XtalView 3.2

XtalView is a crystallographic software package for fitting electron density maps and solving structures by MIR and MAD

• Authors: Duncan E. McRee, Alex Shah, Mark Israel, and Michael Pique
• Distribution
• Academic (free): CCMS
• Commercial: From TSRI (contact:dem@scripps.edu).

• XtalView Guide (PDF file)
• Scattering Factors
• Xheavy Methods
• XtalView References
• Tutorials includes MAD phasing, Xfit auto-fit tracing, photos, native Patterson
• XtalView Man Pages
• Xfit keyboard shortcut (print for handy reference)
• IUCr Crystallographic Computing School Paper A overall description of XtalView including MIR

XtalView 3.2  - New features

• Xfit
• 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
• OS
• IRIX 6
• LINUX "unwanted features" removed

• Xfit
• 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

The new version of XtalView writes Raster3D input. You will need XtalView 3.2+ and Raster3D 2.3+ .

Beta versions of xfit 3.7.1 (updated July 7, 1998)  Also see the hardware stereo versions

Hint: right-click the URL and pull down to Save Link As...

• SGI IRIX5 and IRIX6 improved xhercules_IRIX5_IRIX6
• SGI IRIX5 and IRIX6 xheavy_IRIX5_IRIX6 with anisotropic B refinement and lack-of-isomorphism terms
• SGI IRIX5 and IRIX6 xfit_IRIX5_IRIX6_3.7.1
• DEC alpha (includes some alpha specific bug fixes) xfit_alpha_3.7.1
• DEC alpha xheavy_alpha with anisotropic B refinement and lack-of-isomorphism terms
• Linux xfit_linux_3.7.1

We have had 1066 visits since we started counting 8/1/97 (780 from 8/1-12/17/97)

Contact: ccms-help@sdsc.edu for XtalView help and dem@scripps.edu (Duncan E. McRee) for comments on these pages.