These ebuilds come from http://dev.gentoo.org/~dberkholz/overlay/.
If you have some problems, go to the official site first.
burrow-owl : Visualize multidimensional nuclear magnetic resonance (NMR) spectra ( http://burrow-owl.sourceforge.net/ )
cclib : Library for parsing and interpreting the results of computational chemistry packages ( http://cclib.sourceforge.net/ )
ccp4 : Protein X-ray crystallography toolkit ( http://www.ccp4.ac.uk/ )
ccp4i : Protein X-ray crystallography toolkit, graphical interface ( http://www.ccp4.ac.uk/ )
ccp4mg : This is a sample skeleton ebuild file ( http://www.ysbl.york.ac.uk/~ccp4mg/ )
coot : Crystallographic Object-Oriented Toolkit for model building, completion and validation ( http://www.ysbl.york.ac.uk/~emsley/coot/ )
dssp : The protein secondary structure standard ( http://swift.cmbi.ru.nl/gv/dssp/" elog "Go to ${HOMEPAGE} and return the license agreement. )
dsv : Discovery Studio Visualizer ( http://www.accelrys.com/products/downloads/ds_visualizer/" einfo "Go to ${HOMEPAGE} )
epmr : Crystallographic molecular replacement by evolutionary search ( http://www.epmr.info/" elog "The user manual is available at ${HOMEPAGE} )
espresso : opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization ( http://www.pwscf.org/ )
imosflm : A new GUI for the Mosflm crystallographic data processing tool ( http://www.mrc-lmb.cam.ac.uk/harry/${PN}/" SRC_URI="${HOMEPAGE}/downloads/${P}.tar.gz )
kincontour : Read value/coordinate lists to produce contour maps in kinemage format ( http://kinemage.biochem.duke.edu/software/kincon.php )
king : An interactive system for 3D graphics (primarily molecular) ( http://kinemage.biochem.duke.edu/software/king.php )
mage : Mage is a 3D vector display program which shows 'kinemage' graphics ( http://kinemage.biochem.duke.edu/software/mage.php )
mole-bin : A toolkit for automated location channels, tunnels and pores in molecular structures ( http://mole.chemi.muni.cz/ )
mopac2007-bin : Powerful, fast semi-empirical package ( http://openmopac.net/ )
mopro-bin : Crystallographic structure or charge density refinement ( http://www.lcm3b.uhp-nancy.fr/lcm3b/Logiciels-labo/MoPro.htm )
mosflm : A program for integrating single crystal diffraction data from area detectors ( http://www.mrc-lmb.cam.ac.uk/harry/mosflm/" SRC_URI="${HOMEPAGE}ver${MY_PV}/build-it-yourself/${MY_P}.tgz )
pmb : Automated structure refinement tools for CNS ( http://xray.utmb.edu/PMB/ )
prekin : Prepares molecular kinemages (input files for Mage and KiNG) from PDB-format coordinate files ( http://kinemage.biochem.duke.edu/software/prekin.php )
procheck : Checks the stereochemical quality of a protein structure ( http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html )
profit : Designed to be the ultimate protein least squares fitting program ( http://www.bioinf.org.uk/software/profit/" elog "Download ${ORIG_URI} from ${HOMEPAGE} )
pymol : A Python-extensible molecular graphics system. ( http://pymol.sourceforge.net/ )
pymss : Multiple superposition of proteins, using a genetic algorithm for optimization ( http://reillygroup.cheme.iastate.edu/pymss/ )
qutemol : High quality molecular visualization system that exploits GPU capabilites through OpenGL shaders ( http://qutemol.sourceforge.net/ )
refmac : Macromolecular crystallographic refinement program ( http://www.ysbl.york.ac.uk/~garib/refmac/" SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz )
shelx : Programs for crystal structure determination from single-crystal diffraction data ( http://shelx.uni-ac.gwdg.de/SHELX/" einfo "Go to ${HOMEPAGE} )
theseus : Maximum likelihood superpositioning and analysis of macromolecular structures ( http://www.theseus3d.org/" elog "Download ${ORIG_URI} from ${HOMEPAGE} )
tinker : TINKER is a molecular modeling package that includes force fields for handing large molecules and large systems, such as AMBER and CHARMM. A Java based visualization front end is included. ( http://dasher.wustl.edu/tinker/ )
xia2 : An automated data reduction system for crystallography ( http://www.ccp4.ac.uk/xia/" SRC_URI="${HOMEPAGE}/${P}.tar.bz2 )
zodiac : Software for molecular modelling - computer-aided drug design ( http://www.zeden.org/ )
Add an ebuild in portage :
The ebuild is now in the portage tree.
You can also use layman : emerge layman then layman -a zugaina
For Paludis use this rsync : rsync://gentoo.zugaina.org/zugaina-portage
If you have a problem : ycarus(-at-)zugaina.org