UCSF Chimera Version 1 Build 1700 Release Notes

Changes from the previous release:

• Many menu changes, including:
  • Select menu: Chain and Residue added, Draw Mode removed.
  • Actions menu:
    • Atoms/Bonds, Ribbon, and Surface each include hide/show and representation options.
    • Color targets made clearer and more apparent.
    • New Focus action which adjusts the view and center of rotation to selection.
  • New Tools menu containing previous Settings, Controllers, and Extensions.
  • New Favorites menu for frequently used tools.
• Exiting is faster.
• Tools Preferences replaces the Extension Manager.
• New registered input type: SCOP domain file, automatically retrieved from the ASTRAL Compendium.
• Image Save Panel (and the copy command) can write PNG and JPEG in addition to TIFF.
• Label font/size adjustable (General Preferences).
• Ribbon display changes:
  • Ribbon display is distinct from ribbon representation.
  • Sidechains are now connected to the ribbon representation (were previously often separated).
• Improve the opening of PDB files generated on a different platform.
• Tool changes:
  • Camera tool has new cross-eye, wall-eye, and VRex row stereo options.
  • Model Panel has "write PDB" function.
  • Command Line tool changes:
    • read command implemented.
    • source scripts now update internal state correctly.
    • New focus command acts like focus action.
    • ribcolor command replaces rescolor.
    • ribbon and ribrepr commands replace resrepr.
  • Multalign Viewer new features:
    • Adjustable association criteria.
    • Can write out RSF files.
    • Can focus on structure residue(s).
    • Settings changed to Preferences with Preference sections as separate menu entries.
    • Save/restore with sessions.
  • Collaboratory Start Session interface includes more information and options for control of the collaborative session and participants.
  • collaboratoryHub -g (GUI mode) works on Windows.
  • Effects tool:
    • Can now easily turn off depth cueing.
    • Depth cue color defaults to black instead of background color.
    • Can change subdivision quality for spheres and cylinders.
  • Volume Viewer preferences can be saved (Save button in the Options panel).
• Open File dialog should hang gracefully on slow/bad NFS directories.
• Fixed memory leak with Python wrapped C++ functions taking sequence arguments.
• Make work on SGIs when $CHIMERA is a symbolic link.
• Extensive documentation updates.

Known bugs:

Wire bonds disappear on large PDB models on Mac. Bonds in wire display mode appear correctly when a large model (eg 1aon) is first opened, but then many of them disappear when the model is moved. This is an OpenGL driver bug in Mac OS 10.2.6 that has been reported to Apple.

MSMS surface crashes on Mac. MSMS molecular surfaces of large PDB models (eg 1lta, 6400 atoms) cause Chimera to crash on Mac OS. The problem is caused by the default Mac stack size limit of 512 Kb. This can be fixed by adding the line "ulimit -s 8192" to the Chimera.app/Contents/MacOS/chimera start-up script for the X11 Mac Chimera. For the Aqua Chimera you can set a higher limit in a shell, and run Chimera from the shell instead of clicking on the icon. The next Mac Chimera release increases the stack size on startup.

DelphiViewer data alignment error. DelphiViewer displays potential data shifted by one voxel from the correct alignment. This makes the coloring of MSMS or GRASP molecular surfaces using the potential incorrect. VolumeViewer also displays the potential data (*.phi files) shifted by one voxel. The DelphiViewer trilinear interpolation for surface coloring is also done incorrectly making colors correspond to positions as much as one voxel away.

Copy command makes strange image. Use of the copy command when widgets are in front of the graphics window results in strange images.

Saving JPEG-format images unreliable. Saving an image to JPEG format often fails. If you are saving to JPEG due to the large size of (uncompressed) TIFF-format images, try using PNG format instead [it has built-in compression].

Collaboratory hangs on multiprocessor IRIX.

Mac OS 10.2.4 / Radeon 9000 system crash. On Mac OS 10.2.4 with Radeon 9000 graphics Chimera sometimes causes a system crash when using the side view. This is a graphics driver bug that has been fixed in Mac OS 10.2.5. The crash happens after opening PDB 1gcn with the side view up and switching to sphere representation.

Mac OS 10.2.4 / GeForce 4 Ti system crash. On Mac OS 10.2.4 with GeForce 4 Ti graphics Chimera sometimes causes a system crash when showing large models. This is a graphics driver bug that has been fixed in Mac OS 10.2.5. The crash happens after starting the Benchmark extension and making a standard surface model of size 200.

Partially displayed surfaces Linux / Nvidia. On Linux with the nVidia 3123 driver MSMS surfaces and Volume Viewer isosurfaces are sometimes only partly displayed on GeForce 4 Ti and Quadro 4 graphics cards. This is a bug in the nVidia 3123 driver. The older 2880 driver and the newer 4191 driver do not have this problem. For volume isosurfaces, using a non-zero transparency works around the problem.

Missing selection outline with Mesa. With Mesa 3.4.2 (softare OpenGL sometimes used on Linux and Mac) Chimera selections (atoms, bonds ...) do not show a green outline. The outline is black. Also dragging a selection box with the mouse produces a black box instead of a green box. This is a Mesa bug. Setting Fill mode for selection highlighting in Preferences works around this problem.

Orphaned molecular surfaces. A surface whose structure has been closed causes two problems: session saving fails; the model panel's attributes inspector for the surface will fail.

Command separator ";" bug Multiple command-line commands separated by ';' may not work correctly (e.g. open 1gcn; surface will not properly show a surface).

Bad atom types on Mac. The mac distribution mistakenly includes an obsolete version of the code that computes atom types. In particular, it computes the atom type of carboxylate and nitro-group oxygens to be "O-" (an obsolete type) when they should be "O2-". This causes the FindHBond tool to fail to find hydrogen bonds involving carboxylates and nitro groups.