Uppsala Software Factory - RAVE Package

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Manuals

• AVE for single-crystal averaging
• COMA to find NCS mask using local correlation maps
• COMAP to combine maps during multiple-crystal averaging
• COMDEM to combine multiple domain maps
• CRAVE to auto-generate a C-shell script to do N cycles of averaging over M crystal forms, each with or without NCS
• DATAMAN to manipulate reflection datasets
• ESSENS to do real-space searches for fragments (e.g., helices) or molecules
• IMP to improve NCS operators
• MAMA to manipulate masks
• MAPFIX add spacegroup and symmetry operators to a CCP4 map
• MAPMAN to manipulate maps
• MASKIT to find cross-crystal averaging mask using local correlation maps (VRML world of the correlation map at 0.40 cut-off level for the lipase example discussed in the manual, together with the refined model, chain A of PDB entry 1TCB)
• MAVE for multiple-crystal averaging
• NCS6D to find NCS operators
• O2D to convert plot files (e.g., from MAPMAN or DATAMAN) to PostScript
• PROF to generate electron-density profiles (only in Uppsala at present)
• SITE2RT to find RT-operators between (heavy atom or selenium) sites in different crystal forms
• SOLEX to extract the best solutions from ESSENS runs (and to attempt to auto-trace helices and strands) (A real Solex)
• SPANCSI investigate if your NCS-related molecules have very different average temperature factors, and if so, take special measures during averaging

Examples

• MAPMAN
  • Example of a ROughness density histogram plot.
  • Example of an EXtracted map plot.
  • Example of an 1D_projection plot.
  • Example of a 2D_projection plot.
  • Example of a DH density histogram plot.
  • Example of a VRML display generated with MAPMAN.
• MAMA
  • Example of a VRML display generated with MAMA.
• DATAMAN
  • Example of a WIlson <I> plot after one round of scaling.
  • Example of a WIlson LOG (<I2>/<I1>) plot after one round of scaling.
  • Example of a WIlson <I> plot after two rounds of scaling.
  • Example of a WIlson LOG (<I2>/<I1>) plot after two rounds of scaling.
  • Example of a GEmini plot for non-centrosymmetric data.
  • Example of a GEmini plot for centrosymmetric data.
  • Example of a RAmp ODL file displayed in O.
  • Example of a SCatter plot.
  • Example of a BIn plot.
  • Example of a DOuble plot.
  • Example of an EO plot.
  • Example of an HKl_aniso plot.

Related freebies

• Trouble ftp-ing through your browser ? Look here !
• MAPMAN server to convert ASCII maps in CNS, X-PLOR, MASK (RAVE-style), EZD and OLDEZD format into O-style binary BRIX and DSN6 maps
• mask_atom.omac, an O macro that will set the mask ON in a small volume around an atom
• unmask_atom.omac, an O macro that will set the mask OFF in a small volume around an atom
• bones_mask.mamac, MAMA macro; generate mask from BONES file
• cavities.mamac, MAMA macro; detect cavities using Delaney's method
• extend_mask.mamac, MAMA macro; extend a mask
• mask_new_cell.mamac, MAMA macro; transfer a mask to a new cell etc.
• mask_new_grid.mamac, MAMA macro; transfer a mask to a new grid
• mol_shapes.mamac, MAMA macro; shape similarity of two aligned molecules
• pdb_mask.mamac, MAMA macro; generate mask from PDB file
• cat.mamac, MAMA macro; produce a mask in the shape of a cat (to show that MAMA doubles as a "CAT/CAM program" ;-)
• mappage10.mapmac, MAPMAN macro; read map, make sigma 10.0, mappage for O
• rfree_shell.datmac, DATAMAN macro; generate Rfree reflections in thin resolution shells
• average.csh, script for averaging with RAVE/CCP4
• domain_rave.csh, script for RAVE two-domain averaging
• ncs_waters.csh, script to average difference map & extract possible waters
• plane_extract.csh, script to extract and plot density through a user-defined plane (e.g., a Tyr ring)
  
• Tutorial: Local density correlation used to assess or validate differences between related protein crystal structures.
• Tutorial: Visualisation of tunnels. This explains how to visualise tunnels and other cavities in your protein that are connected to the outside world. The tutorial uses only Uppsala programs (MOLEMAN2, VOIDOO, MAMA, MAPMAN, and O).

Description

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).
• GJ Kleywegt, Acta Cryst., D55, 1878-1884 (1999).
• GJ Kleywegt & TA Jones, Acta Cryst., D55, 941-944 (1999).
• GJ Kleywegt & TA Jones, Acta Cryst., D53, 179-185 (1997).
• GJ Kleywegt & TA Jones, Acta Cryst., D52, 826-828 (1996).
• GJ Kleywegt & TA Jones, CCP4 Proceedings, 1994, 59-66.
• TA Jones, CCP4 Proceedings, 1992, 91-105.

(Another type of RAVE ...)