gpsgibb / tetr_lev00_chimera_plugin Goto Github PK

This repository contains plugins for UCSF Chimera that interfaces it with the
command line utilities Tetr and Lev00.

Tetr is an interactive menu-driven program which allows the creation and 
modification of input files for codes such as VASP, SIESTA, CASTEP etc.
This plugin allows the user to visualise the current model being constructed
in Chimera, whilst allowing the user to select atoms using the GUI and send
that selection into Tetr.

Lev00 is an interactive menu-driven program for post-processing results from DFT
codes, and produces cube files of the charge, spin total and partial densities. These
can be visualised with Chimera.

More information on Tetr and Lev00 can be found at:
http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/index.html

With manuals at
http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/manual_lev00_2-45c+tetr_3-94h6.html
and
http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/node46.html




INSTALLATION INSTRUCTIONS:

*** Tetr and Lev00 only work with UNIX-based operating systems, not MS Windows ****

For these plugins, you require UCSF Chimera, which can be downloaded here:
https://www.cgl.ucsf.edu/chimera/download.html
and Tetr and Lev00, which can both be downloaded here:
http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/index.html

Tetr and Lev00 must be compiled in order to be used. To do this, in the source 
directories of each code, go into the Makefile and alter the line beginning "FCOMPL=" 
to contain the Fortran compiler of your choice (e.g. gfortran, ifort etc...). For
Tetr, set the environment variable HOME_TETR in your shell (e.g. inside your .bashrc)
to point to the Tetr source directory.

Finally, the plugin's directory (tetr_lev00_Chimera_plugin) must be placed inside the 
"share" directory within the Chimera directory tree. In Linux this will be kept in:
/path/to/UCSF_Chimera/share
Whilst on MacOS this will be located in
/path/to/Chimera.app/Contents/Resources/share



USAGE INSTRUCTIONS:

Once installed (see above), the Tetr and Lev00 plugins should be visible in the 
Tools -> Utilities menu in the Chimera GUI.

Upon first launch, the plugins may prompt for the path to the Tetr/Lev00
executable (unless the HOME_TETR environment variable is set). This will be
cached in $HOME/.Tetr/tetr_root.dat and $HOME/.Lev00/lev0_root.dat so you should
not be prompted again.

The plugins will then ask you the path to the working directory you wish
to use.



PLEASE NOTE:
If changing the version of Tetr/Lev00 that is used (e.g. upgrading to a new version) you will have to delete the tetr_root.dat and/or lev00_root.dat files in ~/.Tetr or ~/.Lev00.


ACKNOWLEDGEMENTS:

We would like to thank EPSRC for funding, grant EP/K038583/1. 
The plugin was written by Gordon Gibb, Jeremy Nowell and Iain Bethune from EPCC (Edinburgh, U.K.).