Chimera Beta Version 1.0 Build 1602 Release Notes

Chimera Beta Version 1.0 Build 1602 Release Notes (6 November 2002)

Changes from the previous release:

Initial port to Mac OS X 10.2 -- requires an X server (Aqua port to follow).
Now use an anti-aliased font for labels.
Labels now maintain relative size when saved in a high resolution image.
Some performance optimizations:

large models should open faster.
Model Panel is much faster with large numbers of models.
Side View no longer drawn if containing dialog is closed.
Splash screen shows up faster.

Preferences now has Save/Restore/Reset buttons (changes are not immediately saved).
You are no longer required to press return in entry fields. Moving the cursor outside the entry field has the same effect. This affects attribute panels, Selection Inspector, Preferences, and the Image Save panel.
Write command implemented -- it allows modified molecules to be written out as PDB files.
Select menu reorganization -- Chemistry section including new residue type item, Structure section including new entries for sidechain/mainchain and automatic categories (ligand, main solvent, ions).
Automatic categories (ligand, main, solvent, ions) can be used as command line atom specs.
Color well activation occurs by click anywhere on the well, not just the border.
Chimera window appears at same location as splash screen (even when moved!).
The conic and neon commands now work on UNIX for people who don't have midas installed.
Surfaces and atoms that are default colored now update with the residue color changes.
Delphi Viewer fixes: try to read all types of PHI files; fix color mapping of Delphi (a.k.a. Grasp) surfaces to use correct scale.
Modal dialogs are now centered over invoking dialog.
New Extension:

Benchmark -- measures hardware performance on chimera display tasks with an emphasis on volume models.

Extension changes:

Multalign Viewer now supports region creation according to actual or predicted secondary structure, residue selection based on conservation in alignment, superposition assessment, and automatic loading of PDB structures based on sequence names.
Collaboratory users can send chat messages and see others' pointer positions (color-coded by user); Start Session can now be used within Chimera; password protected sessions.
Phantom documentation integrated into User's Guide.
The Volume Viewer interface has been rearranged and extended. Maximum intensity projections are supported on newer graphics cards. Subregion history and named subregions were added.
The Ribbon Style Editor now allows styles to be saved and retrieved.
Amber 7 support in Movie extension.

Tutorials:

Getting Started tutorial now comes in two versions: one for menu users and one for command line users.
New "Sequences and Structures" tutorial.

Known bugs/workarounds:
On Mac OS 10.2.3 with Radeon 9000 graphics Chimera sometimes causes a system crash when using the side view. This is probably a graphics driver bug. It has been reported to Apple. It can be produced by opening PDB 1gcn with the side view up and switching to sphere representation.
On Mac OS 10.2.4 with GeForce 4 Ti graphics Chimera sometimes causes a system crash when showing large models. This is probably a graphics driver bug. It has been reported to Apple. It can be produced by starting the Benchmark extension and making a standard surface model of size 200.
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.
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.
Adobe Illustrator and Photoshop are unable to open the TIFF files generated by chimera. The workaround/fix is to add the following line to CHIMERA/share/PIL/TiffImagePlugin.py at line 659:
 ifd[COMPRESSION] = 1
	
On Windows, if you're having problems installing or starting up chimera, and you downloaded before 12 Nov 2002, please download again.
On Windows, if you downloaded before 20 Nov 2002, please remove lib\libotf.dll (and keep bin\libotf.dll). The symptom that this fixes is the error "ImportError: DLL load failed: ...." when starting several of the extensions.
Secondary structure records in PDB files written out with the write command need work.
On Windows, collaboratory hub GUI startup (-g option) almost works.
The "conic" command does not work right on non-Tru64 systems. On such non-working systems, Chimera may quit after the "conic" is run.
The "neon" command does not work on systems without MidasPlus previously installed. On such non-working systems, Chimera may quit after "neon" is run.
The "ribbonjr" command does not work on systems without MidasPlus previously installed. This is expected, since "ribbonjr" is not distributed with Chimera. However, on such non-working systems Chimera may quit after "ribbonjr" is run.
Changing the probe radius of an MSMS surface to a very large value may cause to Chimera to quit.
Surfacing unusual structures may cause errors in the MSMS library, which in turn may cause Chimera to quit.