Visualizing Ligand Molecules
in Twilight Electron Density
Academy of Bozen/Bolzano (EURAC),
Viale Druso 1,
We present a software
script for facilitating analysis and visual inspection of ligand
molecules in context of the electron density maps calculated from
experimental data associated with protein structures determined
by X-ray crystallography.
Three-dimensional models of protein structures
determined by X-ray crystallography are based on the
interpretation of experimentally derived electron density maps.
The real-space correlation coefficient (RSCC)
provides an easily comprehensible, objective measure for
residue-based fit of atom coordinates with electron density.
Among protein structure models, protein-ligand complexes are of
special interest, given their contribution to understanding the
molecular underpinnings of biological activity and to drug
design. For consumers of such models it is not trivial to
determine the degree to which ligand structure modelling is
biased by subjective electron density interpretation. We present
a standalone script, Twilight, for analysis, visualization, and annotation of a
pre-filtered set of 2,815 protein/ligand complexes deposited
with the PDB as of January 15, 2012, with ligand
RSCC values that are
below a threshold of 0.6. The script runs on various platforms
and is available for download at
Acta Crystallographica F paper
and its companion in
Acta Crystallographica D
describing the actual findings from the IUCr web site
request a link by email. Please read also the editorial
Expectation bias and information content
M. S. Weiss,
H. Einspahr and
E. N. Baker,
Acta Crystallogr. D69, 141 (2013).
Techniques, tools and best practices for
ligand electron-density analysis and results from their application
to deposited crystal structures.
C. X. Weichenberger and
Acta Crystallogr D69, 150-167 (2013)
Molecules in Twilight Electron Density.
C. X. Weichenberger,
E. Pozharski and
Acta Crystallogr. F69(2), 195-200(2013)
The program distribution comes in a
zip archive file which can be
Here is the readme file for installing
current data files
The distribution comes packaged with the latest datafile
current to the January 13 2016 PDB release (ligands-2016-01-13.tsv). We
archived yearly updates:
The complete data file contains data up to the specified release
date, whereas the yearly data file only contains PDB entries that have
become available between the previous update's release date
and the current release date.
NOTE: The data files are .bz2 compressed files- please
unzip them before starting TWILIGHT
Here is the
readme file for installing
A useful resource if you want to learn more about
protein crystallography, ligand structures, and structure validation
You can still use the web tutorial for free!