= 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. Ticket #7160
 1. Off-screen image saving (using opengl write-to-texture?) so machine does not become unusable during animation encoding. Ticket #7056
 1. Replace mac aqua focus-follows-mouse with click-through. Tk patch probably required. Ticket #7047
 1. Nucleotides: saved in sessions, dialog settings maybe sticky, "nucleotides" command, possibly use in preset. Tickets #5089,#1250,#7163,#7164
 1. integrate Nucleotides Ticket #7162
 1. 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. Ticket #7048
  * Use will specify bond length, angle and dihedral
 1. Minimize Structure: don't call Dock Prep again if all atoms already have amberType and topology has not changed. Ticket #7166
 1. (planned/probable) Measure planes. Ticket #7167
 1. (planned/probable) Rename models using Model Panel. Ticket #7050
 1. (planned/probable) Coulombic surface coloring. Ticket #7051
 1. move Molecule color to Model Ticket #7052
 1. Need "effects" command for controlling all Effects via script. Ticket #7053
 1. Reduce mmcif template file download Ticket #7054
 1. Framework for invoking chimeraservices.rbvi.ucsf.edu and other web services Ticket #7055
  *  Security, transactions with IDs
 1. 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. Ticket #7169
  * (search other databases such as NR? PSI-BLAST on NR?) Ticket #7170
 1. Support PDB v3.2 Ticket #7056
 1. Annotations submenu in Select menu #7190

== 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 Ticket #7171
  * Implement cron job to continuously update mmcif template file
 1. Output compressed TIFF instead of current giant files. Ticket #5604
 1. 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. Ticket #7173
 1. Reposition normal labels with mouse. Ticket #167
 1. (planned/probable) Finish Color Key (X3D output [needed for raytracing]; "key" option to rangecolor command). Ticket #7175
 1. Interpolating ribbons Ticket #7176
 1. Integration/addition of a 2D plotting library (e.g. matplotlib) Ticket #7177
 1. Change depth cueing ramp parameter Ticket #7178
 1. Better label-offset algorithm, particularly when zooming Ticket #7179


=== Documentation ===

 1. Need new image-making tutorial(s) in addition to or replacing the current one. Ticket #7180

=== Core 2 (Software for Interactive Analysis of Large Molecular Assemblies) ===
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 Ticket #7182
  1. move membrane surface along normals while viewing gray levels Ticket #7183
  1. place markers on surfaces Ticket #7184
  1. 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 Ticket #7185

=== Core 4 (Tools for Integrated Sequence/Structure Analysis) ===
 1. ~~allow specifying "sequence to add" by accession code (Uniprot?). Its feature annotations would automatically come along as regions.~~  Ticket #7186 ; mutated into "Annotations submenu" above as 1.4 release priority (still wanted as a feature, just not milestoned for 1.4)
  * ~~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~~
 1. When aligning in a structure sequence, consider secondary structure markups of non-structure sequences Ticket #7187
 1. If gaps are created while adding a sequence, make corresponding gaps in any markups Ticket #7188
 1. Aqua background -> gray, or put black border around sequence-name color swatches Ticket #7189