MOLMOL 2.2.0 Important Information Date: May 2, 1996 DESCRIPTION MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. LEGAL INFORMATION Legal information is contained in the file COPYING, you are required to read this file and agree with its contents before using the program. Users are encouraged to register, please check the section about registration towards the end of this document. OBTAINING MOLMOL The latest version is always available on the following servers: ftp://ftp.mol.biol.ethz.ch/pub/software/MOLMOL ftp://ftp.spectrospin.ch/pub/sag/MOLMOL ftp://ftp.bruker.de/pub/bruker/MOLMOL ftp://ftp.bruker.com/pub/nmr/mirror.bruker.de/MOLMOL The following files can be downloaded: README molmol-2.2.0-doc.tar.Z molmol-2.2.0-bin-aix.tar.Z molmol-2.2.0-bin-dec.tar.Z molmol-2.2.0-bin-lnx.tar.Z molmol-2.2.0-bin-sgi.tar.Z molmol-2.2.0-bin-sol.tar.Z molmol-2.2.0-src.tar.Z README is this file. molmol-2.2.0-doc.tar.Z contains documentation, configuration files, etc. These files are REQUIRED for successful operation of the program. The molmol-2.2.0-bin-*.tar.Z contain executables for IBM (AIX 3.2), Digital Alpha (Digital UNIX V3.2), Linux (ELF format), Silicon Graphics (IRIX 4.0.5 and 5.3) and Sun (Solaris 2.4). If you are using one of these systems, you can just download the corresponding file (together with the doc file) and do not need source code. molmol-2.2.0-src.tar.Z contains the source code. You only need this if there is no executable for the system that you want to use. INSTALLATION Create a directory that holds the program (e. g. /usr/MOLMOL) and unpack the files into that directory: zcat molmol-2.2.0-doc.tar.Z | tar xvf - zcat molmol-2.2.0-bin-xxx.tar.Z | tar xvf - Binaries for multiple architectures can be installed in the same directory, the startup script will automatically select the correct binary. Start the (very simple) installation script: ./INSTALL This only sets the MOLMOLHOME variable in the molmol shell script, you can also do that manually in case of problems, like if your current path looks strange due to using an automounter. You may want to replace the /bin/ksh line in the molmol script by /bin/sh if your system does not have a Korn shell. The Korn shell is taken by default because the Bourne shell on DEC systems cannot handle the script. You can either add the directory where you installed the program to your PATH, copy the script to a directory in your path, or do that as a symbolic link (preferred). E. g.: ln -s /usr/MOLMOL/molmol /usr/local/bin COMPILATION ON SUPPORTED ARCHITECTURE Note that there are binaries for the most common systems, you should only compile the source code if you have a good reason to do so. It is recommended to keep the source code in a directory different from the final installation directory, e. g. in /usr/molmol-src. Unpack the file with the source code: zcat molmol-2.2.0-src.tar.Z | tar xvf - Copy the appropriate makedef.xxx file to makedef: cp makedef.xxx makedef For some architectures there are multiple choices, see the comments at the top of each file for details. After copying, look at the file and edit it to your personal needs if required. You may have to set some path names, etc. The file makedef.gen included explanations for the variables that can be set in makedef. For systems that support the PlotTiff command (see manual), i. e. systems with OpenGL or XGL, you first have to compile the libtiff library (unless you have it on your system already): cd tiff-v3.4 ./configure cd libtiff make cd ../.. If you want to install the library and some useful tools that come with it in a generally accessible place, give these paths when the configure script asks for them, do the "make" one directory level higher, and do a "make install" afterwards. You can optionally create header file dependencies by using the following commands. This step does not work on some architectures (AIX and Linux), and it is unimportant unless you want to do development work on the program, so it is recommended that you leave this step away. cp makedep.devel makedep make depend Compile: make The executable is in the directory src/main, you can now strip that and copy it to the installation directory: cd src/main strip molmol cp molmol /usr/MOLMOL/molmol.xxx Machine specific hints: - the make used by default on DEC cannot handle the include files used in the makefiles, execute the following before compiling: alias make /usr/opt/ultrix/usr/bin/make setenv MAKE /usr/opt/ultrix/usr/bin/make One good reason for compiling the program yourself would be the support of additonal graphics libraries, e. g. the binaries for DEC and IBM use the public domain Mesa library for OpenGL support, not the official OpenGL libraries from the manufacturers. If you have access to these libraries, they may give you better performance, especially on machines with high-end graphics. COMPILATION ON UNSUPPORTED ARCHITECTURE You have to create a makedef file that contains the necessary machine specific definitions for your system. You can either start from the supplied one that is most closely related, or you can take makedef.gen, which contains comments explaining the variables, plus some possible settings: cp makedef.gen makedef edit makedef From here on you can follow the instructions from the previous paragraph for compiling. In addition you have to select a new short system name for the extension, and add the new architecture to the startup script, following the example of an existing one: cd src/main strip molmol cp molmol /usr/MOLMOL/molmol.foo cd /usr/MOLMOL edit molmol In case you have compilation proplems: there should be NO changes necessary in the source code (unless maybe for some #ifdef's in the src/os directory), whenever possible you should get things working by settings in the makedef file (often by -D options). If you find non-portabilities in the code, please notify the authors. Also send your makedef files after successful compilation, so that they can be supplied to other users in the future. PORTING TO DIFFERENT WINDOW SYSTEMS The program runs under Motif, supporting various graphics libraries (GL, OpenGL, XGL, X11). If you would like to port the program to a different window system (e. g. Windows, Mac) or graphics system, please contact the authors. The program has been structured so that this should be possible within reasonable time, but it is still a non-trivial task. Hooks for Windows support (in combination with OpenGL) are present in the source distribution, all that is needed are implementations of the empty functions in the directories src/winogl and src/win. DOCUMENTATION The man subdirectory contains the following files: tutorial.html: tutorial in HTML format manual.dvi: users guide in DVI format manual.ps: users guide in PostScript format ref.ps: reference manual in PostScript format The reference manual is just a copy of all online help pages, you will normally not print that out. ADDITONAL SOFTWARE The aux subdirectory of the distribution contains some "goodies" that can be useful in conjunction with MOLMOL. See the README file in that directory for details. If you your molecules have file formats different from the ones that can be read by MOLMOL, you should check out the conversion program Babel, written by Pat Walters and Matt Stahl. It is available from ftp://joplin.biosci.arizona.edu/pub/Babel/. MOLMOL can generate files for the public domain raytracing program POV-Ray. You can obtain this program from ftp.povray.org, check http://www.povray.org for more information. Note that you have to make the font.inc file from the aux directory accessible to POV-Ray when rendering files created by MOLMOL. When dealing with images (like the ones created by POV-Ray), the netpbm tools for manipulating and converting images are invaluable. They are available from many ftp sites, e. g. wuarchive.wustl.edu. Most systems have an image viewer, but xv, which is also available from many ftp sites (e. g. ftp.cis.upenn.edu), is often the better choice. MOLMOL shares file formats with various other programs developed in the group of Prof. Wuthrich. For information about some of these, check: http://www.mol.biol.ethz.ch/wuthrich/software/ REGISTRATION It is recommended that you get registered as MOLMOL user by sending mail to molmol@mol.biol.ethz.ch or molmol@spectrospin.ch, so that you can be informed about problems, future versions, etc. The easiest way to do this is using the Register command from the Help menu of the program. If there is demand, we might create a mailing list later. CONTRIBUTIONS If you write something that you think could be of use to others, you are very welcome to send it to us, and we will make it generally available. This could include: - macros (preferrably command definitons) - alternate menu or button definitons - non-standard entries for the residue library - additonal examples for the tutorial - shell scripts We also enjoy seeing your pictures if you make nice ones (do not send them by E-mail, please, only pointers to web pages or ftp sites). We would be glad to set up a web page with the best examples. OBTAINING MORE INFORMATION Current information about MOLMOL is available from: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ http://bamsoft.software.bruker.de/packages/molmol/molmol.html If you have problems that you cannot solve AFTER READING THE MANUAL, you can send mail to molmol@mol.biol.ethz.ch. We do not guarantee that it will be answered, but it normally will.