Uppsala Software Factory - DEJAVU Package

| Download executables (SGI|ALPHA|LINUX|OSX) | Download databases & libraries | Manuals | Examples | Freebies | Description | Requirements | References |

Manuals

• DEJAVU to find motifs and to recognise other proteins with a similar fold (includes documentation for DEJANA, PRO1, PRO2 and POST)
• GETSSE to generate an SSE file for DEJAVU from a PDB file of a protein
• LSQMAN to superimpose and analyse multiple models and/or molecules
• O2D to convert LSQMAN plots to PostScript

Examples

• LSQMAN
  • Example of a SOap film in O for two fairly similar structures.
  • Example of a SOap film in O for two fairly different structures.
  • Example of a PHipsi plot.
  • Example of a DIst plot.
  • Example of a QDiff_dist plot.
  • Example of a DDihedral plot.
  • Example of a LEsk plot.
  • Example of a SImilarity plot.
  • Example of a WAter plot.
  • Example of a D1_D2 plot.
  • Example of a MDihedral plot.
  • Example of a MBfactors plot.
  • Example of a normal MRamachandran plot.
  • Example of a polar MRamachandran plot.
  • Example of a MSidechain plot.
  • Example of a normal MTorsion plot.
  • Example of a polar MTorsion plot.
  • Example of a MPlot plot.
  • Example of a MPlot "CD plot".
  • Example of a VMain plot.
  • Example of a VSide plot.

Related freebies

• Trouble ftp-ing through your browser ? Look here !
• Dennis Madsen has written a DEJAVU server. If you are in Uppsala, you can use the full-blown version on the intranet server. Otherwise, you can use this public version. If you want to install a DEJAVU server locally, contact Dennis for a copy of the Perl script.
• align.lsqmac, LSQMAN macro; Gerard's favourite recipe for aligning two protein structures
• sse2odl.f, program to generate an ODL file with solid arrows from a DEJAVU SSE file
• align2.omac, an O macro that runs LSQMAN in BRute_force mode to superimpose any two protein chains, apply the best operator, read the molecule back into O and draw its CA trace
• ana_ncs.lsqmac, LSQMAN macro; generate some standard plots to analyse N-fold NCS (proteins)
• ftp_hits, script to ftp the PDB files of "hits" found by DEJAVU (after running LSQMAN) if these are not available locally
• make_sse, script to generate an SSE-file for DEJAVU from a PDB file (NOTE: this script is obsolete; use the program GETSSE instead !)
• multi_probe, script to generate three probes for Molecular Replacement using multiple aligned NMR models or NCS chains
• align_many.csh, script to align a load of molecules to another (uses LSQMAN)
• cheap_dejavu.csh, script to align your model to any or all structures in the PDB (uses the BRute_force command in LSQMAN)
• Tutorial: Recognising your fold, using DEJAVU, LSQMAN, DEJANA, and O.
• Tutorial: Biomolecular morphing. This explains how to visualise transitions between conformational states etc. in a jiffy, using LSQMAN and a molecular graphics program (e.g., O). The results can be published on the web, e.g. as animated GIF files.

Description

DEJAVU can produce a macro for O which will show your protein with each of the hits found in the database superimposed on top of it. Alternatively, an input file can be generated for the least-squares superpositioning program LSQMAN (included in this package). This program can perform rapid improvement of the least-squares operator of the hits. The results of both DEJAVU and LSQMAN can be "filtered" by another utility program, DEJANA. This can be used to remove spurious matches.

DEJAVU also supports the use of SSE files derived from a skeleton ("bones") to compare these against the database, even though the connectivity and directionality of the SSEs may be unknown. Bones-based SSE files can be generated manually, or using programs from the RAVE package (ESSENS, SOLEX).

The least-squares superpositioning program LSQMAN is also a powerful tool for analysing multiple models or molecules (e.g., in the case of NCS-related molecules and NMR ensembles), and it can be used for "biomolecular morphing" to visualise conformational differences between two forms of a protein.

DEJAVU comes bundled with SSE databases, various pre- and post-processing programs and a C-shell script for generating SSE files from PDB files.

Requirements

References

• GJ Kleywegt, JY Zou, M Kjeldgaard & TA Jones. International Tables for Crystallography, Volume F. Chapter 17.1, pp. 353-356, 366-367 (2001).
• TA Jones & GJ Kleywegt, Proteins: Struct. Funct. Genet. Suppl., 3, 30-46 (1999).
• GJ Kleywegt & TA Jones, Meth. Enzymol., 277, 525-545 (1997).
• GJ Kleywegt, Acta Cryst., D52, 842-857 (1996).
• GJ Kleywegt & TA Jones, Structure, 3, 535-540 (1995).
• GJ Kleywegt & TA Jones, CCP4 Proceedings, 1994, 59-66.