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Twilight: A tool for ligand density validation 

Visualizing Ligand Molecules in Twilight Electron Density

Christian X.  Weichenbergera*,  Edwin  Pozharskib* and  Bernhard  Ruppc

aCenter for Biomedicine, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100, Italy,  bUniversity of Maryland, Baltimore, MD, USA, and  ck.k. Hofkristallamt, 991 Audrey Place, Vista, CA, 92084, USA

Correspondence email:  Christian.Weichenberger@eurac.edu; epozh001@umaryland.edu

Synopsis

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.

Abstract

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 http://www.ruppweb.org/twilight/.

Download this Acta Crystallographica F paper and its companion in Acta Crystallographica D describing the actual findings from the IUCr web site (preferred) or request a link by email. Please read also the editorial Expectation bias and information content Z. Dauter, M. S. Weiss, H. Einspahr and E. N. Baker, Acta Crystallogr. D69, 141 (2013).

 

Citation

Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. E. Pozharski, C. X. Weichenberger and B. Rupp, Acta Crystallogr D69, 150-167 (2013)

Visualizing Ligand Molecules in Twilight Electron Density. C. X. Weichenberger, E. Pozharski and B. Rupp, Acta Crystallogr. F69(2), 195-200(2013)

Download program

The program distribution comes in a zip archive file which can be downloaded here. Here is the readme file for installing Twilight

Update and 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:
Year Release date Complete data (.bz2) Yearly data (.bz2)
2016 Jan 11, 2017 ligands-2017-01-11.tsv newligands-2016.tsv
2015 Jan 13, 2016 ligands-2016-01-13.tsv newligands-2015.tsv
2014 Jan 15, 2015 ligands-2015-01-15.tsv newligands-2014.tsv
2013 Jan 15, 2014 ligands-2014-01-15.tsv newligands-2013.tsv
2012 Jan 16, 2013 ligands-2013-01-16.tsv newligands-2012.tsv
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 Twilight

My texbook

A useful resource if you want to learn more about protein crystallography, ligand structures, and structure validation

For now

You can still use the web tutorial for free!



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