Changes between Initial Version and Version 1 of LargeAssemblyFeatures


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Timestamp:
Dec 24, 2008, 10:53:44 AM (17 years ago)
Author:
Scooter Morris
Comment:

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  • LargeAssemblyFeatures

    v1 v1  
     1== Large Assemblies (Core 2) ==
     2
     3=== Molecular assemblies: Multiscale new user interface and new capabilities. ===
     4   1. user-specified symmetry (e.g. C4, helix, hand-placed copies).
     5   2. mmCIF subassembly display
     6   3. molmap multiscale surfaces to allow quality control
     7   4. user control over hierarchical grouping
     8   5. reduce clutter in graphical interface (aka "button farm")
     9   6. add multiscale command interface
     10   7. allow writing user specified symmetry as BIOMT matrices in PDB file
     11
     12=== Animations: Create a half dozen example movie scripts covering common cases. ===
     13   1. ligand binds to molecule with morph between bound/unbound conformations
     14   2. slice through tomography data plane by plane
     15   3. slice through single particle map with fit pdb showing map slab and thicker pdb slab for illustrating fit
     16   4. simultaneous morph of single particle map and pdb between 2 or more conformations
     17   5. illustration of contact interfaces in an assembly by moving all chains radially like Mac Expose' feature
     18   6. play a molecular dynamics trajectory (needs command interface)
     19
     20  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.
     21
     22=== Tomography + single particle EM maps:  Create, save, restore, use volume masks. ===
     23
     24   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.
     25   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.
     26   3. Restore may need to read from two files (mask array + object info), and need user interface to associate with primary volume data.
     27   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.
     28
     29=== Electron tomography: Visualization of objects embedded in membranes e.g. nuclear pores in nuclear envelope, spikes in virus membranes. ===
     30
     31   1. be able to map volume gray levels onto curved membrane surfaces
     32   2. move membrane surface along normals while viewing gray levels
     33   3. annotate by coloring patches of surface
     34   4. place markers on surfaces
     35   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
     36
     37   
     38=== Single-particle EM: Improve fitting of molecules in maps.  This is one of the most cited features of Chimera. ===
     39
     40   1. avoid steric clashes during fit
     41   2. allow moving any subset of atoms, not just whole molecules
     42   3. avoid clashes between symmetry related copies of molecules
     43   4. allow simultaneous fit of multiple molecules
     44