contained therein.

POVRAY versions prior to V3.5 (e.g. POVRAY V3.1) will NOT work with MolArch+.

For examples of POVRAY graphics and animations generated with MolArch+ see the "molecular graphics and movies" section of this web-site.

VRML
MolArch+ uses VRML (Virtual Reality Modeling Language) to generate high-quality 3D structures of molecules. It is recommended to install a viewer capable of displaying VRML models on your local system. Such viewers are freely available from e.g. http://www.web3d.org/vrml/vrml.htm or http://chromebob.com/vrml/. I highly recommend the commercially developed, but freely distributed program vrmlview available for download from Systems In Motion.

For examples of VRML graphics generated with MolArch+ see the "3D structures" section of this web-site.

Top of Page MolArch+ - Download and Installation
Download

(Currently disabled)

The MolArch+ distribution contains the pre-compiled binary executables, all parameter files, and a variety of examples as an introduction on how to use MolArch+. The latest version of MolArch+ is V7.35 09.MAY.2003. If you have installed a previous version (V7.27 or latter, see command 'molarch+ -V' for your version number), you may upgrade from the Updates and Bug Fixes section.
  • Download the archive "molarch+-v735.tar.gz" (approx. 61.5 MBytes) to a local directory on your system.

    MD5 checksums are as follows: 

    	ls -l molarch+-v735.tar.gz

	-rw-r--r--    1     62884381 May  9 19:57 molarch+-v735.tar.gz

	md5sum molarch+-v735.tar.gz

	d6888ebe32ded97d8fb4238084a41a8b  molarch+-v735.tar.gz
  • Unarchive or unzip the archive using: 
    	gunzip -c molarch+-v735.tar.gz | tar -xvf -
    Then: 
    	cd molarch+
  • There will be two sub-directories named "bin/" and "par/". You need to move (or copy) the binaries to any directory listed by your $PATH variable, I recommend installing the files in the default location "/usr/local/bin". The parameter files should go to a different location, the default used here is "/usr/local/molarch+". You may execute the following while being logged in as "root": 
            mv -i bin/* /usr/local/bin
        mkdir /usr/local/molarch+
        mv -i par/* /usr/local/molarch+
  • The environment variable $MOLARCH must be set to point to the directory where the parameter files are stored. Setting this variable is done by: 
            export MOLARCH="/usr/local/molarch+"
    You may set this variable globally (for all users) on your system by adding the above line to the "/etc/profile" file, or locally (for a single user only) by editing the corresponding "~/.bash_profile" file.

    Note: The shell providing the command line interface of MolArch+ must be invoked with the '--login' flag to indicate that the "/etc/profile" or "~/.bash_profile" files must be executed.

  • The following shortcut 'aliases' may be handy for quick starts of MolArch+: 
            alias m+='molarch+ -sn'
        alias m-='molarch- -sn'
        alias m++='molarch++ -sn'
        alias m--='molarch-- -sn'
    You may add these shortcuts globally (for all users) on your system by adding the above line to the "/etc/profile" file, or locally (for a single user only) by editing the corresponding "~/.bash_profile" file.

  • Upon its first invocation, MolArch+ will create and store a registry key in a file ".molarch.register" in your home directory. Before this is done, MolArch+ will try to send an e-mail containing your user name, the current host name, and the local time to "lemmi@chemie.tu-darmstadt.de" (PD Dr. Stefan Immel). No private information is transmitted. The e-mail may look like this (it will only be used to provide me with some idea how many people are actually using MolArch+, no news letters or any other information are being send in return): 
            To: lemmi@chemie.tu-darmstadt.de
        Subject: MolArch User
        User [your-user-name] on [your-host-name] ([your-ip-address])
        at Fri Mar 28 15:52:20 CET 2003
    The registry key is provided free of charge, the only prerequisite is that the e-mail has been send successfully. All addresses are handled strictly confidential and are not provided to anybody else. If you don't like this procedure, please e-mail me stating your exact UNIX-user name and I will return the registry key for you.
Programs
Please check the list of MolArch+ - Programs and Sub-systems.
Data Files
Please check the list of MolArch+ - Parameter Files and Settings.
File Types
Please check the list of MolArch+ - File Types.
Quick Start
Please check the list of MolArch+ - Quick Start tips.
Commands
Please check the list of MolArch+ - Commands.
Error Messages
Please check the list of MolArch+ - Error Messages.

© Copyright PD Dr. S. Immel