Matthews / Remington Laboratories

SHARP - Statistical Heavy Atom Refinement and Phasing

You will need a password to run SHARP (see Dale)

For more information, check out the SHARP homepage

• Crystallography Packages
• CCP4 V5.0.2
• CCP4i
  
• Phenix
  
• CNS 1.1 (the default version)
• X-ray Data Collection and Reduction
• denzo/scalepack
• HKL2000
• mosflm user guide
• Rotgen     -   Rotation Image Prediction and Analysis  (part of CCP4)
  
• strat
• strategy
• Phasing/Phase Improvement
• EPMR   - Molecular Replacement by Evolutionary Search
• GLRF    - General Locked Rotation Function
• mrchk    - Molecular Replacement by Cai
• rave       - Utilities for Manipulating Maps
  
• SnB       - Automated Location of Heavy Atoms by Direct Methods
• squash   - Density Modification for phase improvement
• solve      - Automated Location of Heavy Atoms
• resolve   - Solvent flattening (usually used after solve)
• Model Building
• COOT      - Latest model building program. A quantum leap from "O". Windows or Linux.
• O(Ver.5.10)
• O(Ver.6.2.2)
• O(Ver.6.2.2) release notes
• O(Ver.7.0) release notes
• rotmap
• xtalview
• Refinement
• ARP/wARP
• shelx
• TNT Reference Manual
• TNT Users Guide
• xplor
• Model Analysis
• DDQ         - Difference Density Quality
• DSSP        - Secondary Sructure of Proteins from 3D coordinates
• edpdb        - many manipulations of pdb files WEBSITE
• hbplus       - lists potential hydrogen bonds in pdb coordinates
• grasp         - calculates electrostatic surfaces of proteins
• match3d    - 3D structure homology surfaces
• MSP          - calculates molecular surfaces
• naccess      - calculates atomic accessible surface of pdb files
• naomi        - analyzes pdb files (maybe out of date...?)
• OS             - calculates occluded surface and atomic packing of proteins
• ovrlap        - optimal superposition of closely or distantly related protein structures
• PASS        - Putative Active Sites with Spheres. Automatically detects and maps binding sites.
• promotif     - identifies structural motifs in proteins
• rasmol       - easy way to look at pdb coordinates
• sarf2          - identifies common secondary structures between two pdb files
• surfnet       - generates surfaces and void regions from pdb files
• whatif        - structure verification (ie. whatcheck)
• x3dna        - analysis of DNA conformation
  
• Data Analysis
• xmgrace
• Sequence analysis
• lalnview     - displays sequence alignments
• sequoia       - sequence and  structure  alignments
  
• Publication
• alscript          - sequence alignment to postscript
• bobscript       - extensions to molscript 1.4
• ESPript         - sequence alignment to postcript
• gnuplot          - interactive plotting program
• gimp             - slow but powerful photoshop clone - access to manual is slow - be patient
• InsightII-95  - makes nice pictures
• Latex             - typesetting language
• ligplot           - plot schematic diagrams of protein-ligand interactions
• molmol
• molscript
• PyMol
• raster3d
• ribbons
• Molecular Dynamics
• InsightII-95
• Crystallographic Subroutine Libraries
• xdl_view    - An X-Windows based toolkit displaying images
  
• Internet
• Apache Web Server

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