UCSF Chimera Release 1.4

Release timeframe: Summer 2009

Feature Discussion

Core Features

1. Pull mmcif connectivity information from a web service. The current mmcif connectivity template file is 20MB uncompressed and constantly out of date. Rather than including the file in our release, the proposal is to include only the most common entries and pull the rest from a web service, as needed. Entries will be cached once they are downloaded, and the user will be able to download the entire file, should they desire.
2. CMS Surface code.
3. 64-bit Mac Aqua build for large volume data applications. TG
   • We had discussed having this happen when OS X 10.6 (Snow Leopard) comes out. It's supposedly slated for Q1 2009. EFP
4. Higher quality lighting and transparency using OpenGL shaders. TG
5. Off-screen image saving (using opengl write-to-texture?) so machine does not become unusable during animation encoding. TG

Project Related Features

Sequence/Structure (Core 4)

Large Assemblies (Core 2)

The four major areas of core 2 are animations, molecular assembly atomic models, electron tomography maps, and single particle EM maps.

I estimate there will only be time to implement one of the following four ideas for the 1.4 release. The work would be about 1/3 time with the other 2/3 of my time devoted to collaborative, service, and dissemination activities. The visualization of membrane objects is work I am considering presenting and the electron tomography conference in Australia, Feb 1, 2009.

Molecular assemblies: Multiscale new user interface and new capabilities.

1. user-specified symmetry (e.g. C4, helix, hand-placed copies).
2. mmCIF subassembly display
3. molmap multiscale surfaces to allow quality control
4. user control over hierarchical grouping
5. reduce clutter in graphical interface (aka "button farm")
6. add multiscale command interface
7. allow writing user specified symmetry as BIOMT matrices in PDB file

Animations: Create a half dozen example movie scripts covering common cases.

1. ligand binds to molecule with morph between bound/unbound conformations
2. slice through tomography data plane by plane
3. slice through single particle map with fit pdb showing map slab and thicker pdb slab for illustrating fit
4. simultaneous morph of single particle map and pdb between 2 or more conformations
5. illustration of contact interfaces in an assembly by moving all chains radially like Mac Expose' feature
6. play a molecular dynamics trajectory (needs command interface)

Main work is to add needed commands. For instance in movie tutorial from 2008 library course 6 python scripts were required to make a simple movie: show first/last trajectory frame, calculate/play pdb morph, set subdivision quality and silhouette edges.

Tomography + single particle EM maps: Create, save, restore, use volume masks.

1. Create means make existing capabilities produce mask arrays (mask command, volume eraser, split by color) and make improved capabilities, e.g. a volume painter tool.
2. Save -- any map file format can save the masks as an array of object indices or as bit masks. Additional info to save includes object names, colors, and groupings (e.g. all microtubules). That may have to be saved in a separate file.
3. Restore may need to read from two files (mask array + object info), and need user interface to associate with primary volume data.
4. Use masks: basic capabilities to hide/show/select objects defined by mask. Ideally would like any volume tool to work also on any masked portion of a volume.

Electron tomography: Visualization of objects embedded in membranes e.g. nuclear pores in nuclear envelope, spikes in virus membranes.

1. be able to map volume gray levels onto curved membrane surfaces
2. move membrane surface along normals while viewing gray levels
3. annotate by coloring patches of surface
4. place markers on surfaces
5. extract volume regions around surface markers for subtomogram averaging (average density for several nuclear pores, virus spikes to achieve higher resolution). Requires alignment capability and handling of tens to thousands of map subregions

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