XTalView

From MarcsHomepage

Introduction

Taken from the XtalView-manual

XtalView is a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model. It organizes and tracks crystallographic data, maintains log files of the computations, and uses standard file formats to facilitate communication between XtalView and programs such as X-PLOR, TNT, and MERLOT.

XtalView takes full advantage of the modern workstation environment with a simple but comprehensive windows-based interface. It is organized around the concept of a crystal --all data that have a common unit cell and space group. All information for a crystal is kept together in a database file. Nearly all of the data files used by XtalView are in ASCII text and have associated history files to help you track them.

XtalView is described in the book Practical Protein Crystallography , by Duncan McRee, who developed the software at the The Scripps Research Institute. The package is distributed by the Computational Center for Macromolecular Structure , located at the San Diego Supercomputer Center.

User Interface

Xtalview small.jpg

XtalView consists of several OpenLook-GUI programs and some more command-line driven tools grouped around a central manager (xtalmgr) which starts the other apps and which can be used for project administration. The main modelling program is xfit, which can read and write coordinate files and electron-density maps, and manipulate them from molecule to atom-level.
Due to the fact, that XtalView uses the OpenLook-toolkit for its interface, commands and the general handling of the program is no as weird as it is in O (files can be read in with "Load" instead of "sam_atom_in" for example ;-) ).

But nevertheless, XtalView is a complex program, which sometimes isn´t too intuitive to use, and OpenLook has sometimes a different approach to common tasks than other nowadays more popular GUI-toolkits (KDE,Gnome, Windows).

The display does not use OpenGL, therefore the program is quite fast even on older machines, if you draw wireframe models only, but can´t benefit from fast 3D-accelerators which are more and more mainstream even for lowcost machines.

Despite this the image quality of the realtime display is quite good, and if your really need superb pictures for publication you can still use other tools like Molscript , Molmol , or SwissPDBViewer or you could use the builtin Raster3D-support to generate raytraced images directly from XtalView.

Features

Taken from the XtalView-homepage

  • Fits Proteins, Nucleic acids, carbohydrates and any arbitrary organic molecule
  • On the fly omit maps
  • Built in FFT - use phases instead of maps
  • Built in Structure Factor Calculations - update density to reflect model changes
  • Automated tracing
  • 20 levels of undo for model changes
  • Cut and paste between models
  • Split residue around active torsion
  • All major UNIX OS's supported (including LINUX)!
  • Refines against map and geometry in real-time
  • Support for ultra high resolution refinement
    • Anisotropic thermal parameters - reads writes U's and displays thermal probabilities
    • Improved disorder handling - can edit each side independently or together
    • SHELX-97 CIF Structure factor files (LIST 6)
  • B-splines - improves accuracy of interpolation without increasing memory use
  • Arbitrary contour grids
  • Improved geometry refinement
    • One-step refinements on Autofit menu:
      • Refine Region - click a residue and then choose this to refine a residue plus its two neighbours, hit spacebar until finished
      • Refine Range - click two endpoints, issue command, hit spacebar until finished
      • Refine-while-fitting - lets you drag atoms while the geometry and fit to density is being continuously updated
    • Phi-psi optimized to Ramachandran plot
    • Chi1 angles optimized by residue type
  • SigmaA maps - SigmaA 2mFo-Dfc and Fo-mFc maps are computed on the fly - combined with the "shake" option in SfCalc window this can greatly reduce phase bias
  • Raster3D interface - Xfit can call Raster3D directly for high quality rendering of map and model
  • Three dictionaries available with a click of the button on the Model window
    • No hydrogens
    • Polar hydrogens
    • Full hydrogens
  • More conformers added to dictionaries
  • Real-time contour levels - contours are adjusted interactively as you change levels
  • Model geometry error list- finds geometry errors - click an error to center it
  • Model window
    • Copy into buffer as well as cut
    • Renumber chain
    • Reverse chain
    • Sort by sequence numbers
    • Make C-terminus (adds second oxygen)
    • Ribosyme - insert now makes peptide bond to previous/next residue automatically
    • Atom level editing - remove an atom - change B/occupancy