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Program Description
Crystallography

ACMI

Automatic Crystallographic Map Interpretation

ACMI is a suite of programs designed to automate construction of a macromolecular model from an electron density map. It is specifically developed to handle low-resolution (3-4 Angstrom resolution) and poorly phased electron density maps.

AMoRe

Stand alone molecular replacement package

ARP/wARP 7.4

ARP/wARP , is a program package for protein structure refinement.

AutoDock 4

Automated Docking of Flexible Ligands to Receptors

ADXV A program to display X-Ray diffraction images

Babel 1.6

Interconvert a number of file formats currently used in molecular modeling.

BnP 1.02 A combination of SnB & Phases:
SnB: A dual-space, direct-methods procedure for determination of MIR and MAD heavy atom substructure.
Phases: derivative refinement and some density leveling.
AutoBuster
BDG
Buster
Gelly
MakeTNT
autoBUSTER is a framework and collection of tools, intended for refining structures with the latest version of the BUSTER-TNT refinement program in conjunction with the geometry module GELLY and the restraints toolbox MakeTNT.

CCP4_6.4

A large collection of programs that covers everything from data reduction to refinement (Tutorial)

CNS_1.3

Phasing and refinement program with many useful utilities

Denzo 1.97.9

Data reduction, integration, merging and scaling of X-ray data

Dock 6.2 DOCK addresses the problem of "docking" molecules to each other.

DockEM

Quantitatively dock, or fit, a crystal structure into an EM map of a molecular compelx that contains that structure

EPMR v11.09

EPMR is a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. (Manual PDF)

Escet 0.6b

A script driven program to analyse and compare three-dimensional protein structures

HKL2000

Data reduction, integration, merging and scaling of X-ray data
HOLE2 HOLE allows the visualization and analysis of the holes through atomic models of ion channels

LaueView

Use for data processing of Laue Frames as an alternative to the CCP4 Laue Program Suite

Main

MAIN is an interactively driven computer program dealing with computational parts of macromolecular crystallography in progressively automated manner

Mead

MEAD is a set of software objects for the purpose of modeling the electrostatics of molecules

MIFit MIFit is a fitting and molecular modeling program (Manual PDF)
Modeller 9v10 A Program for Protein Structure Modeling

Mosflm 7.0.7

Data reduction, integration of X-ray data

Bug for Mosflm & SCALA

MSMS v2.5.5

Molecular Surfaces Computation

User Commands

Muscle

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences.

NAMD

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

User Guide v2.5b1

NUCPLOT A program to generate schematic diagrams of protein-nucleic acid interactions

v1.0 User manual

PHASER-2.3

Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods

PHASES

Bill Furey's program for derivative refinement and some density leveling.

Phenix-1.8-1069

SHARP

Heavy atom refinement program.

SHELX-97

Refinement using structure factor summation-mainly for use with high resolution data

SnB v2.3

A dual-space, direct-methods procedure for determination of MIR and MAD heavy atom substructure.

Solve-2.13 &

ReSolve-2.13

Automated crystollagraphic structure solution for MIR and MAD-locate heavy atoms, calculate phases.

Twister With the three-dimensional coordinates as input, TWISTER uses an original algorithm to determine the local coiled-coil parameters as a function of residue number.

Vega 2.2.0

Creates a bridge between most of the molecular software packages

XDS X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method.

xplor

Model refinement