2.5.0

General bug fixes

• Fix very serious Vista/Windows 7 crash upon loading most pdb files.
• Fix some crashes in Movie Editor.
• Fix some crashes when closing windows or data files, or deleting atom selections.
• Workaround lighting initialization crash with some onboard chipsets.
• Cope with some strangely named H in some pdb files.
• Fix problem with PDB files containing lines beginning with '#'.
• Cope with chains beginning with a number instead of letter.
• Cope with big structure generated by PISA with conflicting chain IDs.
• Fix problem in which some files are not saved in an archive.
• Fix loading of DSSP output files.
• Fix PISA not working if user has used an earlier version.
• Fix Applications->Picture wizard not showing.
• Fix selection of secondary structure types in Selection Browser.
• Fix drawing of lipids and speed up enormously.
• Fix position from which symmetry is calculated.
• Magnification of screenshots fixed.
• Add missing documentation for Geometry module and from some help buttons in preferences dialog.

Render Module

• Fix glitches when there is a transparent background in rendered files.
• Fix clipping of text labels in rendered files.
• Fix position of text labels when rendering.
• Fix a problem with batch rendering and -norestore flag.
• Compress tiff output from render.

Sequence Viewer

• Only populate/update sequence viewer when it is shown.
• Residues selected in sequence viewer appear in Display Table so that style/colouring/selection can be user edited.
• Do not show waters in sequence view or sequences without AA/NA.
• Residues are correctly highlighted in sequence viewer at restart and after alignment.
• Colour models by sequence conservation from an alignment.
• Sequence alignment is restored at program restart.
• Undo a sequence alignment.
• Font size in Sequence Viewer can be changed.

General Enhancements

• Ask user if he/she wishes to restore status at restart.
• Escape exits full-screen mode.
• Show edit zoom factor in status bar.
• Make some large widgets (e.g. residue type colours) scrollable.
• The compact docked display table now has a usable slider for electron density contour level, etc.
• Add a menu with action "Apply to all" to Apply button in preferences. The action is disabled except when the font preferences is selected. For fonts its effect is (currently) to apply to all Annotations.
• Ability to minimize file viewer window and put main window on top of it.
• Hover over molecule name in Display Table shows TITLE and ORGANISM_SCIENTIFIC.
• When loading an MTZ file, if FWT and PHWT are present set them as default.
• Make the Movie Editor somewhat smaller.
• Make the Clip and Fog widget somewhat smaller.
• Allow use of larger fonts.
• Try to guess model associated with a map being loaded better.
• Recentre when loading a single visible file.
• Metals appear separately from monomers in Selection Browser and in separate Display Table objects after running Picture Wizard.
• Graph plotting widget added, which can be used to display (currently) theoretical B-values alongside experimental B-values.
• Thickness of cylinders in cylinder map representation can be changed.
• Beta bulges are yellow by default, just like strands.
• A PDB file can be saved with transformations of current screen view applied to it.
• Surfaces can have a custom colour on the inside.