Qmol Change Log

WIN32 Version 1.4 (2/6/01)

• Added user defined lighting (see "Render | Lighting ..." on the menu bar).
• Improved the default color scheme (i.e. black back ground).
• Improved the depth cueing (switched to the OpenGL linear fog function).

• Fixed bug in read progress bar that caused progress indicator to cycle several times.
• Fixed bug in Kabsch rotation.
• Fixed bug in the handling of -pdb import flag.
• Fixed bug in light control for the wire frame model.
• Fixed visability bug in the save coordinate dialog.
• Added capability to generate uncompressed AVI movies from a molecular trajectory.

• Added user defined resolution for geometric objects.
• Removed the OpenCoordDialog (open a CFileDialog instead).
• Fixed bug in pasting an image to clipboard (windows 95/98 only).

• Added an option to save (or not save) the CONECT records when writing a pdb file.
• Fixed bug saving a pdb file (MODEL records are now written to each pdb file).
• Fixed bug in solvent display (the "Solvent" menu item should now work correctly).

WIN32 Version 1.8

• Added secondary structure assigment via STRIDE (provided by Dr. Dmitrij Frishman).
• Added color-by-secondary structure
• Added trace rendering option to display alpha carbon trace as a wireframe, stick or spline.
• Added variable line widths for wire frame and spline display.
• Fixed color-by-element bug in Color dialog.
• Fixed adjust atom radius dailog.
• Added solid ribbon, flat ribbon, tube (constant raidus, tempature and occupancy based radius).
• Added split-screen stereo.

• Fixed bug in rendering ribbons.
• Added a compile time option to measure frames per second (see QmolView.h).

• Added backface culling the ribbon models (for better looking translucent ribbons).
• Added Protein Data Bank queries (via the File menu). Given a pdb code and a server name, download and display the corresponding file.
• Put the rendering throttle back in OnDraw(). If we don't limit the number of frames per second the message loop can get clogged.
• Misc fixes to PDB parser.

• Improved sphere rendering (now render partial spheres that are always aligned with the viewer).
• Modified file open and save dialogs to always use the current directory.
• Added hydrogen bond detection and display
• Fixed torsion angle rotation bug

• Disbled anti-aliasing for stippled lines. There seems to be a bug (?) in the NVida OpenGL implemetation that causes periodic redrawing of the entire screen when anti-aliasing stippled lines.
• Cleaned up pdb file import to improve speed and code clarity.
• Added the build option to inline ANY suitable function (as opposed to only "inline" functions).
• Added a new option (under "options") to control mouse sensitvity by scaling the virtual trackball size.
• Added support for the wheel found on many pointing devices (the wheel zooms the view).
• Added a command on the menu bar to toggle the display of the status bar at the bottom of the window.
• Improved reading of DCD headers to compute the number of frames in the DCD file (needed for reading VMD generated DCD files).

• Fixed a parsing error that prevented the reading of pdb files that contained concatinated residue names and chain ids.
• Allow the creation of AVI movies containing a single frame.
• Solvent can now only be selected if it is currently being displayed.

• Improved the lighting defaults for solid rendering.
• Increased the range of the custom resolution slider bars.
• Added a DEBUG only option to toggle wire frame models on ('w') and off ('s').
• Added the ability to paste ASCII data from the clipboard into molecular temperature and occupancy values.
• Improved dynamic memory management in STRIDE code.
• Fixed a bug that prevented the reading of multiple model files that failed to specify model numbers (but gave chain ID's instead). This enables Qmol to read multi-layer SwissPDB files.
• Added user defined clipping plane (complete with "cut" sphere rendering to provide the illusion of volume and stereo corrected clipping).
• Added color-by-residue number.
• Improved normalization scheme for pdb temperature and occupancy values.

• Added PostScript export option (via Mark J. Kilgard's OpenGL->EPS code). Adaptive grid needs some adjustment and polygon splitting (to handle overlapping polygons with the painters algorithm) must still be implemented.
• Fixed hydrogen bond line stipple bug.
• Fixed torsion angle rotation bug (Qmol crashed after selecting a torsion!).
• Added material property sliders to the lighting dialog.

• Improved the lighting dialog by removing the gratuitous axes bitmap that caused text alignment problems.
• Added protein sequence tool.
• Fixed the flat ribbon lighting (broken as of 1.98).
• Fixed bug saving multiple model connect records in a pdb file.
• Fixed printing bug (that produced postage stamp images).
• Images are now copied to the clipboard as bitmaps instead of metfiles.

• Improved the rendering of Hydrogen Bonds by stippling "by hand" (i.e. rendering as a set of paralle line segments).
• Changed the clipping plane representation to be a circle instead of a square.
• Modified the save coordinate function to save the current orientation of the molecule(s).
• Reduced the sensitivity of the mouse (for moving molecules).
• Added the ability to read gzip compressed pdb files (which is now the default format when downloading data from the Protein Databank). The zlib library provides the decompression engine.
• Added an "Export Image ..." option. Postscript, BMP and PNG are the supported formats. libpng is the PNG engine.

• Molecular surface rendering has been added. A variety of options are supported, including user-defined surface colors, transparanecy and surface area calculation (by residue and atom). The surface calculation is based on a Marching Cube implementation by Cory Bloyd (corysama@yahoo.com; http://astronomy.swin.edu.au/pbourke/modelling/polygonise/).

• Fixed bug in surface generation (boundary artifacts in small molecules).

• Added the ability to import multiple structures in a pdb file as a molecular trajectory.
• Fixed a bug that prevented setting surface lighting options correctly.
• Added persistant to Qmol settings. Most settings are now stored in the registry to provide consistent behaviour from one session to the next. Options are provided to (a) return to the default configuration and (b) purge the registry of all Qmol values (i.e. an uninstall).
• Added new elements to the status bar, including window size while resizing the window, atom number, atom id and amino acid.
• Added a color-by-amino-acid-index to the color dialog. Useful for distinguishing between the amino and carboxy terminals.

• That's right, version 3.0 -- a major upgrade for Qmol!
• Allow the reading of multiple structures/trajectories into Qmol. Each structure can be moved and adjusted independantly. Each structure can be rendered with a different representation (i.e. lines, ribbons, space-filling, etc.).
• Structures that have been read into Qmol can be duplicated (i.e. "cloned").
• Multiple files can be selected for reading. (using either wildcard import from the command line or the file import dialog).
• Allow the calculation of RMSD between two structures (with user determined atom selection). The structures do not have to be of the same protein or chemical.
• Align two molecules by rigid-body translation and rotation (using a user specified sub-set of atoms).
• Measurement, hydrogen bond determination and RMSD calculation can all be performed in "real" time (i.e. move a molecule and watch dependant values change).
• Added a "scale-to-fit" option to rescale the coordinate system while moving molecules to keep all molecules visible.
• The measurement and torsion angle adjustment mechanism has been (hopefully) improved. Selecting atoms and torsion angles now only occurs when the measurement dialog is displayed (for atoms) or the adjust torsion angle dialog is displayed (for torsion angles).
• Selecting an atom with the pointer displays atom and residue info in the status bar.
• The code for computing the optimal rigid body rotation and translation to minimize the RMSD between two molecules has been fixed to allow alignment of co-planar structures (i.e. ring groups). Co-linear molecules are still not allowed.

• Added the option to preseve molecular center of mass when reading files (see the "Options" | "Read Coord Options ..." dialogbox accessible from the menu bar).
• Document options (like zeroing the center of mass) are now stored in the registry in addition to view options. This required a seperate LoadDocRegistry() function to avoid problems with the document class not being available from the view constructor.
• Fixed more crashes than you can shake a stick at! All were related to deleting one or more molecules without notifying or closing dialogs that assumed a valid activeMol pointer or had a private copy of a mol pointer that was invalid.

WIN 32 Version 4.01 (Jan 2006)

• Qmol now renders ribbons for DNA and RNA strands
• The secondary structure prediction algorithm has been completely changed. The algorithm is cleaner and now assigns turn and bulge structures.
• DNA and RNA strands are now assigned a secondary structure of helix.
• Animation on screen has been slowed down to a manageable speed instead of as fast as possible.
• Export to BMP files now has the correct color.
• Automatically add extension to output files when not specified.
• Improved caching of read coord options in the registry.
• Miscellaneous bug fixes.