UCSF Chimera Release 1.4

Release timeframe: Summer 2009

Features Confirmed for 1.4

These features are high priority for the 1.4 release. If necessary, the release may be postponed if these features are near to completion so that they may be included.

1. CMS Surface code.
2. Off-screen image saving (using opengl write-to-texture?) so machine does not become unusable during animation encoding. TG
3. Replace mac aqua focus-follows-mouse with click-through. Tk patch probably required. TG
4. Nucleotides: saved in sessions, dialog settings maybe sticky, "nucleotides" command, possibly use in preset. ECM
5. integrate Nucleotides GC
6. Build Structure: allow bonding of one clump of atoms to another clump of atoms in a way that automatically repositions one clump instead of requiring the user to attempt to maneuver it into the appropriate bonding position. ECM
   • Use will specify bond length, angle and dihedral
7. Minimize Structure: don't call Dock Prep again if all atoms already have amberType and topology has not changed. ECM
8. (planned/probable) Measure planes. EFP
9. (planned/probable) Rename models using Model Panel. EFP
10. (planned/probable) Coulombic surface coloring. EFP
11. move Molecule color to Model GC
12. Need "effects" command for controlling all Effects via script. ECM
13. Reduce mmcif template file download
14. Framework for invoking chimeraservices.rbvi.ucsf.edu and other web services CH
    • Security, transactions with IDs
15. connect to our own Web service (using the above framework) to BLAST on PDB, provide dialog for choosing which hit structures to open, whether to show pairwise sequence alignment from BLAST (in MAV), whether to superimpose hit and query structures (with Matchmaker). Input is sequence of molecule model already open in Chimera. ECM
    • (search other databases such as NR? PSI-BLAST on NR?)
16. Support PDB v3.2

Features Desired for 1.4

These features would be good to include in 1.4 and effort will be expended to include them, but they are not as high a priority as the "confirmed features" above. We will probably not hold the release if these are not completed.

1. Distribute smaller mmcif template file, but provide a location for users to download the full template file from our web site
   • Implement cron job to continuously update mmcif template file
2. Output compressed TIFF instead of current giant files. ECM
3. Make it easier to get phi,psi,(and maybe chi and omega) torsion values from proteins. For 1.4 will report something to the reply log.
4. Reposition normal labels with mouse. EFP
5. (planned/probable) Finish Color Key (X3D output [needed for raytracing]; "key" option to rangecolor command). EFP
6. Interpolating ribbons GC
7. Integration/addition of a 2D plotting library (e.g. matplotlib)
8. Change depth cueing ramp parameter

Documentation

1. Need new image-making tutorial(s) in addition to or replacing the current one. ECM

Core 2

1. 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. place markers on surfaces
   4. 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

Core 4

1. allow specifying "sequence to add" by accession code (Uniprot?). Its feature annotations would automatically come along as regions. ECM
   • would we want Fetch by ID for sequences? (would we want a sequence with no structure and not aligned with any other sequences?)
   • perhaps allow specifying Uniprot accession or BLAST on Uniprot for existing sequences, retrieve and load feature annotations as sequence regions (would require global alignment to Uniprot sequence for correct mapping of features when the existing sequence is not identical)
   • on my secondary MAV to-do list. EFP
2. When aligning in a structure sequence, consider secondary structure markups of non-structure sequences
3. If gaps are created while adding a sequence, make corresponding gaps in any markups
4. Aqua background -> gray, or put black border around sequence-name color swatches

Features Under Consideration

Core Features

Documentation

1. Need new image-making tutorial(s) in addition to or replacing the current one. ECM

Project Related Features

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 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.

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

Single-particle EM: Improve fitting of molecules in maps. This is one of the most cited features of Chimera.

1. avoid steric clashes during fit
2. allow moving any subset of atoms, not just whole molecules
3. avoid clashes between symmetry related copies of molecules
4. allow simultaneous fit of multiple molecules