About the program `ESCET`

ESCET is a script driven program to analyse and compare three-dimensional protein structures.
The current version (1.00r) is mostly designed for finding the rigid part of protein molecules by comparing different structures.

Some applications are described in:

- Schneider TR
Objective comparison of protein structures: error-scaled difference distance matrices
Acta Cryst. D56, 714-721 (2000). [PDF] [MEDLINE]

- Schneider TR
A genetic algorithm for the identification of conformationally invariant regions in protein molecules
Acta Cryst D58:195-208 (2002). [PDF] [MEDLINE]

- Schneider TR
Domain identification by iterative analysis of error-scaled difference distance matrices
Acta Cryst. D60:2269-2275 (2004). [PDF] [MEDLINE]

The development of ESCET is supported by the Bioinformatics Center Grant from the Italian Association for Cancer research, A.I.R.C..

Download

ESCET is freely available for academic non-profit users. If you are interested in downloading the program and its documentation or if you want to register a version that you 'found' somewhere, please contact me at

The program is available for 64-bit linux .

Supported Architectures

ESCET is available for several platforms. I am grateful for any reports about platforms on which ESCET works / does not work. Here are some notes:

32-bit linux

No known issues
reported to run: Linux 2.6.18-1.2798.fc6 i686 i686 i386 (2 reports)

64-bit linux

No known issues

MAC OS X

At present not supported

Release notes for version 1.00r 04-Apr-2014

This release is based on the same code-base as 0.7h. Only the expiry date was changed.

Release notes for version 0.7i 11-Feb-2011

This release is based on the same code-base as 0.7h. Only the expiry date was changed.

Release notes for version 0.7h 6-Apr-2009

For the first time, executables for 64-Bit linux and Intel-MAC have been prepared.

Release notes for version 0.7e 1-Mar-2006

A number of bugs have been fixed.

Release notes for version 0.7 28-Feb-2005

Version 0.7 introduced a number of major improvements:

The Kabsch-Algorithm for least-squares superposition (Kabsch, 1976) has been implemented. The program will now automatically superimpose the conformers analysed by applying the Kabsch-algorithm to the different conformationally invariant regions. The tranformed coordinates are written to pdb-files for later use.
The pdb-files are named t_XXXX_C_spos_mr#.pdb, where XXXX is the pdb-code of a conformer, C its chain name. '#' is a number indicating the conformationally invariant region used for superposition.
The genetic algorithm for the identification of conformationally invariant regions can now be run in an iterative fashion. This allows to not only find the largest conformationally invariant region, but also other rigid parts of a molecule.
For example, src-kinase can be divided into its four domains using this approach (see (Schneider, 2004) for a explanation). The default number of iterations is 3 and can be changed using the rb_iterate-keyword in the ddm-command. Setting rb_iterate=0 should go back to the pre version 0.7 behaviour of the ddm-command.
Please note that for various technical reasons, the iterative analysis can only be performed on different conformers of the same molecule.
To be able to write complete models after analysis and superposition for visualization purposes and for further analysis, a slight change in the general approach used in ESCET had to be introduced. Previously, the atoms (e.g. CA's) had to be selected before entering the ddm-command. Now this selection is done within the ddm-command using the sele-keyword with a standard selection string. The default for this selection is to select CA-atoms. Thus for most users, nothing will change except that they have to remove the explicit selection of CA-atoms in earlier parts of ESCET -scripts.
Users interested in phophorus atoms as representatives of RNA-structure, can use sele = (name == P) to switch to phosphorus atoms.
People interested in a analysing complex mixtures of atoms can go back to the old behaviour by stating sele = all.
Scripts for visualization of results using pymol are now generated.
The PYMOL-script t_spos_mr1.pml will show all conformers superimposed using rigid region number 1, t_spos_mr2.pml will show the superposition on rigid region number 2 etc.
Various pieces have been added to the html-file, e.g. a table containing statististics about coordinate uncertainties of all conformers, a table containing rmsd-values for all least-squares superpositions done etc. There is also a hyper-linked table of contents at the top of the file.
When atoms with zero-occupancy are read, a warning is generated.

Relases notes of older version can be found here.

Documentation

The following documentation is available online:

A User's Guide describing the use of the program mostly by examples is availaible in pdf-format: escet_user.pdf.
A reference manual, giving the definition of the ESCET-syntax is available as: escet_ref.html

Known Bugs

For multiple chain analyses, the rigid body display on the bottom of the DD-matrices is sometimes messed up. However, the calculations and the RASMOL-, MOLSCRIPT-, and PYMOL-files rasmol are correct.

Contact

Please report all problems/questions/comments directly to

-	Schneider TR Objective comparison of protein structures: error-scaled difference distance matrices Acta Cryst. D56, 714-721 (2000). [PDF] [MEDLINE]
-	Schneider TR A genetic algorithm for the identification of conformationally invariant regions in protein molecules Acta Cryst D58:195-208 (2002). [PDF] [MEDLINE]
-	Schneider TR Domain identification by iterative analysis of error-scaled difference distance matrices Acta Cryst. D60:2269-2275 (2004). [PDF] [MEDLINE]

About the program ESCET