2.10.6

This is a minor bug fix release over 2.10.5, with the following improvements:

• Shadows/occlusion now work on most Windows machines with Intel graphics chips.
• The "Spheres" default radius is now 1.0 van der Waals radius.

2.10.5

This version fixes bugs in 2.10.4 and introduces major improvements to PdbView:

• PdbView
• Works on all platforms.
• Find widget.
• Delete selected atoms/residues/chains.
• Add residue/atom.
• Add symmetry mates.
• Toolbar with icons.
• Sortable by column.
• Fractional coordinate display.
• Edit multiple cells at once.
• Many paste abilities.
• Unsaved indicator in menu bar.
• Edit unit cell parameters.
• User interface
• Picture wizard improvements.
• Atom labels/pick labels can have residue one letter code.
• Remove some keyboard shortcuts which overlapped with standard system ones.
• Fix drag and drop on OS X Yosemite.
• Selection menu shortcut for neighbourhood of ligands.
• Can display bond lengths/angles with user-defined number of decimal places.
• GetMonomer has a searchable selection list.
• Better object movement behaviour.
• Sequence viewer performance increases.
• Saccharides (G) in Simple Display Table.
• Drawing styles
• Glycosolation blocks now has representaions for most sugars.
• Chemistry
• Significant speedup loading molecules with novel ligands.
• Added S-H tolerances.
• Hydrogen bond drawing bug fix.
• Biomolecules can now be generated from mmcif files.
• Various
• Fix bug with restoring status containing vectors.
• Fix bug with restoring mgpic status files with unused custom colour scheme.
• Memory leak fixes.
• Fix centering bug.
• Fix problem with QtPimple with some status file.
• Run as server option ("-serve").

2.10.4

This is a bug-fix version over 2.10.3 which fixes the following:

• XML status files now load successfully again.
• Terminal NME is not treated as a ligand.
• Some missing double-bonds are now drawn properly.

2.10.3

This is a bug-fix version over 2.10.2 which fixes one major bug.

• Fix very bad atom selection bugs.

2.10.2

This version includes many improvements to SMILES string loading, ligand drawing and saccharide representation.

• Add N-H covalent bond tolerances.
• Add correct colours for sugar blocks representations.
• Ligand graph-matching fixes and speed-ups.
• Much better structures generated by default from SMILES strings.
• Options for number of starting confirmations and minimization iterations for structures generated from SMILES strings.
• Name now mandatory for structures generated by default from SMILES strings.
• Standard shapes for NAG in Sugar blocks representation. Sugar blocks renamed Glycosylation blocks.
• Fixes to XML status files.
• Correctly bond H atoms after program restart.

2.10.1

This is a minor bug-fix version over 2.10.0.

• Fix ligand/protein covalent bond in "Site and Ribbons" wizards.
• Use graph matching to check if ligand 3-letter code matches existing 3-letter code.
• Mol2 file format support.
• Fix drawing bug in dihedral angle arrow (and other arc drawings).
• Standard shapes for MAN in Sugar blocks representation. Sugar blocks connections now drawn.

2.10.0

This a major new release, featuring many new ligand drawing features and major internal changes to facilitate integration with the CCP4 suite.

• Ligands
  • 2D depiction of ligands.
  • CIF dictionaries can be loaded from data object menu in Display Table.
  • Load molecule from SMILES string.
  • Load structure from CCP4SRS database.
  • Multiple bond and aromaticity display.
• Drawing
  • Sacchardides treated as ligand by wizards if no other ligands in coordinate file.
  • Ligand-protein covalent bonds are drawn properly.
  • All drawing now done using VBOs when possible.
  • Maps drawn as lines honour transparency.
  • Better hydrogen-bond tolerances.
  • Sugar blocks drawing style.
  • O-H, N-N, C-Cl and C-F bond distance tolerances added.
  • Nucleic base pairs calculation improvements.
• CCP4 integration
  • Use of new CCP4 libraries: MMDB2, SSMv2, CCP4SRS.
  • Many other changes to make incorporation into CCP4 6.5 possible.
  • Ability to load files from running CCP4i2.
• General
  • Opening ccp4 map files works on Windows.
  • Font browser fixes.
  • Fix blank dialog boxes on some versions of OS X.
  • Fix non-compressed stereo tiff files.

2.9.0

• User interface
  • "Simple Display Table" added. New tool for quickly turning on/off lots of related display objects. Particularly useful for looking at large numbers of similar files. (Not a replacement for "full" Display Table, but a useful alternative for some use cases). See Simple Display Table documentation.
  • Improvements to colour by PDB file wizards.
  • Files and atom selections can be saved as CIF files.
  • Hide/show all option at top of display table where it is easier to find.
  • Wizards can be run on just a single chain (with associated ligands).
  • Toolbar allows most buttons to be on it. More on by default.
  • Status files are more portable across OSes.
  • Scene XML file parsing is far more complete.
  • Surface removed as a style option. Must now create a surface object.
  • Make sure vectors are always saved even if user hasn't specified a file.
  • Side-by-side stereo and 3-way view screenshots can be any size.
• Display
  • Fix font size guess in batch rendering.
  • Inside grey option works with oval helices.
  • Speed up drawing of base pair sticks on most platforms.
  • Fix line size of surface mesh in screenshots.
  • Fix bug on some platforms with text labels being hidden by their background.
  • New Bloboids display style.
  • All lighting features work with side-by-side stereo and 3-way view.
  • Fix orientation of lipid cartoon blob in some cases.
  • More sane label/pick label default information display.
  • Text labels can have depth (go behind other objects). User preference.
  • Latex markup allowed in legends and annotations.
• PISA
  • PISA assemblies are now generated the same way as in QtPISA.
  • PISA can be run on files with >10 character names.
  • PISA and superpose work together correctly.
  • Use latest (development) version of PISA.
• ProSMART interface
  • ProSMART interface completely overhauled. Now has tool buttons as major feature and graphs to visualize results.
  • Fix major bug in ProSMART interface which caused massive slowdown.
  • Use latest (development) version of ProSMART.
• Chemistry
  • Improve detection of metal residue types.
  • More residues added to list of "known" solutes.
  • Allow more chemically sensible S-O distances.
• General
  Fix the SF -> map caluculation which was broken in 2.8.1.

2.8.1

• Fix problem that sequence viewer preferences tab may not be available.
• Fix possible crash restoring status with sequence alignment.
• Make sure that correct sequence is sent to blast server even after alignment.
• Fix missing sequence alignment tool on Linux.
• Fix side-by-side stereo and three way view rotation not working properly.
• Fix how slab and zoom work together for line representations (of models and maps).
• Fix problem selecting multiple ligands/monomers in atom picker widgets.

2.8.0

• User interface and related
  • Radical revamp of picture wizards to give more complete and accurate scenes automatically.
  • Calculate and display quickly biomolecules specified in PDB files.
  • Clicking on Peptide->A in selection browser only selects peptide now, not whole of chain A.
  • Sequences can be saved to text files for loading into external programs.
  • Scale bar option on main display.
  • Screen origin displayed in status bar.
  • Drag/drop of files sets file browser default directory to where file was dragged from.
  • Allow saving of PISA assemblies and general bug fixes in PISA interface.
  • Can now save atoms of an individual display object selection to PDB file.
  • Gesamt option for structure superposition.
  • Fix render on Windows when not installed on C: drive or user drive is not on same drive as Program Files.
  • Rib file no longer saved when batch rendering.
  • Superpose and PISA now behave properly together.
  • Fix bug with S-S bridges when doing superposition or other structure movement.
  • Allow user to specify minimum length of alpha helices.
  • Allow use of alternate locations in atom pickers and hence vectors.
  • Fog propery can vary between scenes in movies.
• Electron Density
  • Handle electron density maps up to about 1000 angstroms cubed.
  • Handle electron-microscopy maps properly by not attempted to recalculate with symmetry. Colour by radius option for these maps.
  • Allow loading of gzipped map files.
  • Difference maps are red/green by default.
  • Can specify electron density contour level, etc. to 4 decimal places.
  • Can now download structure factors and calculate map.
• Chemistry
  • Many more monomer types correctly identified as peptide, solute, saccharides, etc.
  • Helix generation tool produces better geometries and now has various beta sheets.
  • More chemically realistic distances used to calculate H-bonds and metal contacts.
• Display
  • Drawing speed 2x faster.
  • Improve quality of "Circles" style, especially with screenshots.
  • Improve quality of thermal ellipsoids.
  • Worms scaled by b-factor and NMR mobility.
  • Custom clip planes.
  • "Clip-capping" for "Perfect spheres" and "Spheres".
  • Ambient occlusion fixes for spheres.
  • Perfect spheres are now lit by all lights.
  • Perfect spheres are now clipped much better.
  • HBonds and Contacts have separate global styles.
  • Text labels can be obscured by nearer objects.
  • Lighting speedups for older nVidia cards.
• General
  • Tutorials and other documentation updates.
  • Speed up program when there are lots of display objects.
  • Fixes for compatibility with various compilers.
  • Use CCP4 version 6.4 libraries.
  • Major overhaul of build system for future compatibility with CCP4 suite.

2.7.3

• Fix Geometry causing crash on Windows/Intel.
• Works on CentOS 5/6 inside VirtualBox, with non-optimal driver.
• Fix drawing of text labels in symmetry mates with some space groups.
• Fogged text better in screenshots.

2.7.2

• OpenGL/ Graphics Drivers
  • Disable use of Vertex Arrays on all Intel Graphics chips on Windows for now, but allow user to override this behaviour. Should now work on all Windows machines, if not optimally.
  • Make sure shadows are smooth when doing screenshot.
  • Fix dark line styles when shadows are on.
  • Shadows work with software Mesa (gallium/llvmpipe, Mesa 9.0 at least).
  • Shadows work with older (HD3000 series) ATI/AMD cards.
  • Shaders/shadows, etc. work with some Intel graphics chips (if shader version >=1.20).
  • Shaders/shadows, etc. work with older nVidia cards (shader version 1.20).
  • Fix reversed z-buffer with screenshots on Windows/Intel.
  • Fix hang/crash at at start-up with new nVidia chips on Linux.
  • Fix dashed lines in non-VBO/VA case (e.g. MS OpenGL 1.1).
  • Fix line colours in non-VBO/VA case (e.g. MS OpenGL 1.1).
  • Fix symmetry for lines in non-VBO/VA case (e.g. MS OpenGL 1.1).
  • EXPERIMENTAL: "Perfect spheres" style. "Ray-traced" spheres in graphics window. Not antialiased however, so screenshot with 2X/4X size recommended. Currently do nothing in "Render".
• User Interface
  • Fix critical bug creating movies on Windows.
  • Restore from XML works on Windows.
  • Fix loading of XML status files with selections with single quotes, e.g. C5' .
  • Fix "Apply all" to Annotation fonts.
  • Sequence viewer option for traffic light or Consurf style colouring.
  • Two new site+(broken)ribbons wizards which colour by molecule instead of chain.
  • Change names of back/forward to undo/redo.
  • Fix undo/redo by always forcing reload of data files.
  • Add download coordinates and screenshot to default toolbar buttons.
  • Only draw half a bond if drawing external to another bond scheme (i.e. not work/ribbon).
  • Selection browser: Allow simple exclusion of CA when group==side (exclude=alpha).
• General
  • Fix R32 symmetry generation from maps.
  • Allow shorter CN bond.
  • Symmetry off by default when an MTZ is loaded.
  • Fixes for running Coot/refmac from CCP4MG.
• Other
  • Fixes for compatibility with CCP4 build systems (no user impact, currently).

2.7.0

• OpenGL (graphics window use of hardware):
  • Shadows. (Display->Lighting->Shadows check-box).
  • Occlusion lighting effect (buried objects are darker than surface ones).
  • Object outlines (edge detection).
  • Shaders working on older (HD3000 series) ATI/AMD cards.
  • Program runs again on Microsoft reference OpenGL 1.1.
  • Fixes for some Windows startup problems.
  • Slighty faster transparency.
  • Text can have a background colour.
  • Text can fade with fog.
  • Speed improvements on Windows.
  • Screenshots up to 8000x8000 pixels on most systems.
• Status files:
  • Portability improvements for status files.
  • Fix saving data files in presentations/archives.
  • Unicode filename fixes.
• Symmetry:
  • Contacts in "Crystal" symmetry method.
  • Symmetry can be on/off for individual display objects; can ignore central symmetry mate.
• User interface:
  • Improvements to PISA interface.
  • Speed up sequence viewer when there are many structures/chains.
  • Clicking on an atom which is labelled from a previous click unlabels it.
  • Atom selections can be given names.
  • Restore the "run Coot" feature.
• "Vibrations" module (normal modes):
  • Clicking on a mode in "Vibrations" when another is already running will switched to the clicked one. Generally more expected behaviour in this GUI.
  • Show theoretical b-values button labels plots much more informatively.
• Picture wizards:
  • Many picture wizards now draw something more sensible by default: broken ribbons are complete ribbons if no range for break is specified; multi-model CA trace works with one model.
  • Wizards support "Crystal" and "View" objects.
  • New way of generating complex scenes with electron density using new XML scene description + new picture wizards. Currently only in batch mode and undocumented.
• Object drawing styles:
  • Edges of ribbons can be coloured grey (colour will be user-specified in 2.7.1).
  • User can specify degree of which loop-shortening effect.
  • Fix drawing of some bonds, e.g. S-S > 2.2 angstroms.
  • Ribbon representation of cyclic polypeptides wraps around on itself correctly.
  • On-screen display of bond/dihedral angles in "Geometry" mode.
  • Fixes for slice and mask density representations.
  • Geoemtry labels behave better on black background.
• Other:
  • Symmetry colours fixed in "Render" module.
  • Fix crash in "Geometry" module.
  • Cope with multiple mtz files on command line.
  • Work with CCP4 6.3.0 libraries and PISA.
  • Install Windows VC++ redistributable package on Windows to fix compatibility with some versions of Windows.

2.6.0

• Improved "File" menu.
  • All loadable files can now be loaded from File->Open. this replaces File->Restore, File->Load archive. Drag and drop works for all file types too.
  • Close all data moved to File menu (from Edit)
  • Creat object moved to Display Table.
  • File->Recent files menu entry.
  • Ctrl+S is now "Save default status". Shift+Ctrl+S is save status to named file.
  • Ctrl+C saves screenshot to clipboard.
• Add Desktop/Documents/Disk drives to file browser left hand pane.
• Support Unicode filenames.
• Support Windows shares in Drag and drop operations.
• Improvements in "Crystal" symmetry drawing:
  • Draw within user specified radius.
  • Works properly when whole molecule is outside defined unit cell.
  • Create crystal option on molecule menu in Display Table.
  • Works with surfaces.
• Speed improvements in "Generate symmetry mates" and also fix bug of drawing long SS bonds.
• Fixes for bugs saving and loading presentations.
• New softer default colours for "by chain", "by model", etc. and for objects created using picture wizard.
• Fix missing ends of "Worms/tubes" representation.
• Sequence viewer improvements:
  • Faster and has more traditional selection behaviour.
  • Can save sequence as PDF or bitmap (png, tiff, etc.)
  • Can colour sequence by secondary structure. Alignment score is more like Consurf.
  • Blast results are cached for later use.
• More test for sensible bond lengths.
• Only use HELIX/SHEET cards if ccp4mg fails to identify secondary structure itself.
• Faster "Circles" representation which also now works with more than one "Circles" object.
• Better initial column selection when opening map files. Option to load difference density at same time as density.
• fcf file support.
• Swap round shift/noshift double click behaviour in "Geometry".
• Speed improvements with some Windows drivers when using VBOs.
• Surface calculation is now parallelized.
• Van der Waals and solvent accessible surfaces.
• New, easier to use light editing GUI.
• Cope with PDB files with >26 chains.
• Support for HTTP proxies.
• "Stop" button for long calculations on Linux (surfaces and lipid cartoon at the moment).
• Acetate,Cl,Br and PEG are now classed as solute.
• Can download data from PDB_REDO straight into CCP4MG.
• Interrupting downloads actually works.
• Can paste text into graphics window: This creates a Legend with pasted text.
• Allow larger than screen size screen shots on OS X.
• OpenGL shaders fixed to work with more drivers.
• User can disable use of VBOs. This should create a workaround for issues with some Windows drivers.
• EXPERIMENTAL: XML status file. XSD

2.5.2

• Do not draw covalent bonds from peptide to metals.
• Use secondary structure definitions in PDB file if present.
• Slightly improve quality of movies.
• Help browser loads now loads PDB links (in external viewer).

2.5.1

• Major speed in improvements from rewriting OpenGL drawing to use Vertex Arrays and Vertex Buffer Objects
• Fix several memory leaks, especially serious ones when saving movie frames and deleting structures.
• Fix translation problem when generating assemblies in PISA interface.
• The Linux binary is now built on CentOS 5 for better compatibilty with more Linux distributions. A build parameter was also changed to increase portability and stability.
• Multiple lights now work when OpenGL shaders active.
• Better transparency of surfaces.
• Flat colour option inside surface with shiny outside with OpenGL shaders.
• Fix problem with clipping of maps after transformation has been applied.
• New drawing style "Circles".
• Small utility to generate idealized α, π and 3₁₀ helices.
• Fix problem with some hydrogen-bonds not being dashed lines when they should.
• Approximate normal modes calculation and visualization.
• Fix problems with bits of file dialog still being visible after closing.
• Support for filenames/directories with non-ASCII names.
• Fix problems with lighting in Render module.
• Selection improvements: much better performance with large structures, use SITE specification in pdb files.
• Improvements in identifying lipids.
• Colour blend goes form blue to red as chain goes N to C.
• Movie preferences simplified.
• Fix problem with R3/H3 symmetry from pdb files.
• Fix the "Error with fixed model" problem when restoring status in Superpose.
• Fix loading of animation from file with multiple models.
• 2FOFCWT, PH2FOFCWT columns selected by default, if present, when loading mtz file.
• Fix problem with long file names in sequence viewer.
• Visual improvement in the "Axes" style of thermal ellipsoids. Fix loading of some clustalw files into sequence viewer.
• Experimental visualization of results of ProSMART calculations. Colour by ProSMART score and superpose using ProSMART transformation matrices implemented.
• Display table docked by default.
• Built-in movie player for Linux. May require some support packages to be installed.
• Some additional options in picture definition file View stanza: scale = 'auto' (zoom to show whole molecule), scale = '25 ang' (zoom to have 25 angstroms from screen top to bottom); add option to orient view along smallest principal component e.g. orientation = {'molData':'toxd','selection':'// /45-46'}

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.

2.4.3

• Fixed crashes when generating/deleting symmetry mates and atom clicking.
• Added an option (Preferences->Display->Render quality->Use shaders) to enable/disable vertex/fragment shaders for (much) smoother lighting. It currently only handles one light, but does behave correctly with fog, slab and transparency. NB. this option is not saved between sessions (yet). This is not available in the CentOS 4 build.
• Movie GUI should be more robust: The combo-box for picking glide frames should work properly and not cause problems if you change type of frame.
• Sync to screen refresh.
• The Sequence viewer has moved to the Applications menu.
• Fixed failure to find sequence alignment executable on OS X.
• Text labels fixed in batch mode rendering and in picture definition save.
• Zalman stereo no longer needs a resize window hack.
• Fullscreen mode.
• Many persistent widgets (Geometry, PISA, Movie Editor, Sequence Viewer) are now docked widgets. The Display Table can also be docked, though this is a user option: Preferences->Behaviour->Advanced->Dock display table.