# Computing

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.

Availability:
Instructions for users:

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.

Licence Details:

Documentation:

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.

### System status

System monitoring page

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