From the homepage: XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.
This program is one of the standard applications loaded so you should find it on your PATH on the workstations. It uses a file called elements to tell it how to display certain atoms. If you wish to use your own custom file rather than the system default then set the variable XM_ELEMENTS to point to your file.
If output of XMakemol is used in publications and you wish to cite it, the authors says to use something like: M. P. Hodges, XMakemol:a program for visualizing atomic and molecular systems, version 5 (2001). and optionally include the URL of the homepage.
The version that ships with Ubuntu isn't GL-enabled. If anyone wants a GL version please contact the Computer Officers.
Manpages
We appear to have dropped the GL-enabled version since 12.04 with no complaints. However if it should be needed again here's how we did it for 10.04.
To build a GL-enabled version for Ubuntu you have to rebuild Mesa with --enable-motif. Getting xmakemol's configure script to see this version of Mesa is fiddly (for one thing, it doesn't do what I expected with LDFLAGS - save yourself the grief and use CFLAGS instead). Eventually I cheated and did this:
#Build Mesa ./configure --enable-motif --with-driver=xlib make # copy Mesa's lib subdirectory into a suitable subdirectory of the place you intend to install xmakemol, I chose 'GL' # build xmakemol pointing it to the GL directory for its libs make clean && CFLAGS="-L /usr/local/shared/xmakemol/x86_64/5.16GL/GL" \ ./configure --prefix=/usr/local/shared/xmakemol/x86_64/5.16GL make rm xmakemol # now relink xmakemol using an rpath and $ORIGIN, I could not figure out # what to pass to configure to make the ORIGIN bit not get substituted for # something empty gcc -Wl,-rpath,'$ORIGIN/../GL' -L /usr/local/shared/xmakemol/x86_64/5.16GL/GL \ -DELEMENTS=\"/usr/local/shared/xmakemol/x86_64/5.16GL/share/xmakemol/elements\"\ -o xmakemol animate.o basename.o bbox.o canvas.o control.o crystal.o draw.o \ edit.o fig.o file.o frames.o gl_funcs.o help.o menus.o region.o rotate.o \ sort.o store.o track.o translate.o utils.o vectors.o view.o xmakemol.o \ gl2ps.o -lGL -lGLU -lGLw -lglut -lXm -lXt -lXext -lXi -lX11 -lm # become root make install
There is a test input file in /usr/local/shared/xmakemol/examples . Make sure the version you end up with is GL-enabled - look for the GL-rendering menu item under Edit.
