Changes between Version 77 and Version 78 of Release1.4


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Timestamp:
Dec 24, 2008, 10:50:59 AM (17 years ago)
Author:
Scooter Morris
Comment:

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  • Release1.4

    v77 v78  
    7272=== Project Related Features ===
    7373
    74 ==== Large Assemblies (Core 2) ====
    75 
    76 The four major areas of core 2 are animations, molecular assembly atomic models, electron tomography maps, and single particle EM maps.
    77 
    78 I estimate there will only be time to implement one of the following five 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.
    79 
    80 Molecular assemblies: Multiscale new user interface and new capabilities.
    81    1. user-specified symmetry (e.g. C4, helix, hand-placed copies).
    82    2. mmCIF subassembly display
    83    3. molmap multiscale surfaces to allow quality control
    84    4. user control over hierarchical grouping
    85    5. reduce clutter in graphical interface (aka "button farm")
    86    6. add multiscale command interface
    87    7. allow writing user specified symmetry as BIOMT matrices in PDB file
    88 
    89 Animations: Create a half dozen example movie scripts covering common cases.
    90    1. ligand binds to molecule with morph between bound/unbound conformations
    91    2. slice through tomography data plane by plane
    92    3. slice through single particle map with fit pdb showing map slab and thicker pdb slab for illustrating fit
    93    4. simultaneous morph of single particle map and pdb between 2 or more conformations
    94    5. illustration of contact interfaces in an assembly by moving all chains radially like Mac Expose' feature
    95    6. play a molecular dynamics trajectory (needs command interface)
    96 
    97   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.
    98 
    99 Tomography + single particle EM maps:  Create, save, restore, use volume masks.
    100 
    101    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.
    102    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.
    103    3. Restore may need to read from two files (mask array + object info), and need user interface to associate with primary volume data.
    104    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.
    105 
    106 Electron tomography: Visualization of objects embedded in membranes e.g. nuclear pores in nuclear envelope, spikes in virus membranes.
    107 
    108    1. be able to map volume gray levels onto curved membrane surfaces
    109    2. move membrane surface along normals while viewing gray levels
    110    3. annotate by coloring patches of surface
    111    4. place markers on surfaces
    112    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
    113 
    114    
    115 Single-particle EM: Improve fitting of molecules in maps.  This is one of the most cited features of Chimera.
    116 
    117    1. avoid steric clashes during fit
    118    2. allow moving any subset of atoms, not just whole molecules
    119    3. avoid clashes between symmetry related copies of molecules
    120    4. allow simultaneous fit of multiple molecules
    121