New version numbering system
Chimera version numbers now have an extra level. The previous production release is now officially 1.0 build 2540. a.k.a. release number 1.0.2540, instead of 1.2540. If a bug fix version of 1.3 comes out, it will be 1.3.1 with the release numbers being 1.3.2 and 1.3.1.X.General:
- Actions... Focus with nothing selected restores default rotation behavior, "center of models"
- added Debug Graphics Driver panel for selectively disabling OpenGL features to find workarounds for graphics driver bugs (opened with startup option --debug-opengl or specified in the General preferences)
- recent commands are remembered between sessions; how many to remember is set in the Command Line preferences (formerly Midas preferences)
- commands can be deleted from the Command History; saving all commands in the history is easier than before
- CASTp pocket measurements can be read from local files that were e-mailed to the user by the CASTp server
- copy/combine function added to Model Panel (creates another copy of a molecule model or combines multiple molecule models into one)
- anisotropic B-factors saved in sessions
- startup option --reverse-stereo and similar setting in Camera to reverse eye views when in sequential stereo; compensates for the reversal introduced by certain devices
- new Mac Aqua-specific preferences: menus in windows (General category), window focus follows mouse (Mouse category)
New Tools:
- Color Key (Utilities) —
- creates labeled color key for figures, saved in sessions
- can be started from Surface Color or Render by Attribute, set to the current coloring scheme
- Write DMS (Structure Editing) — save molecular surface as DMS file (which can be used as input to the sphgen program distributed with DOCK)
- Write Prmtop (Amber) — write Amber parameter/topology file using AmberTools (implementation thanks to Wei Zhang)
Tool Changes:
- Add Charge — includes several choices of Amber force field version (formerly only ff99) to use for standard residues
- Axes (Structure Analysis) —
- helical correction after principal component calculation now optional
- custom axis calculation can be mass-weighted
- axes can be deleted or individually hidden/shown
- option to remove previous axes when creating new ones
- information can be saved to a file
- Build Structure (Structure Editing) — Modify Atom rearranged and simplified, can act on more than one atom at a time
- Distances (Structure Analysis) — table is sortable
- Fourier Transform — removed from Tools menu, now available as an option of the command vop
- MatchMaker (Structure Comparison) — RMSD header shown, other headers hidden in output sequence alignments
- Multalign Viewer (Structure Comparison) — added Ctrl-key editing undo/redo, dialog listing Ctrl-key functions
- Per-Model Clipping (Depiction) — added surface capping button
- Render by Attribute (Depiction, Structure Analysis) — Colors section includes button to create color key
- Sequence (Structure Analysis) — merged into Multalign Viewer, no longer implemented separately
- Side View (Viewing Controls) — added surface capping button
- Surface Color (Volume Data), aka Electrostatic Surface Coloring (Surface/Binding Analysis) —
- Options section includes button to create color key
- default electrostatic coloring scheme no longer includes transparency
- Volume Series (Volume Data) — multiple series can be played simultaneously
- Volume Viewer (Volume Data) —
- Planes interface changed, faster plane display
- surface/mesh styles can be used to show single planes as contour lines and spots
- Coordinates section shows grid indices of XYZ origin rather than XYZ coordinates of grid origin
- solid rendering faster and more efficient; options added for tailoring memory use to the current data and display mode
New Commands:
- combine — combine molecule models into a single model or create another copy of a molecule model
Command Changes:
- addcharge — includes several choices of Amber force field version (formerly only ff99) to use for standard residues
- copy — image pixel width and/or height can be specified
- findclash — allows continuous clash/contact monitoring
- focus — focusing on everything (focus with no arguments or new ~focus command) restores default rotation behavior, "center of models"
- molmap — showDialog option allows suppressing the Volume Viewer dialog
- volume — solid rendering options changed in parallel with Volume Viewer dialog
- vop — added Fourier transform option
Major Bugs Fixed:
- 07/30/2008 restored better-looking default subdivision quality (affects smoothness of curved objects)
- 08/08/2008 Axes measurements based on transformed coordinates rather than untransformed (affects intermodel measurements when the models have been separately transformed)
Known Bugs:
- Mac OS 10.5 / X11 problems (fixed in XQuartz 2.3.2rc3):
- sometimes display does not update (can be forced by slightly moving the view contents with the mouse)
- sometimes saved images have a corrupt or "mis-tiled" appearance. Workarounds to try include:
- showing the Command Line if it is not shown (or if it is shown, hiding it) and then re-saving the image
- saving a session, restoring the session in the Mac Aqua version of Chimera, and then re-saving the image
- surfaces fail for some structures
- incomplete/patchwork surfaces with some Linux versions of libGL (Mesa bug 12141 fixed in Mesa 7.0.2). Commonly observed when running chimera remotely on a Red Hat Enterprise Linux Server 5 and other earlier versions of Linux.
- on Linux, the default font is wrong when using the KDE window manager
- mmCIF NMR ensembles have missing disulfide bonds in all but one structure
- mmCIF structures with hydrogens may be missing N-terminal bonds between hydrogen and nitrogen